From 7396a4471739c38abcf45e54ae0afec54bfc8444 Mon Sep 17 00:00:00 2001 From: Cole Lyman Date: Tue, 27 Feb 2018 22:06:10 -0700 Subject: [PATCH] Squashed commit of the following: MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit commit 92d9eafcca7e6dc208d6163566a259318388cd20 Merge: aeb3a66bf 384354b74 Author: Cole Lyman Date: Tue Feb 27 21:13:37 2018 -0700 Merge branch 'master' of github.com:Colelyman/bioconda-recipes commit aeb3a66bfdd03807f80a4895e0074963ea015bce Author: Ralf Weber Date: Wed Feb 28 00:55:39 2018 +0000 Bump version MetFrag to 2.4.2 (#8022) commit 88497c107cdb5bec6ccc8c081f2bd6d3fd4e9055 Author: Dan Fornika Date: Tue Feb 27 14:21:21 2018 -0800 Kaiju: Version 1.6.2 (#8014) * Update kaiju to 1.6.2 * Update build.sh * Corrected sha256 commit 0fec104044ede39416a2aed66021c830f09c7844 Author: Joachim Wolff Date: Tue Feb 27 23:20:55 2018 +0100 Update tp 2.1-alpha (#8021) * Update tp 2.1-alpha * Update meta.yaml * less strict pinning * fix spelling mistake commit 9aef9708f707a61ee74d0785b318948e6e9885d2 Author: Matthew Fogel Date: Tue Feb 27 14:04:34 2018 -0600 Update Msaboot to 0.1.1 (bug fix) (#8001) * Incremented version number for bug fix * Incremented build number commit 608744216f6bb3b7e422506b41eb8b221c4bb0b8 Author: Michael Knudsen Date: Tue Feb 27 20:14:27 2018 +0100 Bumped GATK version (#8019) commit e7805136f0152d62f9c9e932826a43194995fd25 Author: Daniel Cooke Date: Tue Feb 27 15:19:50 2018 +0000 Add 'DCMAKE_BUILD_TYPE=Release' to octopus cmake options (#7992) Forces release build. commit e3c4ef384dcf85872e877f7ec5e1d8aa09c21caf Author: Jerome Kelleher Date: Tue Feb 27 14:15:43 2018 +0000 Removed svgwrite and msprime recipes. (#8016) These have been superseded by upstream recipes in conda-forge. commit 363877738d4dd58fce923fd9199ae8696b5a9f55 Author: Colin Brislawn Date: Tue Feb 27 01:26:53 2018 -0800 update BBMap (#8009) commit 4a85ceca5b18d26821b855521efe6513fb7a62b2 Author: Andreas Sjödin Date: Tue Feb 27 00:28:59 2018 +0100 Bump flye (#8011) commit 58cdd6d8ac5df8b690dbaa270b61a143cb78ee13 Author: Karel Břinda Date: Mon Feb 26 18:25:16 2018 -0500 SamSift 0.2.5 (#8012) commit 9de0e8f82cca09055b361e70bd529cd10664bff9 Author: Michael T. Wolfinger Date: Mon Feb 26 22:06:11 2018 +0100 update perl-yaml to 1.24 (#7997) * update perl-yaml to 1.24 * add include test for perl-yaml 1.18 * adjusted perl version requirements * fixed typo commit 9e7ad86c9b63e06e49fe3fd920475b7c8e4d78ed Author: Andreas Sjödin Date: Mon Feb 26 21:16:01 2018 +0100 Bump racon (#8010) commit 125077444ac6065c86edf598ab4b360a7ccd18ca Author: Renan Valieris Date: Mon Feb 26 14:59:50 2018 -0300 rebuild filtlong (#8005) commit 5271a61515db3625a7498f3e27d5912bd0b193c5 Author: Will Rowe Date: Mon Feb 26 17:45:34 2018 +0000 updating groot to v0.2 (#8004) commit f2acce2e072970d78d5186bb3d46638d31d18dd8 Author: Renan Valieris Date: Mon Feb 26 14:40:48 2018 -0300 asorted fixes 2 (#8003) * fix detonate * use certificate to download stuff with wget commit 81b626f4f4fd87a59ef31f3da5a00a10db9e7c68 Author: Christian Brueffer Date: Mon Feb 26 14:59:15 2018 +0100 Add bioconductor-hapfabia. (#8000) commit 57602a6e0fe7d591872bd55118eed017e741ef51 Author: Christian Brueffer Date: Mon Feb 26 12:51:14 2018 +0100 Add bioconductor-fabia. (#6726) * Add bioconductor-fabia. * Unconditionally use gcc. * bioconductor-fabia: use clang; drop -lgfortran * bioconductor-fabia: test with toolchain (i.e., -Wl,-rpath,$PREFIX/lib) * bioconductor-fabia: cleanup * bioconductor-fabia: show log for compilation errors * bioconductor-fabia: add libgfortran [osx] to run requirements commit fceee40a8b19ceb89fe2da26ae0218096c73be8c Author: Björn Grüning Date: Mon Feb 26 11:44:48 2018 +0100 rebuild coreutils (#7999) commit 17cd3140f4ac95813306ab0f1eae87c3feb26824 Author: Andreas Sjödin Date: Mon Feb 26 00:25:32 2018 +0100 Bump sourmash (#7998) commit f3f09ef56fd0a43a6181f2412bf0090f8f276165 Author: Andreas Sjödin Date: Sun Feb 25 21:49:51 2018 +0100 Fixing racon (#7978) * Fixing racon * Add missing hash * Add cmake * They released a updated 1.0.0 version... * Cleaning up commit 3419efa675a10a13afcae64f2d9839b079db1c0d Author: John Blischak Date: Sun Feb 25 13:55:15 2018 -0500 Add Bioconductor package scde. (#7859) * Add Bioconductor package scde. * Add libXrender as a dependency for scde. * Add libSM as a dependency for scde. * Add libXext as a dependency for scde. * add libcxx * Pin X11 dependencies. https://github.com/conda-forge/r-rmarkdown-feedstock/pull/5/commits/2e35b271c392509c2c9f96e2630f2fca4f1424f1 commit d3115652ed7e35e4eeb4e80afbdd29122dfb0630 Author: Heng Li Date: Sun Feb 25 10:23:07 2018 -0500 Updated minimap2 and mappy to v2.9 (#7996) commit f9d194d5d051c8933293cda36fd262ba21da6659 Author: Brad Chapman Date: Sun Feb 25 05:11:01 2018 -0500 Update fastp 0.12.3 with polyG improvements (#7995) commit ade4a2b3d53de77e2f9f6b0b4b8a5ed7082d97cc Author: rspreafico Date: Fri Feb 23 22:01:35 2018 -0800 update shortstack (#7994) commit 00ee08eb57545fa90b4a12df06ef58eeb3b01e53 Author: Yasset Perez-Riverol Date: Sat Feb 24 01:57:11 2018 +0000 identifiers added to the abyss container (#7940) commit 2d8243356ad528334e7b0731639de9624f8ca9ad Author: Slugger70 Date: Sat Feb 24 08:35:38 2018 +1100 chewBBACA version bump to 2.0.6 (#7982) commit 0affd3550e5d08079bc14f55c35d527eabdef987 Author: Renan Valieris Date: Fri Feb 23 17:11:35 2018 -0300 asorted fixes (#7984) * asorted fixes * pin bzip2 * add hash * add cflags for samtools * try update r-spp and skip osx commit d04e12831cad2e343c92e52efb9a5226e3824928 Author: Kevin R. Thornton Date: Fri Feb 23 11:59:32 2018 -0800 update recipe to fwdpy11 0.1.3.post2 (#7991) * update recipe to fwdpy11 0.1.3.post2 * bump version yet again b/c I goofed the sdist for .post2 commit 60c35fc58108f90e38c6004f7ac6dea875b7208d Author: Erik Clarke Date: Fri Feb 23 12:57:06 2018 -0500 new rbt release (#7990) commit 62ff725b6a4712d36e8f5f3f4a11ca21ca06b56c Author: Christian Brueffer Date: Fri Feb 23 18:03:57 2018 +0100 Remove redundant R packages. (#7989) * Remove r-fnn. It is a general package and exists on conda-forge in the same version. * Remove r-factominer, it exists on conda-forge. * Remove r-ggthemes. It is a general package and exists on conda-forge in the same version. commit a931916a89522e1045e8c109250a295a0ebf8312 Author: Davide Chicco Date: Fri Feb 23 11:50:51 2018 -0500 behst2.9 (#7988) commit 4880c5feb15a0dbf550b02b9d76f94662d48ae4b Author: David Laehnemann Date: Fri Feb 23 17:13:06 2018 +0100 Unblacklist prosolo (#7973) * prosolo: attempt unblacklisting * workaround for conda-build bug workaround for the bug that seems to be behind the error that got this and other rust recipes blacklisted * make unsetting safer thanks to @mbargull at: https://github.com/bioconda/bioconda-recipes/issues/7712#issuecomment-367803930 commit b30f1f4ffc462d65e6a48384180b5d5b7811b194 Author: Christian Brueffer Date: Fri Feb 23 17:02:08 2018 +0100 Remove r-ggsignif. (#7985) It is a general package and exists on conda-forge in the same version. commit fd032223e0ce752660f354bb095c3fe8009394c7 Author: Brad Chapman Date: Fri Feb 23 06:50:06 2018 -0500 Update: bcbio with effects/trim CWL support (#7980) commit 5462f14636dcc660915d6537124d392e4b293c1b Author: Davide Chicco Date: Thu Feb 22 18:32:42 2018 -0500 behst2.8 (#7977) commit 6918532f77613c5f9b172237f15904c71f90743f Author: Andreas Sjödin Date: Thu Feb 22 22:40:30 2018 +0100 Bump swga (#7976) commit a56e2c7d52e886140c30ca3596df07f5e2236d0d Author: zachcp Date: Thu Feb 22 16:09:35 2018 -0500 Downpore12 (#7926) * bump version * move new src subdirectories * mapping is a newer directory than last release commit 6fb993241fd706c7e58abc64df92165cefde43bc Author: Davide Chicco Date: Thu Feb 22 15:28:47 2018 -0500 version behst2.7 in Python3.5 (#7974) BEHST package for Python3.5 commit a6e6c4412981a4eb99a7b6dd0bdf93a666f3f41c Author: Peter Cock Date: Thu Feb 22 18:34:33 2018 +0000 kodoja v0.0.3 (#7970) commit 1e519214eb78d06b8e6289a5f2ad348c0cfcd489 Author: Michael T. Wolfinger Date: Thu Feb 22 19:04:42 2018 +0100 add recipe for treekin (#7971) * add recipe for treekin * added home URL commit 44dfc9e94cf8f0b5d3c0f5fa2a8481560254b517 Author: Andreas Sjödin Date: Thu Feb 22 17:19:08 2018 +0100 Bump racon to 1.0.0 (#7969) commit e37eb5ae15378e3a34c9949d8b9d9b1894dc5e5b Author: Gildas Le Corguillé Date: Thu Feb 22 13:43:46 2018 +0100 add r-asics (#7953) commit c7223a272e58798bfed4f0709fbddad2f151ac32 Author: Michael Kluge Date: Thu Feb 22 13:25:13 2018 +0100 new watchdog release 1.2.6 (#7966) commit c2656db73dfea609d70e584817e5dc3a1b470240 Author: Will Rowe Date: Thu Feb 22 10:58:00 2018 +0000 update groot to v0.2 (#7960) * adding recipe for groot * adding recipe for groot * adding recipe for groot * adding recipe for groot * adding recipe for groot * switching to compile GROOT from source * switching to compile GROOT from source * updating GROOT to v0.2 * updating GROOT to v0.2 * updating GROOT to v0.2 * updating GROOT to v0.2 * updating GROOT to v0.2 * updating GROOT to v0.2 * updating GROOT to v0.2 * updating GROOT to v0.2 commit 4dbf875456ce98b02ce44798823621b987c17c26 Author: Wei Shen Date: Thu Feb 22 16:18:17 2018 +0800 update csvtk to v0.13.0 (#7964) commit 6a5b6781441426c3a209fbe2515c70fcfc4c49d0 Author: Jens Preußner Date: Thu Feb 22 08:39:14 2018 +0100 Bumped comb-p version to 0.48 (#7958) commit 4602ca450dc4d8f14afe00a543eeb1a18a03610f Author: Michael T. Wolfinger Date: Wed Feb 21 21:59:38 2018 +0100 added tests to bio-perl-viennangs(#7961) commit 081cd7437bd2871de85b37ee88164e80417bbdbf Author: Michael T. Wolfinger Date: Wed Feb 21 20:26:09 2018 +0100 add recipe for perl-bio-viennangs v0.18 (#7955) * add recipe for perl-bio-viennangs v0.18 * typo fixed * removed perl-bio-sequtils dependency * added ucsc-fatotwobit dependency * added ucsc-bedtobigbed dependency * removed file-basename dependency commit f78b0cc9f6eb6a7ee41bae22bf670e063d1d894a Author: Marcel Martin Date: Wed Feb 21 18:23:37 2018 +0100 Cutadapt 1.16 (#7957) commit 1b963b5d872c56bdebb568e4898c210cff0f3c61 Author: Karl Nordström Date: Wed Feb 21 17:49:20 2018 +0100 Adding Bis-SNP v0.82.2. (#7397) * Adding Bis-SNP v0.82.2. The bioconda code is built upon the picard code commit 6831a0dd473d60598b77511642b51ee5303d3375 Author: Michael T. Wolfinger Date: Wed Feb 21 17:39:57 2018 +0100 add recipe for perl-file-share (#7959) commit c6f951bb16cafd902ee77954ebddfd38741dfab0 Author: Johannes Köster Date: Wed Feb 21 12:25:31 2018 +0100 snakemake 4.7.0 (#7952) * snakemake 4.7.0 * Add missing dependency. commit f55c4f31bd298c5a12e6b58f134366afb0c61d43 Author: Michael T. Wolfinger Date: Tue Feb 20 22:44:35 2018 +0100 add recipe for perl-ipc-cmd (#7951) commit 9185d701d3256ac16fc1738ee8ccf9c42e944a27 Author: David Laehnemann Date: Tue Feb 20 21:27:55 2018 +0100 prosolo: update to version 0.4.0 (#7948) commit 1d4480049a8d83a7dc8352e1e71c7186fa1028e1 Author: Florian Eggenhofer Date: Tue Feb 20 20:33:04 2018 +0100 Added libxml2 dependency, unblacklisted cmv recipe (#7860) * Added libxml2 dependency, unblacklisted cmv recipe * Changed constraint on libgmp * Updated stack, gmp * Updated gmp * Added pthread-stubs * Updated linker flags * Updated linker flags - again * Updated linker flags - 3 * Updated linker flags - 4 * Updated linker flags - 5 * Updated linker flags - 6 * Switched requested ghc variant * Updated linker flags - 7 * Updated - 8 * Updated - 9 * Updated - 10 * Updated library path * Passing threaded option to ghc * Passing stack install options also to setup * Changed stack setup options * Updated stack to 1.6.5 * Added lib and lib64 * Fixed extra lib path * Switched to /usr/lib64 * Simplifying recipe * Simplified recipe 2 commit ade8b7f1ced822c0c896758b4a80dcf88b6a42b7 Author: Michael T. Wolfinger Date: Tue Feb 20 20:06:29 2018 +0100 add perl-module-load-conditional 0.68 (#7946) commit 811a844ae0b2b4f4b3ffd33500bce4cc54e6ab0c Author: Davide Chicco Date: Tue Feb 20 13:11:59 2018 -0500 behst2.6 (#7945) commit 8bc76775fdec2f68aabbf15003ddb92a7fb7fbcc Author: Michael T. Wolfinger Date: Tue Feb 20 18:53:46 2018 +0100 add recipe for perl-module-corelist (#7944) commit f4c57db142c9521d551eee2c3114badf40bcde76 Author: Philippe Bordron Date: Tue Feb 20 18:25:21 2018 +0100 Stacks update to 2.0Beta8c (#7868) * Update to 2.0Beta8c * Update meta.yaml * revert back to linux only * Update meta.yaml * stacks 2.0: enable osx builds commit c3121f522a3006b023378c281ebbfff351533749 Author: Michael T. Wolfinger Date: Tue Feb 20 18:20:46 2018 +0100 add recipe for perl-test-file-contents (#7943) commit 0f8cb2039fcdc26780a7f3ee00b18fcc341be44b Author: Karl Nordström Date: Tue Feb 20 16:46:13 2018 +0100 update Bamutil (#7935) * bamutil: - push build number - switched build script to use curl - add zlib, curl and openssl as dependencies - disabled profiling in makefile as this stopped compilation - apply sed fix only to OPTFLAG_PROFILE line - adding review suggestions from mbargull - documenting the modification of the makefile - adding checksum for libStatGen - and adding the corresponding dependencies for the the check commit 611d3773084bad78cbee2386dd6cd3825b51b5fb Author: Davide Chicco Date: Tue Feb 20 09:51:33 2018 -0500 Behst2.5 (#7923) * Fixed the problem on the Python2.7 * edited python commands * Update build.sh * Update run_test.sh commit ca8cb8cf2402f5d204c729402dbcca023f49704d Author: Christian Brueffer Date: Tue Feb 20 15:27:07 2018 +0100 Add bioconductor-flowq. (#7936) commit 9ea7be364e28ce29d217225d3dd418b820d95c44 Author: Christian Brueffer Date: Tue Feb 20 14:29:53 2018 +0100 Remove r-idpmisc. (#7937) It is a general package and exists in conda-forge in the same version as in bioconda, thus our recipe is redundant. commit 1517b10c31b83f463be8ff5e807742d33f822cb1 Author: Christian Brueffer Date: Tue Feb 20 14:06:10 2018 +0100 Update Picard to 2.17.10. (#7934) commit 43fcd91ab60028c3b366f7d0612e4f3e47d26436 Author: Brad Chapman Date: Tue Feb 20 07:57:19 2018 -0500 Update: cwltool, cwltest, toil, arvados and deps (#7933) Updates cwltool to latest release shared by Toil and Arvados CWL runner. Includes matching updates to cwltool dependencies: cgcloud, cwltest and schema-salad. Unpins boto in toil, avoiding issues with old version of boto. Fixes chapmanb/bcbio-nextgen-vm#167 commit 6b53732252d4cde2f6ae388ad4b564b29e14d7f5 Author: Ralf Weber Date: Tue Feb 20 11:16:06 2018 +0000 Bump version dimspy (#7932) commit 368ffd42acbabd16ad5e6d2467d6145d24e6e94d Author: Michael T. Wolfinger Date: Tue Feb 20 11:52:54 2018 +0100 add perl-test-prereq (#7931) commit 8fa27a8fac754d07e2152fa2f64f8c082082bf91 Author: Michael T. Wolfinger Date: Tue Feb 20 11:22:53 2018 +0100 Perl module extract use (#7930) * add perl-module-extract-use commit 491664ec5a2d9a6cc1d0c9aaad316ec94919aac7 Author: Michael T. Wolfinger Date: Tue Feb 20 10:49:26 2018 +0100 Perl ppi (#7924) * add perl-ppi * added perl-hook-lexwrap dependency * add perl-class-xsaccessor dependency * removed comments commit 660796790cc8f85a8e746c46643000a335344b53 Author: Michael T. Wolfinger Date: Tue Feb 20 09:36:04 2018 +0100 Perl test subcalls (#7865) * add perl-test-subcalls * fixed perl-test-builder-tester dependency * add perl-hook-lexwrap dependency commit d60d36ee4a5bfaa0c227147f75d354712def67f5 Author: Michael T. Wolfinger Date: Tue Feb 20 08:11:30 2018 +0100 add perl-class-xsaccessor (#7925) commit ca62523f8b3dc86a88dd6c989bbeed7d1c544ee5 Author: Christian Brueffer Date: Tue Feb 20 00:59:57 2018 +0100 Add r-tidygenomics. (#7929) commit 831566d4f04e7e6dd079eb4d88c24af275ed3d43 Author: ArneKr Date: Mon Feb 19 21:34:12 2018 +0100 Added recipe for cisPath (#7875) commit 68ea9b79d9ff32098aee0dd5dffc374d0315480a Author: ArneKr Date: Mon Feb 19 21:33:46 2018 +0100 Added recipe for ClassifyR (#7874) commit 40d1c2e175e20ba8a8691aaef165f166d9901ffb Author: ArneKr Date: Mon Feb 19 21:33:33 2018 +0100 Added recipe for CINdex (#7876) commit a0168ce576775bb4a5ed6c0ba267a6ece8de8324 Author: ArneKr Date: Mon Feb 19 21:33:19 2018 +0100 Added recipe for chromstaR (#7877) commit 94080b4a78ede7f03a4c18a2227e40415acad25b Author: ArneKr Date: Mon Feb 19 21:33:03 2018 +0100 Added recipe for ChromHeatMap (#7878) commit 38b8497d04efadbfc3d186413b6aa9832613664b Author: ArneKr Date: Mon Feb 19 21:32:29 2018 +0100 Added recipe for chopsticks (#7879) commit 395d53cd6dc5f56809c5446e7f1a67c3ae4982b6 Author: ArneKr Date: Mon Feb 19 21:31:56 2018 +0100 Added recipe for CGHnormaliter (#7882) commit 4944fedba12247cd6c62a443ae39e88a9b0a8167 Author: ArneKr Date: Mon Feb 19 21:30:47 2018 +0100 Added recipe for iCOBRA (#7883) commit b37ab5be03b7eeb5366d01ddaa03982461eab05a Author: ArneKr Date: Mon Feb 19 21:30:33 2018 +0100 Added recipe for iChip (#7884) commit 8680b5e53fc79b8a08dcd05421154802112029b1 Author: ArneKr Date: Mon Feb 19 21:15:39 2018 +0100 Added recipe for cleanUpdTSeq (#7873) commit 41dd406278999ac768d15ffc47ece1a99b360598 Author: ArneKr Date: Mon Feb 19 21:15:17 2018 +0100 Added recipe for clonotypeR (#7872) commit d22bed87ef04a16dc6ffa46978425f743e863b43 Author: ArneKr Date: Mon Feb 19 21:14:57 2018 +0100 Added recipe for clstutils (#7871) commit 19d5661362a63a572ce51b254e073b5a5fd2d4b5 Author: ArneKr Date: Mon Feb 19 21:14:36 2018 +0100 Added recipe for ibh (#7885) commit d9087168d9ed8bdb480f9df2668ed879b8e91708 Author: ArneKr Date: Mon Feb 19 21:14:12 2018 +0100 Added recipe for iASeq (#7886) commit 873f4af0e3aad26a7839fe80b144b4ab92a91765 Author: ArneKr Date: Mon Feb 19 21:12:50 2018 +0100 Added recipe for CancerInSilico (#7887) commit 649b44ce2edd2aa702f7ff6d1bcf17e5bf28b87e Author: ArneKr Date: Mon Feb 19 21:12:37 2018 +0100 Added recipe for BUS (#7888) commit 60aaee4246659bd07a3dba3373fec18868f5d9a5 Author: ArneKr Date: Mon Feb 19 21:12:26 2018 +0100 Added recipe for BufferedMatrixMethods (#7889) commit 63270220ff728ba221cc6d68f662d48fc98ccd67 Author: ArneKr Date: Mon Feb 19 21:11:47 2018 +0100 Added recipe for BrowserVizDemo (#7890) commit 0dd4f6cc5a10a85ff0f8924ffe28420cf838d3a5 Author: ArneKr Date: Mon Feb 19 21:11:30 2018 +0100 Added recipe for bridge (#7891) commit 1732cad70dda834e7d08fa50da8a5707e5332617 Author: ArneKr Date: Mon Feb 19 21:10:52 2018 +0100 Added recipe for BrainStars (#7892) commit 1521cde047f286dca20457ee0abd28ae6ba286df Author: ArneKr Date: Mon Feb 19 21:10:41 2018 +0100 Added recipe for BiRewire (#7893) commit e56203461322252832f436a95948c7f2cb6dd03a Author: ArneKr Date: Mon Feb 19 21:10:21 2018 +0100 Added recipe for BioQC (#7895) commit bb6791a311a4e258bb514e0c40ef6355197fd701 Author: ArneKr Date: Mon Feb 19 20:09:52 2018 +0100 Added recipe for biosvd (#7894) commit 7487c126415414581bd5cdbdb00ac455e7602c6c Author: ArneKr Date: Mon Feb 19 20:09:40 2018 +0100 Added recipe for hopach (#7901) commit 56792d451e88c3acc7658cccaed54395f540a6f8 Author: Paolo Di Tommaso Date: Mon Feb 19 20:06:32 2018 +0100 nextflow 0.27.6 (#7864) commit 78cacc91edf17111c69c6b344bffa35fc8181ead Author: ArneKr Date: Mon Feb 19 20:06:04 2018 +0100 Added recipe for BioMVCClass (#7896) commit 356f46fd181495bae0f2f82a11258f82c8e2e7ac Author: ArneKr Date: Mon Feb 19 20:02:45 2018 +0100 Added recipe for hyperdraw (#7897) commit b8c3bff0cee1efa1318be8fade5b3b2bf73ba2a5 Author: ArneKr Date: Mon Feb 19 20:02:28 2018 +0100 Added recipe for HybridMTest (#7898) commit f7e5b8d6dbb18e037096f6e91e4f8007295c9c5b Author: ArneKr Date: Mon Feb 19 20:01:19 2018 +0100 Added recipe for htSeqTools (#7899) commit 398d27b46aac58e54e6cafe2ad1ee633835f3330 Author: ArneKr Date: Mon Feb 19 19:35:18 2018 +0100 Added recipe for HTqPCR (#7900) commit 5184537aed24cccae1aaa08713e2ba1428c0f662 Author: ArneKr Date: Mon Feb 19 19:18:35 2018 +0100 Added recipe for HiTC (#7902) commit 3f120a09032cc9b532707e2ced9e9ecdfe48b0a7 Author: ArneKr Date: Mon Feb 19 19:00:00 2018 +0100 Added recipe for HIBAG (#7903) commit 35832be06334043ac08fa26a01090a254acf5f28 Author: ArneKr Date: Mon Feb 19 18:59:42 2018 +0100 Added recipe for HEM (#7904) commit 3c04f152889dca8e904d054e840c0660084fe956 Author: ArneKr Date: Mon Feb 19 18:54:30 2018 +0100 Added recipe for HELP (#7905) commit eb95f49690655bf720ae3cfe935d918d71df0ecf Author: ArneKr Date: Mon Feb 19 18:50:23 2018 +0100 Added recipe for Harshlight (#7906) commit af0f2dc6022a851b0d15beed4b19f8f9acb59c7e Author: ArneKr Date: Mon Feb 19 18:50:10 2018 +0100 Added recipe for Harman (#7907) commit 4103c4fe56eb97192a4f61abcb10fc5276dfe683 Author: ArneKr Date: Mon Feb 19 18:43:49 2018 +0100 Added recipe for GSRI (#7908) commit bc5e0e08552b6369a456d5b11794e756fe1272d4 Author: ArneKr Date: Mon Feb 19 18:29:29 2018 +0100 Added recipe for GSReg (#7909) commit 4fa732f24cddd558b74fc1d3d1f1e5d9c3bfa3e6 Author: Michael T. Wolfinger Date: Mon Feb 19 18:23:53 2018 +0100 add perl-test-object (#7921) commit 07a60076e50b30e0da8031d33e978db3202c6d26 Author: ArneKr Date: Mon Feb 19 18:22:58 2018 +0100 Added recipe for GSEAlm (#7910) commit 6aa3f9f7f823a928825ea7bc4b5fa445b15003de Author: ArneKr Date: Mon Feb 19 18:22:35 2018 +0100 Added recipe for GSCA (#7911) commit 35a903d706f7f663992feaa379b80229eb8efdb9 Author: ArneKr Date: Mon Feb 19 18:22:11 2018 +0100 Added recipe for GSALightning (#7912) commit f87e8f0babd75b4dccc7b7a8304375545e991579 Author: ArneKr Date: Mon Feb 19 18:21:52 2018 +0100 Added recipe for GRmetrics (#7913) commit 73c58dfa5144ffa6f0de07d1624d96d1755206eb Author: ArneKr Date: Mon Feb 19 18:21:35 2018 +0100 Added recipe for GraphAT (#7914) commit 0487b213def927148ad5a582b988ce88a3a74332 Author: ArneKr Date: Mon Feb 19 18:12:41 2018 +0100 Added recipe for ChIPXpress (#7880) commit f47f67dd55dc8804814ee9080cded9a5eb692897 Author: ArneKr Date: Mon Feb 19 18:12:21 2018 +0100 Added recipe for ChIPsim (#7881) commit 459c7e7a8596b0d0a1d0287cc1ad6b450c86d611 Author: Michael T. Wolfinger Date: Mon Feb 19 18:11:44 2018 +0100 add perl-file-remove (#7870) commit 615430729e9a4f7c8fd6ee57f3b8e4a7d6a2a538 Author: ArneKr Date: Mon Feb 19 18:11:25 2018 +0100 Added recipe for gpls (#7915) commit 15145ca5ec4438347789bccc8ad1673681bebfae Author: ArneKr Date: Mon Feb 19 18:02:19 2018 +0100 Added recipe for goTools (#7916) commit 7898f493a8e3c3769a673f02c4df3e180ea3b74f Author: ArneKr Date: Mon Feb 19 17:56:35 2018 +0100 Added recipe for wateRmelon (#7917) commit d712bb15af4eeda235286174e4747dc2cf3792f4 Author: ArneKr Date: Mon Feb 19 17:31:33 2018 +0100 Added recipe for waveTiling (#7918) commit 68f0f068375f130fc5f9ebc3c2718f4a44adfceb Author: Jim Johnson Date: Mon Feb 19 09:43:29 2018 -0600 flashlfq_0.1.101 (#7919) * flashlfq_0.1.101 Update flashlfq to version 0.1.101 * flashlfq_0.1.101 update sha256 commit 1c12b3aba79ac8251b7e5c2139fb315446848a1e Author: Renan Valieris Date: Mon Feb 19 10:16:00 2018 -0300 fix metavelvet recipe (#7813) * fix metavelvet recipe commit 109b6f10c5703fcc65a219ee255d3d1bdaeaba1c Author: Michael T. Wolfinger Date: Mon Feb 19 11:30:06 2018 +0100 add perl-hook-lexwrap (#7863) commit 51eed1481db69a43c7b86e85dbba5ee86987907a Author: Michael T. Wolfinger Date: Mon Feb 19 08:34:53 2018 +0100 update perl-pathtools -> 3.73 (#7862) * update perl-pathtools -> 3.73 * added tests commit 04936800915d16839e25eb8f4d30dd4f55f3cae6 Author: Bérénice Batut Date: Mon Feb 19 00:12:27 2018 +0100 Add metaphlan2 2.7.5 (#7861) commit d6615c2316649d551ef30c622b5f6263f00ccb09 Author: ArneKr Date: Sun Feb 18 17:39:08 2018 +0100 Added recipe for interactiveDisplay (#7852) commit 99b99f7d53f8b0173053b6d8b8d9277a8c3c84b5 Author: ArneKr Date: Sun Feb 18 17:38:55 2018 +0100 Added recipe for inveRsion (#7851) commit 681dcc590e065cd0a3a8f5b6f75fc456cb97d07a Author: ArneKr Date: Sun Feb 18 17:38:45 2018 +0100 Added recipe for IPPD (#7850) commit d8d5dc508d22460bc9e802d56d3f442ab736fa5b Author: ArneKr Date: Sun Feb 18 17:38:34 2018 +0100 Added recipe for iSeq (#7849) commit e2a9db68cb6f05d9c8992f7eac1c448839bdadd4 Author: ArneKr Date: Sun Feb 18 17:38:25 2018 +0100 Added recipe for ISoLDE (#7848) commit cda3242dcdb7d80c75794b678d09286b67477c34 Author: ArneKr Date: Sun Feb 18 17:37:41 2018 +0100 Added recipe for iterativeBMA (#7847) commit de2d757122bb1d33721899384814a065194c680c Author: ArneKr Date: Sun Feb 18 17:37:34 2018 +0100 Added recipe for iterativeBMAsurv (#7846) commit 21ae3249cef94cc7a4c1687efb956a2932380edb Author: ArneKr Date: Sun Feb 18 17:37:26 2018 +0100 Added recipe for MCRestimate (#7845) commit 3ccf0050d80b1116ab6b3bde2c0024021a8813b1 Author: ArneKr Date: Sun Feb 18 17:37:19 2018 +0100 Added recipe for KEGGlincs (#7844) commit 024eaa8c1dda5b132bb03cbdbf0cf5803f68af36 Author: ArneKr Date: Sun Feb 18 17:37:09 2018 +0100 Added recipe for keggorthology (#7843) commit 5affeb1b850762a47c58c26025635b14e1027964 Author: ArneKr Date: Sun Feb 18 17:34:42 2018 +0100 Added recipe for kimod (#7842) commit 9b6c93d4ff5ddebedf80b79598c92fb44d93ba86 Author: ArneKr Date: Sun Feb 18 17:34:37 2018 +0100 Added recipe for LBE (#7841) commit 4b4355a6f07420ae0aa4a6c5e2ba5b4a414881dc Author: ArneKr Date: Sun Feb 18 17:34:27 2018 +0100 Added recipe for les (#7840) commit 85a2a0519e9005e66ead5210e35fe508ea896395 Author: ArneKr Date: Sun Feb 18 17:34:17 2018 +0100 Added recipe for lfa (#7839) commit 9d277158aef743e7da90fde7e576ac42d6403ae9 Author: ArneKr Date: Sun Feb 18 17:34:00 2018 +0100 Added recipe for LINC (#7838) commit 462294a6902625cefc3f4431f7eaf02d39304478 Author: ArneKr Date: Sun Feb 18 17:33:53 2018 +0100 Added recipe for CMA (#7837) commit 5a7f50c07eb8bfb36f2bb15e135e4adb06888603 Author: ArneKr Date: Sun Feb 18 17:33:48 2018 +0100 Added recipe for cn.farms (#7836) commit d4b20632ef941d7643c0baba80aa7bcc431a5c45 Author: ArneKr Date: Sun Feb 18 17:33:41 2018 +0100 Added recipe for LiquidAssociation (#7835) commit 296f0c1f6461036563778bcc695369bf812ac4f3 Author: ArneKr Date: Sun Feb 18 17:33:33 2018 +0100 Added recipe for lmdme (#7833) commit ab586c21abf0e5f88a3e2f13d3edf199674803bb Author: ArneKr Date: Sun Feb 18 17:33:26 2018 +0100 Added recipe for CNVPanelizer (#7832) commit 87c5376fa5932039e1f3a9a7433477b7f2d664c9 Author: ArneKr Date: Sun Feb 18 17:33:12 2018 +0100 Added recipe for LOBSTAHS (#7831) commit 1fe51b48e40a5988ebb6476d32ca573571a366cf Author: ArneKr Date: Sun Feb 18 17:32:44 2018 +0100 Added recipe for CNVtools (#7830) commit 65c567fcc7485a1654777b79ef5bb3377434ae02 Author: ArneKr Date: Sun Feb 18 17:32:19 2018 +0100 Added recipe for INSPEcT (#7853) commit ff51b3819da54ce8d4544a5ec559586247cb8b65 Author: ArneKr Date: Sun Feb 18 17:29:20 2018 +0100 Added recipe for INPower (#7854) commit ba0d7d5f734c5765021f18aaf800149db2321dae Author: ArneKr Date: Sun Feb 18 17:28:54 2018 +0100 Added recipe for ImpulseDE (#7855) commit a2a0bbf2dece573dc4a4d67e3084552ddc08ab5c Author: ArneKr Date: Sun Feb 18 17:25:42 2018 +0100 Added recipe for clusterStab (#7856) commit 064df095e36aae59a61d2567a245717d42b11087 Author: ArneKr Date: Sun Feb 18 17:25:29 2018 +0100 Added recipe for ClusterSignificance (#7857) commit 2c61e34eac4d92b1e50e52ce7d224e18f59eaeac Author: ArneKr Date: Sun Feb 18 17:23:32 2018 +0100 Added recipe for CNORfuzzy (#7834) commit bdcdb57634855dff1a9f64abc71c8bb6c4f0b38e Author: ArneKr Date: Sun Feb 18 17:22:09 2018 +0100 Added recipe for clustComp (#7858) commit e6826bb5adadd0250b0e47702554e3b7ad5e530d Author: ArneKr Date: Sun Feb 18 17:16:20 2018 +0100 Added recipe for lol (#7829) commit b9cf497976ba3c82de862a17fb43bb5255c0221c Author: Paolo Di Tommaso Date: Sun Feb 18 17:14:58 2018 +0100 nextflow 0.27.5 (#7817) commit 189b08ff36423d21de413a2f45c2ec7331e832fb Author: Michael T. Wolfinger Date: Sun Feb 18 00:20:04 2018 +0100 add perl-moosex-clone (#7826) * add perl-moosex-clone * Update build.sh * removed comments from meta.yaml commit 6f5d5294ec9303b2d6249a681fe734ba50852991 Author: Michael T. Wolfinger Date: Sat Feb 17 23:53:02 2018 +0100 added perl-data-visitor and perl-tie-toobject (#7812) * added perl-data-visitor and perl-tie-toobject * fixed runtime perl requirements * Update build.sh commit 56cfbde81d6e80520a2b16f08af1e16a638f6aeb Author: Florian Eggenhofer Date: Sat Feb 17 23:46:51 2018 +0100 Updated to version 2.1.3 (#7828) commit df2937f2ffa5e40091d6602cf919031cbcad5dc0 Author: Christian Brueffer Date: Sat Feb 17 23:12:28 2018 +0100 Add bioconductor-ffpe. (#7388) commit 1b4d77cd6605853746d3bfb9f20c3c5e11cd9cae Author: Björn Grüning Date: Sat Feb 17 18:29:28 2018 +0100 Update meta.yaml (#7825) commit d7a7d03c969e4379ff00218a8bb1012a0e0f5c82 Author: Michael T. Wolfinger Date: Sat Feb 17 18:24:39 2018 +0100 Perl hash util fieldhash compat (#7821) * added recipe for perl-tie-refhash * updated license * added recipe for perl-tie-refhash-weak * add perl-hash-util-fieldhash-compat recipe * fixed perl dependencies commit 9fbdb9d18d714d6d43d4376fbcf967ce6055ab7f Author: Michael T. Wolfinger Date: Sat Feb 17 10:41:17 2018 +0100 added recipe for perl-tie-refhash (#7801) * added recipe for perl-tie-refhash * updated license * added recipe for perl-tie-refhash-weak commit 960a2b127c487f5263229541df5d3e5567040b87 Author: Johannes Köster Date: Sat Feb 17 09:42:22 2018 +0100 Pin bamtools (#7701) * Pin bamtools * Pin bamtools. * fix build string. * increase build number * Fix lints. * fix constraint commit 5fbf388903e6d0dc70bfb1f351ea4216d047af1f Author: Dan Fornika Date: Fri Feb 16 17:54:02 2018 -0800 Update MentaliST to v0.2.1 (#7824) commit 68e8b620728059ebb75bf1366e225dd41df3902d Author: Dan Fornika Date: Fri Feb 16 16:18:15 2018 -0800 Move MentaLiST v0.1.3 recipe to separate directory (#7818) * Add MentaLiST v0.1.3 recipe to separate dir * mentalist 0.1.3: workaround SSL certificate issue commit 29cacdfc0ad0004ddfc09475dbddaaa0ecc2e104 Author: Phillip Brooks Date: Fri Feb 16 16:15:00 2018 -0800 Bump kaiju to latest version (#7213) * Changed url to master from latest version Modified url to master from latest release to take advantage of recent changes including gzip compatibility. * Updated url to reference latest commit Modified url from master to latest commit to enable reproducibility * Change to released version * Trying to fix OS10 error - Modified fn * Attempting to fix macOS build error * Update meta.yaml * troubleshooting kaiju build on macOS added -p per https://github.com/bioinformatics-centre/kaiju/issues/20 * Changed -p to -e troubleshooting macos build. Linux build is passing. Getting the following error '''File "/tmp/workspace/miniconda/bin/conda-build", line 6, in sys.exit(conda_build.cli.main_build.main()) File "/tmp/workspace/miniconda/lib/python3.6/site-packages/conda_build/cli/main_build.py", line 342, in main execute(sys.argv[1:]) File "/tmp/workspace/miniconda/lib/python3.6/site-packages/conda_build/cli/main_build.py", line 333, in execute noverify=args.no_verify) File "/tmp/workspace/miniconda/lib/python3.6/site-packages/conda_build/api.py", line 97, in build need_source_download=need_source_download, config=config) File "/tmp/workspace/miniconda/lib/python3.6/site-packages/conda_build/build.py", line 1524, in build_tree config=config) File "/tmp/workspace/miniconda/lib/python3.6/site-packages/conda_build/build.py", line 1147, in build utils.check_call_env(cmd, env=env, cwd=src_dir) File "/tmp/workspace/miniconda/lib/python3.6/site-packages/conda_build/utils.py", line 628, in check_call_env return _func_defaulting_env_to_os_environ(subprocess.check_call, *popenargs, **kwargs) File "/tmp/workspace/miniconda/lib/python3.6/site-packages/conda_build/utils.py", line 624, in _func_defaulting_env_to_os_environ return func(_args, **kwargs) File "/tmp/workspace/miniconda/lib/python3.6/subprocess.py", line 291, in check_call raise CalledProcessError(retcode, cmd) subprocess.CalledProcessError: Command '['/bin/bash', '-x', '-e', '/tmp/workspace/miniconda/conda-bld/kaiju_1517006552538/work/kaiju-1.6.0/conda_build.sh']' returned non-zero exit status 2.''' * Updating test command as per suggestion from @mbargull * kaiju: update to 1.6.1 * kaiju: fix no_link entry commit de71fa6bb2455dcf61a9e9a2d04567169d37a078 Author: Marcel Bargull Date: Sat Feb 17 00:19:19 2018 +0100 stacks 2.0: add lower bound for libgcc version (#7815) * stacks 2.0: add lower bound for libgcc version * stacks 2.0: remove never used [linux32] * stacks 2.0: nearly forgot to bump build number! commit f609a6c37e5a1df8b3b418e15b24ed02292b536f Author: Brad Chapman Date: Fri Feb 16 17:57:57 2018 -0500 Update: bcbio to avoid htslib pinning (#7820) Avoids downgrades of bcbio on htslib changes. commit 685f80c4c27330b8bf9a9b3cd6abcadfa773308c Author: Marcel Bargull Date: Fri Feb 16 23:46:41 2018 +0100 edlib: update to 1.2.3 (#7697) * edlib: update to 1.2.3 * edlib: cleanup; remove subdirs of unmaintained old versions * edlib: add a note about the aligner exe rename commit e08546f666e5184d098222ed8a549f645de893ef Author: ArneKr Date: Fri Feb 16 15:41:00 2018 +0100 Added recipe for codelink (#7811) commit 3d023871794a16247d84b35ebd5e0d1ad2e1fd4c Author: ArneKr Date: Fri Feb 16 15:40:49 2018 +0100 Added recipe for cogena (#7810) commit 2c5257e3145e029654647e5edb93c11456d18919 Author: ArneKr Date: Fri Feb 16 15:40:38 2018 +0100 Added recipe for coGPS (#7809) commit 20e13504ec0a461e452514c39e480d19fd47d392 Author: ArneKr Date: Fri Feb 16 15:40:25 2018 +0100 Added recipe for COHCAP (#7808) commit 73c8558079f53606535b02b9798332575163ea4b Author: ArneKr Date: Fri Feb 16 15:40:16 2018 +0100 Added recipe for COMPASS (#7807) commit 76f193a8f3af37792dde863b141331b832f57239 Author: ArneKr Date: Fri Feb 16 15:40:03 2018 +0100 Added recipe for consensusSeekeR (#7806) commit bd17cf50b63b169de2d5d5489fea3684a1e47197 Author: ArneKr Date: Fri Feb 16 15:39:53 2018 +0100 Added recipe for contiBAIT (#7805) commit 2a3284fa555463f820b96c6e509d1b454c226208 Author: ArneKr Date: Fri Feb 16 15:39:39 2018 +0100 Added recipe for CopywriteR (#7804) commit 9a4c23a346831361d0facdcbc7a7b840ec662a18 Author: ArneKr Date: Fri Feb 16 15:39:29 2018 +0100 Added recipe for Cormotif (#7803) commit 474da29ecdb802dc17702324a159e0d6d0d4b504 Author: ArneKr Date: Fri Feb 16 15:39:16 2018 +0100 Added recipe for CORREP (#7802) commit af2846bf3a15239256647935f6af16c2f676db2f Author: ArneKr Date: Fri Feb 16 12:13:20 2018 +0100 Added recipe for cosmiq (#7800) commit d1d74e7aca1d1fe8f8c11f5f20fdaab0e8a93a8e Author: ArneKr Date: Fri Feb 16 12:13:05 2018 +0100 Added recipe for LPEadj (#7799) commit d55cdbcee9910ee38da2ba47870dd963a6e51ba5 Author: ArneKr Date: Fri Feb 16 12:12:40 2018 +0100 Added recipe for lpNet (#7798) commit ca39a394931046ca0dc3daea8dad0792c40fc244 Author: ArneKr Date: Fri Feb 16 11:02:45 2018 +0100 Added recipe for LVSmiRNA (#7797) commit 6f1fd7162a2f40054ea88d1f39d6f2e08ff4b840 Author: ArneKr Date: Fri Feb 16 11:02:35 2018 +0100 Added recipe for M3D (#7796) commit 4f36b1dcfff1ad38fb09afd152a98dc9080e075e Author: ArneKr Date: Fri Feb 16 11:02:26 2018 +0100 Added recipe for MADSEQ (#7795) commit b8710ea15aec03fd7d5423b5dfa489f1abf795ac Author: ArneKr Date: Fri Feb 16 11:02:16 2018 +0100 Added recipe for maigesPack (#7794) commit af45c76c859307f3e4089b1c637acc2b9aad36ce Author: ArneKr Date: Fri Feb 16 11:02:05 2018 +0100 Added recipe for maPredictDSC (#7793) commit f43643c4eb2615af584d092ee9c608d8f72ddab4 Author: ArneKr Date: Fri Feb 16 11:01:54 2018 +0100 Added recipe for maskBAD (#7792) commit be2288e92449d99222ba6c3f8c1adb7a9df4bb9b Author: ArneKr Date: Fri Feb 16 11:01:43 2018 +0100 Added recipe for MeasurementError.cor (#7791) commit 97447fd7cc2afc4a3f8d0835379e562e4b12eafc Author: ArneKr Date: Fri Feb 16 11:01:32 2018 +0100 Added recipe for covRNA (#7790) commit 2c7b1db449e2a5dc6eefddff5b5bb3711c8d4bdf Author: ArneKr Date: Fri Feb 16 11:01:19 2018 +0100 Added recipe for cpvSNP (#7789) commit 4a9e9315bd53b336affea2295da513e443cc66c6 Author: ArneKr Date: Fri Feb 16 11:01:08 2018 +0100 Added recipe for CRImage (#7788) commit 28c271a65e128054fc2448a1f82ca1364f400b8c Author: ArneKr Date: Fri Feb 16 11:00:57 2018 +0100 Added recipe for crisprseekplus (#7787) commit eb9a61579fc6b7939b4fec3adafeba3d710a963e Author: ArneKr Date: Fri Feb 16 11:00:48 2018 +0100 Added recipe for CrispRVariants (#7786) commit 7c00edec35ea441323e24b6bfaa6e55cd74b9aff Author: ArneKr Date: Fri Feb 16 11:00:38 2018 +0100 Added recipe for ctsGE (#7785) commit 7fd3290d20079942141270dd3046f99c0c9f9542 Author: ArneKr Date: Fri Feb 16 11:00:27 2018 +0100 Added recipe for CVE (#7784) commit 701554008788f1acf6e6e5ae269b9ebaa2a18873 Author: ArneKr Date: Fri Feb 16 10:59:27 2018 +0100 Added recipe for daMA (#7783) commit ecbe68afb9621d2bfef8f7343665dd53e1bc7ece Author: ArneKr Date: Fri Feb 16 10:59:17 2018 +0100 Added recipe for DBChIP (#7782) commit 5a81b3668bc43104528cee7c172fa48d3a663f2f Author: ArneKr Date: Fri Feb 16 10:59:07 2018 +0100 Added recipe for dcGSA (#7781) commit e04cfa5106e4d9cbeaccd3fb703d8d2eeb7a6717 Author: ArneKr Date: Fri Feb 16 10:58:57 2018 +0100 Added recipe for DChIPRep (#7780) commit 0dbfaa94ef87e9015c489a21f68097b5f1008474 Author: ArneKr Date: Fri Feb 16 10:58:46 2018 +0100 Added recipe for MEDME (#7779) commit 91e133ff7e435af4167c0ecd6d850aa21a83c723 Author: ArneKr Date: Fri Feb 16 10:58:36 2018 +0100 Added recipe for MEIGOR (#7778) commit 7539cb1f7b176c457d03cce0fb6b819056a93ac8 Author: ArneKr Date: Fri Feb 16 10:58:27 2018 +0100 Added recipe for ddCt (#7777) commit fa1db5afa6e7c8d11a27848ea41a2ad0c2b4cb37 Author: ArneKr Date: Fri Feb 16 10:58:17 2018 +0100 Added recipe for meshes (#7776) commit 48596f67f7bf9fc7d7334391dc7b56df9bd14d55 Author: ArneKr Date: Fri Feb 16 10:58:06 2018 +0100 Added recipe for Metab (#7775) commit 1eee769d731a4db9104ba6d40d756d90aaadc378 Author: ArneKr Date: Fri Feb 16 10:57:56 2018 +0100 Added recipe for MetaboSignal (#7774) commit 7213e2202b5ac6e41b9f0c5bc13cadd0c97a6fa9 Author: ArneKr Date: Fri Feb 16 10:57:46 2018 +0100 Added recipe for methyAnalysis (#7773) commit bc0ae5f97c05f209b453c88038d1bcb5ce65a616 Author: ArneKr Date: Fri Feb 16 10:57:34 2018 +0100 Added recipe for DEDS (#7772) commit ee795343e7981a097f7c8f4e9cf70e8dacbfe890 Author: ArneKr Date: Fri Feb 16 10:52:04 2018 +0100 Added recipe for DNABarcodes (#7771) commit 192652e2e11f1e02cc3a9a38b29c4f73eb00723c Author: ArneKr Date: Fri Feb 16 10:51:54 2018 +0100 Added recipe for DOQTL (#7770) commit 9c1cee43f363004080d03b2506638bcb4880947d Author: ArneKr Date: Fri Feb 16 10:51:44 2018 +0100 Added recipe for DrugVsDisease (#7769) commit a1d85fcdd34576fbd2b6aa5f2fff50a2ae200ced Author: ArneKr Date: Fri Feb 16 10:51:34 2018 +0100 Added recipe for DeepBlueR (#7768) commit 23dc220d680c9b1da32715aff3f25bd0d78cabc7 Author: ArneKr Date: Fri Feb 16 10:51:25 2018 +0100 Added recipe for DEFormats (#7767) commit f2dfd95625f94356d3da230f054f213fa7393fe8 Author: ArneKr Date: Fri Feb 16 10:51:15 2018 +0100 Added recipe for DEGraph (#7766) commit 9773eca6b4061621c3a8cb4ee767edaf78078caa Author: ArneKr Date: Fri Feb 16 10:51:06 2018 +0100 Added recipe for DeMAND (#7765) commit 083d18eaab39c67a0792432f432734daa826e308 Author: ArneKr Date: Fri Feb 16 10:50:57 2018 +0100 Added recipe for MineICA (#7764) commit 5724e1a14927500a2577c62d8a71406ba1897e0e Author: ArneKr Date: Fri Feb 16 10:50:47 2018 +0100 Added recipe for MinimumDistance (#7763) commit ca5c4cf85d04c2c26abc65b7cd6a92dd439c034e Author: ArneKr Date: Fri Feb 16 10:50:37 2018 +0100 Added recipe for mirIntegrator (#7762) commit 77848f99a6a2faff12e66bef93b5271cbf0ccb68 Author: ArneKr Date: Fri Feb 16 10:50:27 2018 +0100 Added recipe for miRNAmeConverter (#7761) commit ef45abfdf51b61745b86d0ff21de952c06cba394 Author: ArneKr Date: Fri Feb 16 10:50:17 2018 +0100 Added recipe for dexus (#7760) commit 7429059fb12426ebec87d69f5363d920cb7e91bd Author: ArneKr Date: Fri Feb 16 10:50:07 2018 +0100 Added recipe for DFP (#7759) commit a34957866e222039370226ced200fd693d4bb01b Author: ArneKr Date: Fri Feb 16 10:49:57 2018 +0100 Added recipe for diffGeneAnalysis (#7758) commit 7c28f72c284b123548bcd20a3c01ca6c0272ddcf Author: ArneKr Date: Fri Feb 16 10:49:47 2018 +0100 Added recipe for diffloop (#7757) commit 06bbc6382d7e91c2b0fb93cd2ae8e991d907f523 Author: ArneKr Date: Fri Feb 16 10:49:39 2018 +0100 Added recipe for Director (#7756) commit 4cfe24096a9253201744279dcd1d61119516ecbe Author: ArneKr Date: Fri Feb 16 10:48:03 2018 +0100 Added recipe for easyRNASeq (#7755) commit 8e462b47e429f8a832e2c549a0881b7e945f6a1d Author: ArneKr Date: Fri Feb 16 10:47:52 2018 +0100 Added recipe for missMethyl (#7754) commit bbe4aa297b1e235f5a6202dfe10f62e45a5a0b93 Author: ArneKr Date: Fri Feb 16 10:47:39 2018 +0100 Added recipe for mQTL.NMR (#7753) commit 6e2949b5636bccadf429dff385b4da1fc54ca2dd Author: ArneKr Date: Fri Feb 16 10:47:28 2018 +0100 Added recipe for EDDA (#7752) commit 4da3d9a235745fb635728d826fb2e9b6113d6b76 Author: ArneKr Date: Fri Feb 16 10:47:15 2018 +0100 Added recipe for MSnID (#7751) commit cfb9dfda7c14d6e3ff3d1bb34da6eb0da67ee27d Author: ArneKr Date: Fri Feb 16 10:47:04 2018 +0100 Added recipe for EmpiricalBrownsMethod (#7750) commit d038257fa5ab7d07780eec0f094b83dfa722baff Author: ArneKr Date: Fri Feb 16 10:46:50 2018 +0100 Added recipe for ENCODExplorer (#7749) commit 49dfeba173c068c00d77c8f90242ce6c924f2af9 Author: ArneKr Date: Fri Feb 16 10:46:38 2018 +0100 Added recipe for EnrichmentBrowser (#7748) commit f3d9beceb7b0a140f01b768f877e00ba3655f469 Author: ArneKr Date: Fri Feb 16 10:46:27 2018 +0100 Added recipe for epigenomix (#7747) commit bada3577172e6996275aa096ee424b563a40d24c Author: ArneKr Date: Fri Feb 16 10:46:13 2018 +0100 Added recipe for MultiAssayExperiment (#7746) commit b59ea711067ca0c5d0688d0b3f620268d41859a0 Author: ArneKr Date: Fri Feb 16 10:46:05 2018 +0100 Added recipe for multiClust (#7745) commit d7299a87a53a0c7fb7a491740493e7e06b3ae23f Author: ArneKr Date: Fri Feb 16 10:45:54 2018 +0100 Added recipe for epivizrStandalone (#7744) commit f5598f5bce28e88046598c632bd53a5adec4716a Author: ArneKr Date: Fri Feb 16 10:45:43 2018 +0100 Added recipe for esetVis (#7743) commit 939d4b3244e6de4abe8b004c26c2a35edb836f5f Author: ArneKr Date: Fri Feb 16 10:45:32 2018 +0100 Added recipe for eudysbiome (#7742) commit c3e7457e7707f5dfc6056e6d35acdee4eab59dc0 Author: ArneKr Date: Fri Feb 16 10:45:21 2018 +0100 Added recipe for ExiMiR (#7741) commit e863f1e38728a851c3a06a26959b5ac8ae51cce8 Author: ArneKr Date: Fri Feb 16 10:45:10 2018 +0100 Added recipe for exomePeak (#7740) commit 18f13941934f6beddd776ce9ab6de8ac7fcc660b Author: ArneKr Date: Fri Feb 16 10:28:10 2018 +0100 Added recipe for FindMyFriends (#7739) commit c7c6fa93cd6adeeac57c2360de0731f6a5eff5cb Author: ArneKr Date: Fri Feb 16 10:27:53 2018 +0100 Added recipe for flowMatch (#7738) commit cfe965bbb3c1dee53cf06ce06d63a5e67c9f5a95 Author: ArneKr Date: Fri Feb 16 10:27:33 2018 +0100 Added recipe for geneRxCluster (#7737) commit c1ceebd1cf909f4bc3d2658fabb1b217d2a6d7cc Author: ArneKr Date: Fri Feb 16 10:27:23 2018 +0100 Added recipe for GeneSelector (#7736) commit 31be69de6867c9952edb589c8e976fd5912a2832 Author: ArneKr Date: Fri Feb 16 10:27:09 2018 +0100 Added recipe for PathoStat (#7735) commit 5a3d7d941fc0f173719ac5d995c3fbcd08755dc8 Author: ArneKr Date: Fri Feb 16 10:27:00 2018 +0100 Added recipe for pathRender (#7734) commit 61a797ba8838f2862bbfc5f2bc83c12b32ad7744 Author: ArneKr Date: Fri Feb 16 10:26:50 2018 +0100 Added recipe for pathVar (#7733) commit f5814e77455759c32eaaf24f1c4dd406d3cc36ab Author: ArneKr Date: Fri Feb 16 10:26:40 2018 +0100 Added recipe for Pbase (#7732) commit 9ba28aeed3682c88e5a1f4f79693e80806d62709 Author: ArneKr Date: Fri Feb 16 10:26:30 2018 +0100 Added recipe for geNetClassifier (#7731) commit 4c46c37026adbb87133008ad716529a35de3b2b2 Author: ArneKr Date: Fri Feb 16 10:26:19 2018 +0100 Added recipe for GeneticsDesign (#7730) commit 407f986496282d408e818210f21bc101c36ad8b3 Author: ArneKr Date: Fri Feb 16 10:23:56 2018 +0100 Added recipe for pcaGoPromoter (#7729) commit 13df0553bb2f8bb3e82c5102c87f3bfe84178047 Author: ArneKr Date: Fri Feb 16 10:23:45 2018 +0100 Added recipe for GenoGAM (#7728) commit 6119e849fbea7b9ca345a5d27ff305e9c91d6159 Author: ArneKr Date: Fri Feb 16 10:23:27 2018 +0100 Added recipe for PCpheno (#7727) commit e57e477c6eedb1cc7d697d97df9f5e070f8d8858 Author: ArneKr Date: Fri Feb 16 10:23:16 2018 +0100 Added recipe for GenRank (#7726) commit bd3ef4ed0b15dc65fb49a12a3edd258152558a11 Author: ArneKr Date: Fri Feb 16 10:23:06 2018 +0100 Added recipe for GEOsubmission (#7725) commit da7fb2f1725c48f4f361b047ae6707d3335d986a Author: ArneKr Date: Fri Feb 16 10:09:30 2018 +0100 Added recipe for pRolocGUI (#7724) commit 5bae735a184bff94a9c742dcc43a52cea5c6bcdf Author: ArneKr Date: Fri Feb 16 10:09:15 2018 +0100 Added recipe for qsea (#7723) commit a135a47526d87777436f70d745398649e7f946b0 Author: ArneKr Date: Fri Feb 16 10:08:47 2018 +0100 Added recipe for QuartPAC (#7722) commit 03ae80f0640245a3d27c76658979e72b99e26bda Author: ArneKr Date: Fri Feb 16 10:08:35 2018 +0100 Added recipe for QuaternaryProd (#7721) commit 11aba2ddd2d3d6a2d7d57f57a3698afcbcf62f78 Author: ArneKr Date: Fri Feb 16 10:08:22 2018 +0100 Added recipe for RareVariantVis (#7720) commit 5483ac702389de27b7cb39524baa947dbb1d6b65 Author: ArneKr Date: Fri Feb 16 10:08:11 2018 +0100 Added recipe for Rariant (#7719) commit 91704c72c8320901e2dcc4c58897d116cc0b8a9a Author: ArneKr Date: Fri Feb 16 10:07:46 2018 +0100 Added recipe for GAprediction (#7718) commit 74732d92c5e1c919b235a84a634be4f91de1ea58 Author: ArneKr Date: Fri Feb 16 10:07:00 2018 +0100 Added recipe for gcatest (#7716) commit 4fe7bdb4d7ed42e68fcb199d3659321762eaff81 Author: Philip Reiner Kensche Date: Fri Feb 16 10:04:06 2018 +0100 Perl json create (#7525) * Perl JSON::Create. * Fix. * Changed perl-threaded to perl. commit e947f4895df0622c2451dffb2b45c6cf38ea66a4 Author: Michael T. Wolfinger Date: Fri Feb 16 10:00:52 2018 +0100 add recipe fore perl-filedirutil (#7715) commit 01f6c50c11266729b6e9f7d3f97792f7fc7460fd Author: Michael T. Wolfinger Date: Fri Feb 16 07:22:14 2018 +0100 added recipes/perl-params-coerce (#7710) * added recipes/perl-params-coerce * updated perl-params-coerce meta.yaml * fixed meta.yaml * Delete bld.bat * specified acceptable perl versions commit ce2abe1491faf2f01bb4969f24607d84ac8300a0 Author: Andreas Sjödin Date: Thu Feb 15 23:13:56 2018 +0100 Fixing perl-net-ssleay (#7713) * Add perl-mime-base64 * Bump perl-net-ssleay * simplify test commit 1f9ec5890d7d67c075a134906796ffc0962ceeae Author: Björn Grüning Date: Thu Feb 15 21:50:16 2018 +0100 merge bulk into master (#7711) * Update bulk (#6274) * new version of graphicsmagick with --enable-symbol-prefix option when building (#6120) * add bioconductor v3.4 versions (#6124) * update r-aroma* (#6126) * create recipe for perl-types-standard (#6125) * Create build.sh * Create meta.yaml * Create recipe for perl-bio-cigar (#6118) * Create build.sh * Create meta.yaml * Update meta.yaml * Update meta.yaml * Update meta.yaml * Update meta.yaml * Update meta.yaml * Update meta.yaml * Update meta.yaml * remove bioconductor-peca from blacklist (#6129) * rebuild r-packages (#6128) * Update meta.yaml (#6134) * Add BamM package (#6133) * Add bamm * Update galaxy_sequence_utils to 1.1.1 (#6136) * updated recipe (#6138) * add bioconductor-jaspar2014 (#6137) * Haystack 0.5.2 (#6140) * updated recipe * updated recipe * dr-disco v0.11.0 (#6142) * Add several R and Bioconductor recipes (#5428) * initial version of recipes * remove last lines * add missing dependencies * added missing dependencies * added recipe for r-sfsmisc * move r-recipes to conda-forge and remove empty lines in bioc recipes * remove recipes that have been already added since last push * remove r-sfsmisc * Update gffread to 0.9.9. (#6146) * Add recipe for bioconductor-scran (#6143) * Initial recipe of bioconductor-scran * Modified R dependency * Updated cmv to version 1.0.6 (#6147) * Hansel | Pinning attrs version (#6135) * Added recipe for "Heidelberg Subtyping". This includes tailoring of the python environment within the build.sh file. * Fixing the directory within build.sh * Fixing the ordering of the sed command, moving to after the pip install. * Removing SED tailoring for now, and adding "which" as a test command. * Changing repository as we have now migrated to the PHAC NML repository. * Changing to official release branch now. * Fixing MD5 value. * Fixing requirements and test command. * Changing the testing command, as the new help contains invalid characters. * Removing list of authors from summary within meta.yaml. * Adding Detailed Summary Added detailed summary including authors. * Deleting python version file. Deleting un-needed file. * Changing recipe to rely on PyPi and fixed the build script. * Adding python setup parameters. * Removing pinning, and adding skip for Python 2. * Changing URL to standard. Added variable for hash type and val. * Pinning version of attrs. * Update trim_galore to 0.4.4. (#6148) * Downgrade networkx dependency (#6094) Networkx has recently been updated to 2.0, which is incompatible with `colormath` - `spectra` dependency (see https://github.com/ewels/MultiQC/pull/561 and https://github.com/ewels/MultiQC/issues/592). Until a new `colormath` version is released, we have to downgrade networkx dependency for MultiQC. * Updating Last (lastal) to v874 (#6141) * updating to last 874 * switch for OSX specific compilation with new makefile * adding 8 byte binaries (for large DBs using big RAM) * Snakemake 4.1.0 (#6150) * Update Bamm (#6156) * bump gnu-getopt build (#6157) gnu-getopt depends on gettext, which had a linking issue with 0.19.8 (fixed in 0.19.8.1). This bumps gnu-getopt to hopefully trigger a rebuild with gettext 0.19.8.1 from conda-forge * [WIP] add sis (#6055) * [WIP] add sis init * [wip] sis build passes local * [WIP] added python req * [WIP] changed build script * Add package MentaLiST-0.1.2 (#5856) * Initial commit * Updated to v0.1.2 * Updated url and sha256 hash * Filled in missing fn field * Added requirement mpfr * Specify openblas build to force conda-forge build of julia * Revert last change * Updated build section to skip osx build (no julia available) * Moved MentaLiST.jl -> mentalist symbolic link command to build.sh * Mapsembler2 (#6159) * Remove unneeded samtools run requirement (#6155) CrossMap uses pysam. * update shovill (#6152) * bumped shovill version to 0.8.0 * added conda_perl * added version requirements * discosnp (#6149) * discosnp * fix sed compatibility * pin zlib against {{CONDA_ZLIB}}* * Haystack 0.5.2 (#6164) * updated recipe * updated recipe * updated sha256 * Haystack 0.5.2 (#6165) * updated sha256 * fixed build number * Kissplice (#6154) * Kissplice * pin zlib against {{CONDA_ZLIB}}* * add python libraries * remove make test * fix python dependency * uncomment make test * IntaRNA v2.0.5 (#6160) * v2.0.5 released * reset build number to 0 * Update: bcbio-vm for ansible 2.x compatibility (#6167) * Adds Deeptools 1.5.8.2 and 1.5.9.1 (#6166) * deeptools: add old 1.5.8.2 version * deeptools: minor update for linux build * deeptools: add missing requirement for ucsc-bedgraphtobigwig * deeptools: add 1.5.9.1 * Perl io gzip (#6158) * first commit * first commit * Remove zlib-devel dependency * Add a dependency to zlib (zlib-devel not found) * Update build.sh with CFLAGS and LDFLAGS * update build.sh with CFLAGS and LDFLAGS * Add zlib reuirement * Back to the perl-io-html model * Back to the perl-io-html model + env vars for compliation and ld * [lint skip uses_setuptools for recipes/qcumber] * [lint skip uses_setuptools for recipes/qcumber] * [lint skip uses_setuptools for recipes/qcumber] * [lint skip uses_setuptools for recipes/qcumber] * [lint skip uses_setuptools for recipes/qcumber] * [lint skip uses_setuptools for recipes/qcumber] * pin zlib * bump build number (#6174) * Added recipe for bioconductor-copynumber (#6170) * Haystack 0.5.2 (#6176) * updated recipe * updated recipe * updated sha256 * fixed build number * updated hash * improved patch (#6173) * Update meta.yaml (#6179) Oups, I forgot to check the build number * Update Bamm (#6180) * Discosnp fix dependencies (#6182) * discosnp * fix sed compatibility * pin zlib against {{CONDA_ZLIB}}* * fix dependencies binaries not found during the execution * Bump mash to 2.0 (#6168) * Bump mash to 2.0 * Pin zlib * Discosnp fix scripts path in .sh (#6185) * discosnp * fix sed compatibility * pin zlib against {{CONDA_ZLIB}}* * fix dependencies binaries not found during the execution * fix scripts path in .sh * fix dbh5 path for copy * Update mssttitch version to 2.5 (#6181) * Update mssttitch version to 2.5 * Fix setup.py for conda after linting * GraphProt (#6183) * add GraphProt version 1.1.6 * update shiver (#6175) * update Graphprot version 1.1.7 (#6188) * add python3 dependency, need at least weblogo 3 * version bump * Tantan (#6189) Adding tantan: a utility for masking low complexity sequences * Updated haystack sha256 (#6178) * updated sha256 * updated sha256 * Haystack bio (#6190) * updated haystack 0.5.3 * updated haystack 0.5.3 * updated sha256 * updated sha256 * updated sha256 * updated sha256 * updated last aligner to 876 (#6191) * updated last aligner to 876 * updated spades to 3.11.1 bug-fix release (#6192) * updated sha256sum (#6193) * adding mappy (#6195) * adding mappy * adding import test * removed double whitelines * fixing yaml * fixing yaml - adding build * fixing yaml - removed space * fixing yaml - no idea * fixed files - maybe * added zlib * dummy change * trying environmental variables in build.sh * removed comments * specified CONDA zlib in requirements * adding nanolyse (#6196) * adding mappy * adding import test * removed double whitelines * fixing yaml * fixing yaml - adding build * fixing yaml - removed space * fixing yaml - no idea * fixed files - maybe * added zlib * dummy change * trying environmental variables in build.sh * removed comments * specified CONDA zlib in requirements * adding nanolyse * lowercase name * corrected import test * Fix url and description (#6197) * Update vcf2db to 2017.09.14. (#5433) * Bumped STAR-Fusion version (#6198) * HUMAnN2 requires diamond<0.9.0 (#6194) * HUMAnN2 requires diamond<0.9.0 * Fix pre-existing linting errors * Increment build numbers * update r-sartools (#6201) * Update: latest version with CollectErccMetrics (#6205) * Takeabreak software (#6145) * first commit for takeabreak * add zlib requirement * fix sed compatibility * pin zlib against {{CONDA_ZLIB}}* * delete decrease of memory * Mapsembler2 (#6206) * Mapsembler2 * fi mapsembler2 deps * Htseq 0.9.1 (#6204) * Add recipe for HTSeq-0.9.1 * Delete files * Add recipe for htseq * Update vsearch to 2.4.4 (#6211) * Update picard to 2.13 (#6212) * bump to 0.8.1 (#6058) * bump to 0.8.1 * change patch file to reflect updated code * add cflag to use C99 in the compiler. this is due toa new error in the new scrappie code * Add recipe for hicrep by Tao Yang. (#6213) * Explicit set of LGPL license (#6210) * Explicit set of LGPL license and move license link to license_file meta field * refer license_file to source directory * set explicit license instead of reference to LICENSE source file (#6208) * set explicit license instead of reference to LICENSE source file * add license_file info * update CIRCexplorer2 from 2.3.0 to 2.3.1 (#6214) * Flexbar 2.5.0 (#6187) * initial commit * move to separate dir and start 3.0.2 version * prepare version 3.0.3 * dont do 303 * enable osx and pin bzip2 and zlib * unpin bzip2 * have to create documentation directory * remove libgcc build dep * Add yanagiba (#6217) * Add yanagiba * Fix url * Remove duplicated dep * Skip py27 * update Graphprot tests to run in docker setup (#6218) * add python3 dependency, need at least weblogo 3 * version bump * remove libgcc runtime tep * see if libcxx is required at all * directly get test files from github * fix tests for wget download of test files * add wget runtime dependency for downloading testing data within docker * remove explicit python stuff, depends implicitely on python via weblogo * clean up test calls again * use curl instead of wget * Update bcftools to v1.6 (#6221) * [update] pyquant-ms to 0.2.1 (#6222) * Update version * Skip python 3 build * Commet recipe (#6220) * add commet recipe * add python dependency :) * Fix invalid license link (#6209) * Fix invalid license link Explicit set of license and add correct link to license file on github * add skip-lints as source uses only git_url, upstream not providing tags or archives * refer to license in source code instead of github link * use archive instead of git_url * increase build number to force new release update after modification of source url instead of git_url, increatse build number to get a new fresh built * fix license file location * Create recipe for rad_haplotyper (#6202) * Create build.sh * Create meta.yaml * Update meta.yaml * Update meta.yaml * Update snpEff, SnpSift to 4.3.1r. (#6224) * Update SnpSift to 4.3.1r. * Update snpEff to 4.3.1r. * Pairix 0.3.0 (#6223) * Update meta.yaml * Update build.sh * Update build.sh * Update build.sh * update sequana to version 0.5.2 (#6226) * Ped parser 1.6.6 (#6229) * Save ped_parser 1.6.5. * Update ped_parser to 1.6.6. * Fix LINT check setup_py_install_args. * Update htsbox to r340. (#6230) * ViennaRNA 2.4.1 (#6228) * build.sh of v2.3.5 * meta.yaml of v2.3.5 * tutorial build disabled * v2.4.1 enabled * summary tag indention * RNAlocmin disabled since not compiling * canu 1.6 (#6216) * canu 1.6 * set machine requirements * fix * remove the second test * Sift4g recipe (#6227) * Add recipe for HTSeq-0.9.1 * Add recipe for sift4g * Updating Hansel to version 0.2.0 (#6225) * Added recipe for "Heidelberg Subtyping". This includes tailoring of the python environment within the build.sh file. * Fixing the directory within build.sh * Fixing the ordering of the sed command, moving to after the pip install. * Removing SED tailoring for now, and adding "which" as a test command. * Changing repository as we have now migrated to the PHAC NML repository. * Changing to official release branch now. * Fixing MD5 value. * Fixing requirements and test command. * Changing the testing command, as the new help contains invalid characters. * Removing list of authors from summary within meta.yaml. * Adding Detailed Summary Added detailed summary including authors. * Deleting python version file. Deleting un-needed file. * Changing recipe to rely on PyPi and fixed the build script. * Adding python setup parameters. * Removing pinning, and adding skip for Python 2. * Changing URL to standard. Added variable for hash type and val. * Bumping version of bio_hansel to 0.2.0 * Fixing - to _ * add cassiopee index/search sequence tool (#6215) * add cassiopee index/search sequence tool * pin boost version * add boost related libraries as requirements though should be done by boost * try setting boost options on cmake for linux/travis case * add debug info to find why boost does not find deps * add LDFLAG to PREFIX/lib * add some C FLAGS for compilation to try to find missing deps * pin bioconda dep libs and append xFLAGS instead of set * Set hstlib version to use as recipe clone master branch (#6207) * Set hstlib version to use as recipe clone master branch and does not compile anymore. Recipe may be improved to use htslib conda package but this fix at least only rebuild of the package. Add hash to source. * fix manpage copy for osx * Update NucleoATAC to version 0.3.4 (#6177) * Update NucleoATAC to version 0.3.4 Added imports test, which forces a build Add fix for zlib.h not found Preserve nucleoatac version 0.3.1 * Use template-vars for nucleoatac package info * Cleaning up some test code * Update vcf2maf to 1.6.14. (#6232) * Commet apply patch (#6233) * add commet recipe * add python dependency :) * patch commet to load dependencis correctly * add build number * Update biobambam to 2.0.78. (#6234) * Update galaxy_sequence_utils to 1.1.2 (#6235) * Recipes for R packages alakazam and prestor. (#6199) * Recipes for R packages alakazam and prestor. * Added missing dependencies. * Removed #win specific things and updated gcc/llvm dependencies. * Anvio to versino 3 (#6238) * moving to anvio 3 * adding centrifuge as a run dependency * bowtie2 2.3.3.1 (#6241) * Update gffcompare to 0.10.1. (#6243) * Update bcftools-snvphyl-plugin to 1.6 (#6237) Depend on bcftools instead of conflicting with it. * Lordec (#6144) * first commit * test changes and add comments * fix command line * remove binary * remove stderr redirection * fix testin adding || true * fix command line test * add zlib to recipe * Bump vsearch version and add .gz support (#6239) * Update peddy to 0.3.1. (#6236) * Update peddy to 0.3.1. * Update dependencies. * Work around API changes in networkx >=2.0. * Remove running the unit tests as suggested by @daler. This was running into trouble with the minimal docker containers. * Samtools 0.1.x (#6200) * samtools: add version 0.1.12 till 0.1.15 with one semi test * samtools: resolving dependencies for new versions - i hope * samtools: pin requirements and expand CFLAGS * samtools: fix incorrect sha256 and change back to md5 * samtools: os dependend Makefile adjustment * patch ViennaRNA 2.4.1 RNAlocmin (#5994) * bump viennarna * increment bn * Enable RNAlocmin * Bump KneadData to 0.6.1 (#6244) * Augustus deps (#6242) * use latest augustus * use latest augustus * fix augustus, maker and busco recipes * typo... * typo... * bump build numbers * some problem with tests * pin zlib * try to fix test case * fix test * bioconductor-limma - add statmod as dependency (#6247) * bioconductor-limma - add statmod as dependency * bioconductor-limma - update build number * Update meta.yaml * VEP: bumped subversion (#6249) * Cyvcf 0.8.0 (#6251) * Preserve CyVCF 0.7.2. * Update CyVCF to 0.8.0. * Update IRFinder to 1.2.3. (#6252) * Gecode 5.1.0 (#6253) * Preserve Gecode 5.0.0. * Update Gecode to 5.1.0. * Genehunter-Modscore v3.1 (#6248) * genehunter recipe * skip osx * Gmap 2017 09 30 (#6255) * Preserve GMAP 2017.05.08. * Update GMAP to 2017.09.30. * Bump mashtree to 0.25 (#6258) * Update Oncofuse to 1.1.1. (#6259) * Freebayes seems to need libbz2 (#6260) * Freebayes seems to need libbz2 * Pin zlib and bzip2 * Update meta.yaml * Peptide shaker 1.16.14 (#6261) * Preserve peptide-shaker 1.16.13. * Update PeptideShaker to 1.16.14. * Omero 5.4.0 (#6256) * Bump OMERO recipe to version 5.3.4 - Bump version number and SHA1 - Add range to the zero-ice dependency - User HTTPS * Add skip-lints * Fix character * Bump to OMERO.py 5.4.0 * Do not skip lint * Update: mosdepth 0.1.9 (#6264) Includes breaking changes relative to 0.1.8: chapmanb/bcbio-nextgen#2094 Has fixes for changed install.sh: Fixes #6263 * Add conda for tgDist #BioCon2017 (#6257) * Add conda for tgDist #BioCon2017 * Correct comments after pull request * fix runtime dep * add cmake as buld time dependency * skip build on OSX * some recipes has been update for character format (#6267) * Lelievrey (#6266) * Add the pyasp recipe * Correction of the version * Add the missing summary * Update build.sh * small fixes * Snakemake 4.2.0 (#6270) * Bioconductor 3.5 build bumps (#6203) * new version of graphicsmagick with --enable-symbol-prefix option when building (#6120) * add bioconductor v3.4 versions (#6124) * update r-aroma* (#6126) * create recipe for perl-types-standard (#6125) * Create build.sh * Create meta.yaml * Create recipe for perl-bio-cigar (#6118) * Create build.sh * Create meta.yaml * Update meta.yaml * Update meta.yaml * Update meta.yaml * Update meta.yaml * Update meta.yaml * Update meta.yaml * Update meta.yaml * remove bioconductor-peca from blacklist (#6129) * rebuild r-packages (#6128) * Update meta.yaml (#6134) * Add BamM package (#6133) * Add bamm * Update galaxy_sequence_utils to 1.1.1 (#6136) * updated recipe (#6138) * add bioconductor-jaspar2014 (#6137) * Haystack 0.5.2 (#6140) * updated recipe * updated recipe * dr-disco v0.11.0 (#6142) * Add several R and Bioconductor recipes (#5428) * initial version of recipes * remove last lines * add missing dependencies * added missing dependencies * added recipe for r-sfsmisc * move r-recipes to conda-forge and remove empty lines in bioc recipes * remove recipes that have been already added since last push * remove r-sfsmisc * Update gffread to 0.9.9. (#6146) * Add recipe for bioconductor-scran (#6143) * Initial recipe of bioconductor-scran * Modified R dependency * Updated cmv to version 1.0.6 (#6147) * Hansel | Pinning attrs version (#6135) * Added recipe for "Heidelberg Subtyping". This includes tailoring of the python environment within the build.sh file. * Fixing the directory within build.sh * Fixing the ordering of the sed command, moving to after the pip install. * Removing SED tailoring for now, and adding "which" as a test command. * Changing repository as we have now migrated to the PHAC NML repository. * Changing to official release branch now. * Fixing MD5 value. * Fixing requirements and test command. * Changing the testing command, as the new help contains invalid characters. * Removing list of authors from summary within meta.yaml. * Adding Detailed Summary Added detailed summary including authors. * Deleting python version file. Deleting un-needed file. * Changing recipe to rely on PyPi and fixed the build script. * Adding python setup parameters. * Removing pinning, and adding skip for Python 2. * Changing URL to standard. Added variable for hash type and val. * Pinning version of attrs. * Update trim_galore to 0.4.4. (#6148) * Downgrade networkx dependency (#6094) Networkx has recently been updated to 2.0, which is incompatible with `colormath` - `spectra` dependency (see https://github.com/ewels/MultiQC/pull/561 and https://github.com/ewels/MultiQC/issues/592). Until a new `colormath` version is released, we have to downgrade networkx dependency for MultiQC. * Updating Last (lastal) to v874 (#6141) * updating to last 874 * switch for OSX specific compilation with new makefile * adding 8 byte binaries (for large DBs using big RAM) * Snakemake 4.1.0 (#6150) * Update Bamm (#6156) * bump gnu-getopt build (#6157) gnu-getopt depends on gettext, which had a linking issue with 0.19.8 (fixed in 0.19.8.1). This bumps gnu-getopt to hopefully trigger a rebuild with gettext 0.19.8.1 from conda-forge * [WIP] add sis (#6055) * [WIP] add sis init * [wip] sis build passes local * [WIP] added python req * [WIP] changed build script * Add package MentaLiST-0.1.2 (#5856) * Initial commit * Updated to v0.1.2 * Updated url and sha256 hash * Filled in missing fn field * Added requirement mpfr * Specify openblas build to force conda-forge build of julia * Revert last change * Updated build section to skip osx build (no julia available) * Moved MentaLiST.jl -> mentalist symbolic link command to build.sh * Mapsembler2 (#6159) * Remove unneeded samtools run requirement (#6155) CrossMap uses pysam. * update shovill (#6152) * bumped shovill version to 0.8.0 * added conda_perl * added version requirements * discosnp (#6149) * discosnp * fix sed compatibility * pin zlib against {{CONDA_ZLIB}}* * Haystack 0.5.2 (#6164) * updated recipe * updated recipe * updated sha256 * Haystack 0.5.2 (#6165) * updated sha256 * fixed build number * Kissplice (#6154) * Kissplice * pin zlib against {{CONDA_ZLIB}}* * add python libraries * remove make test * fix python dependency * uncomment make test * IntaRNA v2.0.5 (#6160) * v2.0.5 released * reset build number to 0 * Update: bcbio-vm for ansible 2.x compatibility (#6167) * Adds Deeptools 1.5.8.2 and 1.5.9.1 (#6166) * deeptools: add old 1.5.8.2 version * deeptools: minor update for linux build * deeptools: add missing requirement for ucsc-bedgraphtobigwig * deeptools: add 1.5.9.1 * Perl io gzip (#6158) * first commit * first commit * Remove zlib-devel dependency * Add a dependency to zlib (zlib-devel not found) * Update build.sh with CFLAGS and LDFLAGS * update build.sh with CFLAGS and LDFLAGS * Add zlib reuirement * Back to the perl-io-html model * Back to the perl-io-html model + env vars for compliation and ld * [lint skip uses_setuptools for recipes/qcumber] * [lint skip uses_setuptools for recipes/qcumber] * [lint skip uses_setuptools for recipes/qcumber] * [lint skip uses_setuptools for recipes/qcumber] * [lint skip uses_setuptools for recipes/qcumber] * [lint skip uses_setuptools for recipes/qcumber] * pin zlib * bump build number (#6174) * Added recipe for bioconductor-copynumber (#6170) * Haystack 0.5.2 (#6176) * updated recipe * updated recipe * updated sha256 * fixed build number * updated hash * improved patch (#6173) * Update meta.yaml (#6179) Oups, I forgot to check the build number * Update Bamm (#6180) * Discosnp fix dependencies (#6182) * discosnp * fix sed compatibility * pin zlib against {{CONDA_ZLIB}}* * fix dependencies binaries not found during the execution * Bump mash to 2.0 (#6168) * Bump mash to 2.0 * Pin zlib * Discosnp fix scripts path in .sh (#6185) * discosnp * fix sed compatibility * pin zlib against {{CONDA_ZLIB}}* * fix dependencies binaries not found during the execution * fix scripts path in .sh * fix dbh5 path for copy * Update mssttitch version to 2.5 (#6181) * Update mssttitch version to 2.5 * Fix setup.py for conda after linting * GraphProt (#6183) * add GraphProt version 1.1.6 * update shiver (#6175) * update Graphprot version 1.1.7 (#6188) * add python3 dependency, need at least weblogo 3 * version bump * Tantan (#6189) Adding tantan: a utility for masking low complexity sequences * Updated haystack sha256 (#6178) * updated sha256 * updated sha256 * Haystack bio (#6190) * updated haystack 0.5.3 * updated haystack 0.5.3 * updated sha256 * updated sha256 * updated sha256 * updated sha256 * updated last aligner to 876 (#6191) * updated last aligner to 876 * updated spades to 3.11.1 bug-fix release (#6192) * updated sha256sum (#6193) * adding mappy (#6195) * adding mappy * adding import test * removed double whitelines * fixing yaml * fixing yaml - adding build * fixing yaml - removed space * fixing yaml - no idea * fixed files - maybe * added zlib * dummy change * trying environmental variables in build.sh * removed comments * specified CONDA zlib in requirements * adding nanolyse (#6196) * adding mappy * adding import test * removed double whitelines * fixing yaml * fixing yaml - adding build * fixing yaml - removed space * fixing yaml - no idea * fixed files - maybe * added zlib * dummy change * trying environmental variables in build.sh * removed comments * specified CONDA zlib in requirements * adding nanolyse * lowercase name * corrected import test * Fix url and description (#6197) * Update vcf2db to 2017.09.14. (#5433) * Bumped STAR-Fusion version (#6198) * HUMAnN2 requires diamond<0.9.0 (#6194) * HUMAnN2 requires diamond<0.9.0 * Fix pre-existing linting errors * Increment build numbers * update r-sartools (#6201) * add easy build version bumps * run diff to origin/bulk * fix line wraps, build numbers reset to 0, and template bioc version * version bumps for relatively simple packages * data packages remove existing build.sh from recipes; add post-link.sh. A handful have already been created, so their build numbers were not bumped. * Update: latest version with CollectErccMetrics (#6205) * Takeabreak software (#6145) * first commit for takeabreak * add zlib requirement * fix sed compatibility * pin zlib against {{CONDA_ZLIB}}* * delete decrease of memory * Mapsembler2 (#6206) * Mapsembler2 * fi mapsembler2 deps * Htseq 0.9.1 (#6204) * Add recipe for HTSeq-0.9.1 * Delete files * Add recipe for htseq * Update vsearch to 2.4.4 (#6211) * first round of non-straightforward recipes e.g., libgcc, skipped on osx, readline deps * dexseq maintain custom build script; no version change so reset to build: 0 * Update picard to 2.13 (#6212) * dirichletmultinomial updates ensure custom GSL, blas, gcc etc make it into recipe * bump to 0.8.1 (#6058) * bump to 0.8.1 * change patch file to reflect updated code * add cflag to use C99 in the compiler. this is due toa new error in the new scrappie code * dnacopy update prev recipe listed gcc as build dep; changed it to the standard linux/osx build deps. * dose, and new dependency fgsea prev version of DOSE had gmp listed as run and build deps, so retaining it here * ebimage update orig recipe skipped osx; try not skipping for now * flowcore update retain custom parts of build script * flowworkspace update No version change, so build number set to 0. Build deps included autoconf/automake for some reason, but gcc was not included. I kept autoconf in there for now, and added gcc. Note that many of the deps changes are just sort order. * genefilter update prev recipe included gcc, so keeping it here. No version bump, so build number kept at 0. * genomation updates prev version of package 1.6.0 had r-rcpp as dep, but 1.8.0 does not any more. Keeping it (and the custom osx lines in build.sh) just in case. * geoquery build.sh must have missed this in a prev commit * gosemsim update new version no longer depends on r-rcpp, but keeping it just in case * ipo update prev version was skipped for OSX, removing skip for now * lsymphony update prev recipe depended on gcc, retaining here * methylkit update keeping build number: 0; prev recipe had libgcc as dep * monocle update parsing DESCRIPTION has an empty dep; skipped for osx. Since this was added relatively recently, pretty sure it should stay skipped. * fetch remote branch for diffs * Add recipe for hicrep by Tao Yang. (#6213) * Explicit set of LGPL license (#6210) * Explicit set of LGPL license and move license link to license_file meta field * refer license_file to source directory * set explicit license instead of reference to LICENSE source file (#6208) * set explicit license instead of reference to LICENSE source file * add license_file info * update CIRCexplorer2 from 2.3.0 to 2.3.1 (#6214) * Flexbar 2.5.0 (#6187) * initial commit * move to separate dir and start 3.0.2 version * prepare version 3.0.3 * dont do 303 * enable osx and pin bzip2 and zlib * unpin bzip2 * have to create documentation directory * remove libgcc build dep * Add yanagiba (#6217) * Add yanagiba * Fix url * Remove duplicated dep * Skip py27 * update Graphprot tests to run in docker setup (#6218) * add python3 dependency, need at least weblogo 3 * version bump * remove libgcc runtime tep * see if libcxx is required at all * directly get test files from github * fix tests for wget download of test files * add wget runtime dependency for downloading testing data within docker * remove explicit python stuff, depends implicitely on python via weblogo * clean up test calls again * use curl instead of wget * Update bcftools to v1.6 (#6221) * [update] pyquant-ms to 0.2.1 (#6222) * Update version * Skip python 3 build * Commet recipe (#6220) * add commet recipe * add python dependency :) * Fix invalid license link (#6209) * Fix invalid license link Explicit set of license and add correct link to license file on github * add skip-lints as source uses only git_url, upstream not providing tags or archives * refer to license in source code instead of github link * use archive instead of git_url * increase build number to force new release update after modification of source url instead of git_url, increatse build number to get a new fresh built * fix license file location * Create recipe for rad_haplotyper (#6202) * Create build.sh * Create meta.yaml * Update meta.yaml * Update meta.yaml * Update snpEff, SnpSift to 4.3.1r. (#6224) * Update SnpSift to 4.3.1r. * Update snpEff to 4.3.1r. * Pairix 0.3.0 (#6223) * Update meta.yaml * Update build.sh * Update build.sh * Update build.sh * update sequana to version 0.5.2 (#6226) * Ped parser 1.6.6 (#6229) * Save ped_parser 1.6.5. * Update ped_parser to 1.6.6. * Fix LINT check setup_py_install_args. * Update htsbox to r340. (#6230) * ViennaRNA 2.4.1 (#6228) * build.sh of v2.3.5 * meta.yaml of v2.3.5 * tutorial build disabled * v2.4.1 enabled * summary tag indention * RNAlocmin disabled since not compiling * canu 1.6 (#6216) * canu 1.6 * set machine requirements * fix * remove the second test * Sift4g recipe (#6227) * Add recipe for HTSeq-0.9.1 * Add recipe for sift4g * Updating Hansel to version 0.2.0 (#6225) * Added recipe for "Heidelberg Subtyping". This includes tailoring of the python environment within the build.sh file. * Fixing the directory within build.sh * Fixing the ordering of the sed command, moving to after the pip install. * Removing SED tailoring for now, and adding "which" as a test command. * Changing repository as we have now migrated to the PHAC NML repository. * Changing to official release branch now. * Fixing MD5 value. * Fixing requirements and test command. * Changing the testing command, as the new help contains invalid characters. * Removing list of authors from summary within meta.yaml. * Adding Detailed Summary Added detailed summary including authors. * Deleting python version file. Deleting un-needed file. * Changing recipe to rely on PyPi and fixed the build script. * Adding python setup parameters. * Removing pinning, and adding skip for Python 2. * Changing URL to standard. Added variable for hash type and val. * Bumping version of bio_hansel to 0.2.0 * Fixing - to _ * add cassiopee index/search sequence tool (#6215) * add cassiopee index/search sequence tool * pin boost version * add boost related libraries as requirements though should be done by boost * try setting boost options on cmake for linux/travis case * add debug info to find why boost does not find deps * add LDFLAG to PREFIX/lib * add some C FLAGS for compilation to try to find missing deps * pin bioconda dep libs and append xFLAGS instead of set * Set hstlib version to use as recipe clone master branch (#6207) * Set hstlib version to use as recipe clone master branch and does not compile anymore. Recipe may be improved to use htslib conda package but this fix at least only rebuild of the package. Add hash to source. * fix manpage copy for osx * Update NucleoATAC to version 0.3.4 (#6177) * Update NucleoATAC to version 0.3.4 Added imports test, which forces a build Add fix for zlib.h not found Preserve nucleoatac version 0.3.1 * Use template-vars for nucleoatac package info * Cleaning up some test code * Update vcf2maf to 1.6.14. (#6232) * Commet apply patch (#6233) * add commet recipe * add python dependency :) * patch commet to load dependencis correctly * add build number * Update biobambam to 2.0.78. (#6234) * Update galaxy_sequence_utils to 1.1.2 (#6235) * Recipes for R packages alakazam and prestor. (#6199) * Recipes for R packages alakazam and prestor. * Added missing dependencies. * Removed #win specific things and updated gcc/llvm dependencies. * Anvio to versino 3 (#6238) * moving to anvio 3 * adding centrifuge as a run dependency * bowtie2 2.3.3.1 (#6241) * Update gffcompare to 0.10.1. (#6243) * Update bcftools-snvphyl-plugin to 1.6 (#6237) Depend on bcftools instead of conflicting with it. * Lordec (#6144) * first commit * test changes and add comments * fix command line * remove binary * remove stderr redirection * fix testin adding || true * fix command line test * add zlib to recipe * Bump vsearch version and add .gz support (#6239) * Update peddy to 0.3.1. (#6236) * Update peddy to 0.3.1. * Update dependencies. * Work around API changes in networkx >=2.0. * Remove running the unit tests as suggested by @daler. This was running into trouble with the minimal docker containers. * Samtools 0.1.x (#6200) * samtools: add version 0.1.12 till 0.1.15 with one semi test * samtools: resolving dependencies for new versions - i hope * samtools: pin requirements and expand CFLAGS * samtools: fix incorrect sha256 and change back to md5 * samtools: os dependend Makefile adjustment * patch ViennaRNA 2.4.1 RNAlocmin (#5994) * bump viennarna * increment bn * Enable RNAlocmin * Bump KneadData to 0.6.1 (#6244) * Augustus deps (#6242) * use latest augustus * use latest augustus * fix augustus, maker and busco recipes * typo... * typo... * bump build numbers * some problem with tests * pin zlib * try to fix test case * fix test * bioconductor-limma - add statmod as dependency (#6247) * bioconductor-limma - add statmod as dependency * bioconductor-limma - update build number * Update meta.yaml * VEP: bumped subversion (#6249) * Cyvcf 0.8.0 (#6251) * Preserve CyVCF 0.7.2. * Update CyVCF to 0.8.0. * Update IRFinder to 1.2.3. (#6252) * comment out custom build.sh lines and meta.yaml deps * comment out custom gmp dep * comment out custom build.sh lines * comment out automake build dep * comment out previous genomation build.sh lines and r-rcpp * gosemsim: comment out prev r-rcpp * lpsymphony: comment out prev gcc * comment out patch for methylkit * comment out monocle skip for osx * deseq2 update comment out deps that are not listed in DESCRIPTION * mosaics update comment out prev version's libgcc run dep * motifbreakr update comment out osx skip * motiv updates comment out custom build.sh lines and deps * mzr: comment out custom build deps and osx skip * ncdfflow: comment out prev custom deps * oligo: comment out previous extra deps, add separate build script * oligoclasses update comment out custom deps from prev recipe * update pcamethods * pchicdata update to make it a proper data package recipe * phyloseq: comment out prev gmp dep * piano update comment out previous libgcc/llvm * qdnaseq update: rm extra `r-` dep from empty DESCRIPTION entry * rcas update rm "r-" dep from empty DESCRIPTION * rgalaxy update: rm "r-" empty dep * rgraphviz: comment out prev patch and gcc * rhdf5 update: comment out osx patch and gcc * rhtslib update: comment out patches, gcc, and custom build.sh line * risa update: comment out readline dep; reset build to 0 * rtracklayer update: fix dep version numbers which had "-" in them * scan.upc update keep build number at 0; comment out prev r-rsqlite dep and osx skip * shortread: comment out custom build lines * signer update: comment out build lines and prev deps * sva update: comment out prev deps * systempiper: comment out prev osx skip * add diffbind * Gecode 5.1.0 (#6253) * Preserve Gecode 5.0.0. * Update Gecode to 5.1.0. * Genehunter-Modscore v3.1 (#6248) * genehunter recipe * skip osx * Gmap 2017 09 30 (#6255) * Preserve GMAP 2017.05.08. * Update GMAP to 2017.09.30. * Bump mashtree to 0.25 (#6258) * Update Oncofuse to 1.1.1. (#6259) * Freebayes seems to need libbz2 (#6260) * Freebayes seems to need libbz2 * Pin zlib and bzip2 * Update meta.yaml * Peptide shaker 1.16.14 (#6261) * Preserve peptide-shaker 1.16.13. * Update PeptideShaker to 1.16.14. * Omero 5.4.0 (#6256) * Bump OMERO recipe to version 5.3.4 - Bump version number and SHA1 - Add range to the zero-ice dependency - User HTTPS * Add skip-lints * Fix character * Bump to OMERO.py 5.4.0 * Do not skip lint * Update: mosdepth 0.1.9 (#6264) Includes breaking changes relative to 0.1.8: chapmanb/bcbio-nextgen#2094 Has fixes for changed install.sh: Fixes #6263 * Add conda for tgDist #BioCon2017 (#6257) * Add conda for tgDist #BioCon2017 * Correct comments after pull request * fix runtime dep * add cmake as buld time dependency * skip build on OSX * some recipes has been update for character format (#6267) * Lelievrey (#6266) * Add the pyasp recipe * Correction of the version * Add the missing summary * Update build.sh * small fixes * Snakemake 4.2.0 (#6270) * update and otherwise unify r recipes * try removing r-base restrictions * bioconductor-rhtslib additional deps * rm r-base restriction on anything < 3.2.2 * rm a few more r-base restrictions * a small round of bioconductor fixes * try adding openblas * bump ebimage version * add bioconductor-matter * rm r-base pin * add zlibbioc dep to mzr * add treeio * re-enable libglu dep for r-mixomics * add r-mqtl * update s4vectors * rm r restriction in biomformat * fix ebiimage * add libnetcdf dep to mzr * rm r-base restriction for causalr * update biocgenerics to try fixing s4vectors * bump iranges * add bioconductor-msnbase * gcc for osx for fortran * gcc for osx for fortran * try libgfortran to get rhtslib to compile * r-impute -> bioconductor-impute * bump genomeinfodb * assorted fixes * assorted fixes 2 * assorted fixes 3 * assorted fixes 4 * assorted fixes 5 * try to fix shortread * readd bioc-graph patch * assorted fixes 6 * assorted fixes 7 * assorted fixes 8 * rebuild gosemsim * add llvm for motiv and synergyfinder * update rpath patches for rhdf5 and rgraphviz * fix for bioconductor-dose * try gcc for motiv? * gcc for rhdf5? * fix r-latticeextra dependency thanks to @nsoranzo for spotting! * Update meta.yaml * fix buildstring for motiv * skipping remaining osx packages * add bioconductor-masigpro dev version as subdir * bioconductor 3.6 updates * bioconductor 3.6 remaining updates * update bioconductor-treeio * add bioconductor-rcy3 * update rDGIdb and SWATH2stats * fix biocparallel * update complexheatmap * update DelayedArray * update edgeR * temporarily skip osx for rhdf5 and dep * update rGREAT and matter * add r-bh as dep to flowcore * rm post-link for jaspar2018 * update rols * add bioconductor-singlecellexperiment * add bioconductor-raggedexperiment * bump phyloseq * increase subdags for bulk branch * update annotationhub * bump total subdag count * update go.db * update orgdb pkgs * add rhtslib as dep for methylkit * update org.Cf.eg.db * add zlibbioc as dep for mzr * update PSICQUIC and scran * bump Rnits and methylumi * add r-ncdf4 * fix checksum * new version * add bioconductor-rhdf5lib * add bioconductor-beachmat * add r-rcpparmadillo * increase version * add bioconductor-rhdf5lib * add boost back to mzR * upgrade to new version * add hdf5array * upgrade * add the two new deps * add genemeta * add missing dep * fix link * add missing deps * add bioc-cytolib * add rprotobuflib * add missing deps * add missing deps * add additional deps * add automake dep to rprotobuflib * minor formatting * update BioC 3.5 packages recently added to master to BioC 3.6 cc @cbrueffer * add r-bh to chemminer * add missing dep * fix automake to version 1.14 * add protobuf * fix autoconf * fix automake * round 2 of ucsc updates * blacklist remaining bioconductor build failures * back to a single subdag * skip isomirs on osx * try additional fixes * fix rprotobuflib * revert #6758 * whitespace * whitespace test * add nloptr dep to flowdensity * whitespace * revert whitespace * whitespace * add egesa * add data pack * add data pack * add padog * add glimma * add keggdzpathqaysgeo * add scpipe * add egseadata * add updated, existing ucsc packages * fix template for pkgs needing stringify * fix template and build script for fetchchromsizes on osx * add new tools in v357 * remove calc and ave * cleanup * more ucsc cleanup * more ucsc fixes * fix expMatrixBarchartBed * another fix for expMatrixToBarchartBed * various special-casing for expMatrixToBarchartBed * patch expMatrixToBarchartBed to support py3 * Fix Bioconductor data packages (#7116) * Update: ensembl-vep, cnvkit (#6880) - ensembl-vep: Fix loftee plugin installation to include recent splice site updates: https://github.com/chapmanb/bcbio-nextgen/issues/2158#issuecomment-346031639 - cnvkit: incorporate empty weight patch merged upstream * VEP: bumped subversion (#6882) * Adding vcfpy v0.11.0 (#6879) * bulk ucsc updates (#6884) * Update bulk (#6274) * new version of graphicsmagick with --enable-symbol-prefix option when building (#6120) * add bioconductor v3.4 versions (#6124) * update r-aroma* (#6126) * create recipe for perl-types-standard (#6125) * Create build.sh * Create meta.yaml * Create recipe for perl-bio-cigar (#6118) * Create build.sh * Create meta.yaml * Update meta.yaml * Update meta.yaml * Update meta.yaml * Update meta.yaml * Update meta.yaml * Update meta.yaml * Update meta.yaml * remove bioconductor-peca from blacklist (#6129) * rebuild r-packages (#6128) * Update meta.yaml (#6134) * Add BamM package (#6133) * Add bamm * Update galaxy_sequence_utils to 1.1.1 (#6136) * updated recipe (#6138) * add bioconductor-jaspar2014 (#6137) * Haystack 0.5.2 (#6140) * updated recipe * updated recipe * dr-disco v0.11.0 (#6142) * Add several R and Bioconductor recipes (#5428) * initial version of recipes * remove last lines * add missing dependencies * added missing dependencies * added recipe for r-sfsmisc * move r-recipes to conda-forge and remove empty lines in bioc recipes * remove recipes that have been already added since last push * remove r-sfsmisc * Update gffread to 0.9.9. (#6146) * Add recipe for bioconductor-scran (#6143) * Initial recipe of bioconductor-scran * Modified R dependency * Updated cmv to version 1.0.6 (#6147) * Hansel | Pinning attrs version (#6135) * Added recipe for "Heidelberg Subtyping". This includes tailoring of the python environment within the build.sh file. * Fixing the directory within build.sh * Fixing the ordering of the sed command, moving to after the pip install. * Removing SED tailoring for now, and adding "which" as a test command. * Changing repository as we have now migrated to the PHAC NML repository. * Changing to official release branch now. * Fixing MD5 value. * Fixing requirements and test command. * Changing the testing command, as the new help contains invalid characters. * Removing list of authors from summary within meta.yaml. * Adding Detailed Summary Added detailed summary including authors. * Deleting python version file. Deleting un-needed file. * Changing recipe to rely on PyPi and fixed the build script. * Adding python setup parameters. * Removing pinning, and adding skip for Python 2. * Changing URL to standard. Added variable for hash type and val. * Pinning version of attrs. * Update trim_galore to 0.4.4. (#6148) * Downgrade networkx dependency (#6094) Networkx has recently been updated to 2.0, which is incompatible with `colormath` - `spectra` dependency (see https://github.com/ewels/MultiQC/pull/561 and https://github.com/ewels/MultiQC/issues/592). Until a new `colormath` version is released, we have to downgrade networkx dependency for MultiQC. * Updating Last (lastal) to v874 (#6141) * updating to last 874 * switch for OSX specific compilation with new makefile * adding 8 byte binaries (for large DBs using big RAM) * Snakemake 4.1.0 (#6150) * Update Bamm (#6156) * bump gnu-getopt build (#6157) gnu-getopt depends on gettext, which had a linking issue with 0.19.8 (fixed in 0.19.8.1). This bumps gnu-getopt to hopefully trigger a rebuild with gettext 0.19.8.1 from conda-forge * [WIP] add sis (#6055) * [WIP] add sis init * [wip] sis build passes local * [WIP] added python req * [WIP] changed build script * Add package MentaLiST-0.1.2 (#5856) * Initial commit * Updated to v0.1.2 * Updated url and sha256 hash * Filled in missing fn field * Added requirement mpfr * Specify openblas build to force conda-forge build of julia * Revert last change * Updated build section to skip osx build (no julia available) * Moved MentaLiST.jl -> mentalist symbolic link command to build.sh * Mapsembler2 (#6159) * Remove unneeded samtools run requirement (#6155) CrossMap uses pysam. * update shovill (#6152) * bumped shovill version to 0.8.0 * added conda_perl * added version requirements * discosnp (#6149) * discosnp * fix sed compatibility * pin zlib against {{CONDA_ZLIB}}* * Haystack 0.5.2 (#6164) * updated recipe * updated recipe * updated sha256 * Haystack 0.5.2 (#6165) * updated sha256 * fixed build number * Kissplice (#6154) * Kissplice * pin zlib against {{CONDA_ZLIB}}* * add python libraries * remove make test * fix python dependency * uncomment make test * IntaRNA v2.0.5 (#6160) * v2.0.5 released * reset build number to 0 * Update: bcbio-vm for ansible 2.x compatibility (#6167) * Adds Deeptools 1.5.8.2 and 1.5.9.1 (#6166) * deeptools: add old 1.5.8.2 version * deeptools: minor update for linux build * deeptools: add missing requirement for ucsc-bedgraphtobigwig * deeptools: add 1.5.9.1 * Perl io gzip (#6158) * first commit * first commit * Remove zlib-devel dependency * Add a dependency to zlib (zlib-devel not found) * Update build.sh with CFLAGS and LDFLAGS * update build.sh with CFLAGS and LDFLAGS * Add zlib reuirement * Back to the perl-io-html model * Back to the perl-io-html model + env vars for compliation and ld * [lint skip uses_setuptools for recipes/qcumber] * [lint skip uses_setuptools for recipes/qcumber] * [lint skip uses_setuptools for recipes/qcumber] * [lint skip uses_setuptools for recipes/qcumber] * [lint skip uses_setuptools for recipes/qcumber] * [lint skip uses_setuptools for recipes/qcumber] * pin zlib * bump build number (#6174) * Added recipe for bioconductor-copynumber (#6170) * Haystack 0.5.2 (#6176) * updated recipe * updated recipe * updated sha256 * fixed build number * updated hash * improved patch (#6173) * Update meta.yaml (#6179) Oups, I forgot to check the build number * Update Bamm (#6180) * Discosnp fix dependencies (#6182) * discosnp * fix sed compatibility * pin zlib against {{CONDA_ZLIB}}* * fix dependencies binaries not found during the execution * Bump mash to 2.0 (#6168) * Bump mash to 2.0 * Pin zlib * Discosnp fix scripts path in .sh (#6185) * discosnp * fix sed compatibility * pin zlib against {{CONDA_ZLIB}}* * fix dependencies binaries not found during the execution * fix scripts path in .sh * fix dbh5 path for copy * Update mssttitch version to 2.5 (#6181) * Update mssttitch version to 2.5 * Fix setup.py for conda after linting * GraphProt (#6183) * add GraphProt version 1.1.6 * update shiver (#6175) * update Graphprot version 1.1.7 (#6188) * add python3 dependency, need at least weblogo 3 * version bump * Tantan (#6189) Adding tantan: a utility for masking low complexity sequences * Updated haystack sha256 (#6178) * updated sha256 * updated sha256 * Haystack bio (#6190) * updated haystack 0.5.3 * updated haystack 0.5.3 * updated sha256 * updated sha256 * updated sha256 * updated sha256 * updated last aligner to 876 (#6191) * updated last aligner to 876 * updated spades to 3.11.1 bug-fix release (#6192) * updated sha256sum (#6193) * adding mappy (#6195) * adding mappy * adding import test * removed double whitelines * fixing yaml * fixing yaml - adding build * fixing yaml - removed space * fixing yaml - no idea * fixed files - maybe * added zlib * dummy change * trying environmental variables in build.sh * removed comments * specified CONDA zlib in requirements * adding nanolyse (#6196) * adding mappy * adding import test * removed double whitelines * fixing yaml * fixing yaml - adding build * fixing yaml - removed space * fixing yaml - no idea * fixed files - maybe * added zlib * dummy change * trying environmental variables in build.sh * removed comments * specified CONDA zlib in requirements * adding nanolyse * lowercase name * corrected import test * Fix url and description (#6197) * Update vcf2db to 2017.09.14. (#5433) * Bumped STAR-Fusion version (#6198) * HUMAnN2 requires diamond<0.9.0 (#6194) * HUMAnN2 requires diamond<0.9.0 * Fix pre-existing linting errors * Increment build numbers * update r-sartools (#6201) * Update: latest version with CollectErccMetrics (#6205) * Takeabreak software (#6145) * first commit for takeabreak * add zlib requirement * fix sed compatibility * pin zlib against {{CONDA_ZLIB}}* * delete decrease of memory * Mapsembler2 (#6206) * Mapsembler2 * fi mapsembler2 deps * Htseq 0.9.1 (#6204) * Add recipe for HTSeq-0.9.1 * Delete files * Add recipe for htseq * Update vsearch to 2.4.4 (#6211) * Update picard to 2.13 (#6212) * bump to 0.8.1 (#6058) * bump to 0.8.1 * change patch file to reflect updated code * add cflag to use C99 in the compiler. this is due toa new error in the new scrappie code * Add recipe for hicrep by Tao Yang. (#6213) * Explicit set of LGPL license (#6210) * Explicit set of LGPL license and move license link to license_file meta field * refer license_file to source directory * set explicit license instead of reference to LICENSE source file (#6208) * set explicit license instead of reference to LICENSE source file * add license_file info * update CIRCexplorer2 from 2.3.0 to 2.3.1 (#6214) * Flexbar 2.5.0 (#6187) * initial commit * move to separate dir and start 3.0.2 version * prepare version 3.0.3 * dont do 303 * enable osx and pin bzip2 and zlib * unpin bzip2 * have to create documentation directory * remove libgcc build dep * Add yanagiba (#6217) * Add yanagiba * Fix url * Remove duplicated dep * Skip py27 * update Graphprot tests to run in docker setup (#6218) * add python3 dependency, need at least weblogo 3 * version bump * remove libgcc runtime tep * see if libcxx is required at all * directly get test files from github * fix tests for wget download of test files * add wget runtime dependency for downloading testing data within docker * remove explicit python stuff, depends implicitely on python via weblogo * clean up test calls again * use curl instead of wget * Update bcftools to v1.6 (#6221) * [update] pyquant-ms to 0.2.1 (#6222) * Update version * Skip python 3 build * Commet recipe (#6220) * add commet recipe * add python dependency :) * Fix invalid license link (#6209) * Fix invalid license link Explicit set of license and add correct link to license file on github * add skip-lints as source uses only git_url, upstream not providing tags or archives * refer to license in source code instead of github link * use archive instead of git_url * increase build number to force new release update after modification of source url instead of git_url, increatse build number to get a new fresh built * fix license file location * Create recipe for rad_haplotyper (#6202) * Create build.sh * Create meta.yaml * Update meta.yaml * Update meta.yaml * Update snpEff, SnpSift to 4.3.1r. (#6224) * Update SnpSift to 4.3.1r. * Update snpEff to 4.3.1r. * Pairix 0.3.0 (#6223) * Update meta.yaml * Update build.sh * Update build.sh * Update build.sh * update sequana to version 0.5.2 (#6226) * Ped parser 1.6.6 (#6229) * Save ped_parser 1.6.5. * Update ped_parser to 1.6.6. * Fix LINT check setup_py_install_args. * Update htsbox to r340. (#6230) * ViennaRNA 2.4.1 (#6228) * build.sh of v2.3.5 * meta.yaml of v2.3.5 * tutorial build disabled * v2.4.1 enabled * summary tag indention * RNAlocmin disabled since not compiling * canu 1.6 (#6216) * canu 1.6 * set machine requirements * fix * remove the second test * Sift4g recipe (#6227) * Add recipe for HTSeq-0.9.1 * Add recipe for sift4g * Updating Hansel to version 0.2.0 (#6225) * Added recipe for "Heidelberg Subtyping". This includes tailoring of the python environment within the build.sh file. * Fixing the directory within build.sh * Fixing the ordering of the sed command, moving to after the pip install. * Removing SED tailoring for now, and adding "which" as a test command. * Changing repository as we have now migrated to the PHAC NML repository. * Changing to official release branch now. * Fixing MD5 value. * Fixing requirements and test command. * Changing the testing command, as the new help contains invalid characters. * Removing list of authors from summary within meta.yaml. * Adding Detailed Summary Added detailed summary including authors. * Deleting python version file. Deleting un-needed file. * Changing recipe to rely on PyPi and fixed the build script. * Adding python setup parameters. * Removing pinning, and adding skip for Python 2. * Changing URL to standard. Added variable for hash type and val. * Bumping version of bio_hansel to 0.2.0 * Fixing - to _ * add cassiopee index/search sequence tool (#6215) * add cassiopee index/search sequence tool * pin boost version * add boost related libraries as requirements though should be done by boost * try setting boost options on cmake for linux/travis case * add debug info to find why boost does not find deps * add LDFLAG to PREFIX/lib * add some C FLAGS for compilation to try to find missing deps * pin bioconda dep libs and append xFLAGS instead of set * Set hstlib version to use as recipe clone master branch (#6207) * Set hstlib version to use as recipe clone master branch and does not compile anymore. Recipe may be improved to use htslib conda package but this fix at least only rebuild of the package. Add hash to source. * fix manpage copy for osx * Update NucleoATAC to version 0.3.4 (#6177) * Update NucleoATAC to version 0.3.4 Added imports test, which forces a build Add fix for zlib.h not found Preserve nucleoatac version 0.3.1 * Use template-vars for nucleoatac package info * Cleaning up some test code * Update vcf2maf to 1.6.14. (#6232) * Commet apply patch (#6233) * add commet recipe * add python dependency :) * patch commet to load dependencis correctly * add build number * Update biobambam to 2.0.78. (#6234) * Update galaxy_sequence_utils to 1.1.2 (#6235) * Recipes for R packages alakazam and prestor. (#6199) * Recipes for R packages alakazam and prestor. * Added missing dependencies. * Removed #win specific things and updated gcc/llvm dependencies. * Anvio to versino 3 (#6238) * moving to anvio 3 * adding centrifuge as a run dependency * bowtie2 2.3.3.1 (#6241) * Update gffcompare to 0.10.1. (#6243) * Update bcftools-snvphyl-plugin to 1.6 (#6237) Depend on bcftools instead of conflicting with it. * Lordec (#6144) * first commit * test changes and add comments * fix command line * remove binary * remove stderr redirection * fix testin adding || true * fix command line test * add zlib to recipe * Bump vsearch version and add .gz support (#6239) * Update peddy to 0.3.1. (#6236) * Update peddy to 0.3.1. * Update dependencies. * Work around API changes in networkx >=2.0. * Remove running the unit tests as suggested by @daler. This was running into trouble with the minimal docker containers. * Samtools 0.1.x (#6200) * samtools: add version 0.1.12 till 0.1.15 with one semi test * samtools: resolving dependencies for new versions - i hope * samtools: pin requirements and expand CFLAGS * samtools: fix incorrect sha256 and change back to md5 * samtools: os dependend Makefile adjustment * patch ViennaRNA 2.4.1 RNAlocmin (#5994) * bump viennarna * increment bn * Enable RNAlocmin * Bump KneadData to 0.6.1 (#6244) * Augustus deps (#6242) * use latest augustus * use latest augustus * fix augustus, maker and busco recipes * typo... * typo... * bump build numbers * some problem with tests * pin zlib * try to fix test case * fix test * bioconductor-limma - add statmod as dependency (#6247) * bioconductor-limma - add statmod as dependency * bioconductor-limma - update build number * Update meta.yaml * VEP: bumped subversion (#6249) * Cyvcf 0.8.0 (#6251) * Preserve CyVCF 0.7.2. * Update CyVCF to 0.8.0. * Update IRFinder to 1.2.3. (#6252) * Gecode 5.1.0 (#6253) * Preserve Gecode 5.0.0. * Update Gecode to 5.1.0. * Genehunter-Modscore v3.1 (#6248) * genehunter recipe * skip osx * Gmap 2017 09 30 (#6255) * Preserve GMAP 2017.05.08. * Update GMAP to 2017.09.30. * Bump mashtree to 0.25 (#6258) * Update Oncofuse to 1.1.1. (#6259) * Freebayes seems to need libbz2 (#6260) * Freebayes seems to need libbz2 * Pin zlib and bzip2 * Update meta.yaml * Peptide shaker 1.16.14 (#6261) * Preserve peptide-shaker 1.16.13. * Update PeptideShaker to 1.16.14. * Omero 5.4.0 (#6256) * Bump OMERO recipe to version 5.3.4 - Bump version number and SHA1 - Add range to the zero-ice dependency - User HTTPS * Add skip-lints * Fix character * Bump to OMERO.py 5.4.0 * Do not skip lint * Update: mosdepth 0.1.9 (#6264) Includes breaking changes relative to 0.1.8: chapmanb/bcbio-nextgen#2094 Has fixes for changed install.sh: Fixes #6263 * Add conda for tgDist #BioCon2017 (#6257) * Add conda for tgDist #BioCon2017 * Correct comments after pull request * fix runtime dep * add cmake as buld time dependency * skip build on OSX * some recipes has been update for character format (#6267) * Lelievrey (#6266) * Add the pyasp recipe * Correction of the version * Add the missing summary * Update build.sh * small fixes * Snakemake 4.2.0 (#6270) * Bioconductor 3.5 build bumps (#6203) * new version of graphicsmagick with --enable-symbol-prefix option when building (#6120) * add bioconductor v3.4 versions (#6124) * update r-aroma* (#6126) * create recipe for perl-types-standard (#6125) * Create build.sh * Create meta.yaml * Create recipe for perl-bio-cigar (#6118) * Create build.sh * Create meta.yaml * Update meta.yaml * Update meta.yaml * Update meta.yaml * Update meta.yaml * Update meta.yaml * Update meta.yaml * Update meta.yaml * remove bioconductor-peca from blacklist (#6129) * rebuild r-packages (#6128) * Update meta.yaml (#6134) * Add BamM package (#6133) * Add bamm * Update galaxy_sequence_utils to 1.1.1 (#6136) * updated recipe (#6138) * add bioconductor-jaspar2014 (#6137) * Haystack 0.5.2 (#6140) * updated recipe * updated recipe * dr-disco v0.11.0 (#6142) * Add several R and Bioconductor recipes (#5428) * initial version of recipes * remove last lines * add missing dependencies * added missing dependencies * added recipe for r-sfsmisc * move r-recipes to conda-forge and remove empty lines in bioc recipes * remove recipes that have been already added since last push * remove r-sfsmisc * Update gffread to 0.9.9. (#6146) * Add recipe for bioconductor-scran (#6143) * Initial recipe of bioconductor-scran * Modified R dependency * Updated cmv to version 1.0.6 (#6147) * Hansel | Pinning attrs version (#6135) * Added recipe for "Heidelberg Subtyping". This includes tailoring of the python environment within the build.sh file. * Fixing the directory within build.sh * Fixing the ordering of the sed command, moving to after the pip install. * Removing SED tailoring for now, and adding "which" as a test command. * Changing repository as we have now migrated to the PHAC NML repository. * Changing to official release branch now. * Fixing MD5 value. * Fixing requirements and test command. * Changing the testing command, as the new help contains invalid characters. * Removing list of authors from summary within meta.yaml. * Adding Detailed Summary Added detailed summary including authors. * Deleting python version file. Deleting un-needed file. * Changing recipe to rely on PyPi and fixed the build script. * Adding python setup parameters. * Removing pinning, and adding skip for Python 2. * Changing URL to standard. Added variable for hash type and val. * Pinning version of attrs. * Update trim_galore to 0.4.4. (#6148) * Downgrade networkx dependency (#6094) Networkx has recently been updated to 2.0, which is incompatible with `colormath` - `spectra` dependency (see https://github.com/ewels/MultiQC/pull/561 and https://github.com/ewels/MultiQC/issues/592). Until a new `colormath` version is released, we have to downgrade networkx dependency for MultiQC. * Updating Last (lastal) to v874 (#6141) * updating to last 874 * switch for OSX specific compilation with new makefile * adding 8 byte binaries (for large DBs using big RAM) * Snakemake 4.1.0 (#6150) * Update Bamm (#6156) * bump gnu-getopt build (#6157) gnu-getopt depends on gettext, which had a linking issue with 0.19.8 (fixed in 0.19.8.1). This bumps gnu-getopt to hopefully trigger a rebuild with gettext 0.19.8.1 from conda-forge * [WIP] add sis (#6055) * [WIP] add sis init * [wip] sis build passes local * [WIP] added python req * [WIP] changed build script * Add package MentaLiST-0.1.2 (#5856) * Initial commit * Updated to v0.1.2 * Updated url and sha256 hash * Filled in missing fn field * Added requirement mpfr * Specify openblas build to force conda-forge build of julia * Revert last change * Updated build section to skip osx build (no julia available) * Moved MentaLiST.jl -> mentalist symbolic link command to build.sh * Mapsembler2 (#6159) * Remove unneeded samtools run requirement (#6155) CrossMap uses pysam. * update shovill (#6152) * bumped shovill version to 0.8.0 * added conda_perl * added version requirements * discosnp (#6149) * discosnp * fix sed compatibility * pin zlib against {{CONDA_ZLIB}}* * Haystack 0.5.2 (#6164) * updated recipe * updated recipe * updated sha256 * Haystack 0.5.2 (#6165) * updated sha256 * fixed build number * Kissplice (#6154) * Kissplice * pin zlib against {{CONDA_ZLIB}}* * add python libraries * remove make test * fix python dependency * uncomment make test * IntaRNA v2.0.5 (#6160) * v2.0.5 released * reset build number to 0 * Update: bcbio-vm for ansible 2.x compatibility (#6167) * Adds Deeptools 1.5.8.2 and 1.5.9.1 (#6166) * deeptools: add old 1.5.8.2 version * deeptools: minor update for linux build * deeptools: add missing requirement for ucsc-bedgraphtobigwig * deeptools: add 1.5.9.1 * Perl io gzip (#6158) * first commit * first commit * Remove zlib-devel dependency * Add a dependency to zlib (zlib-devel not found) * Update build.sh with CFLAGS and LDFLAGS * update build.sh with CFLAGS and LDFLAGS * Add zlib reuirement * Back to the perl-io-html model * Back to the perl-io-html model + env vars for compliation and ld * [lint skip uses_setuptools for recipes/qcumber] * [lint skip uses_setuptools for recipes/qcumber] * [lint skip uses_setuptools for recipes/qcumber] * [lint skip uses_setuptools for recipes/qcumber] * [lint skip uses_setuptools for recipes/qcumber] * [lint skip uses_setuptools for recipes/qcumber] * pin zlib * bump build number (#6174) * Added recipe for bioconductor-copynumber (#6170) * Haystack 0.5.2 (#6176) * updated recipe * updated recipe * updated sha256 * fixed build number * updated hash * improved patch (#6173) * Update meta.yaml (#6179) Oups, I forgot to check the build number * Update Bamm (#6180) * Discosnp fix dependencies (#6182) * discosnp * fix sed compatibility * pin zlib against {{CONDA_ZLIB}}* * fix dependencies binaries not found during the execution * Bump mash to 2.0 (#6168) * Bump mash to 2.0 * Pin zlib * Discosnp fix scripts path in .sh (#6185) * discosnp * fix sed compatibility * pin zlib against {{CONDA_ZLIB}}* * fix dependencies binaries not found during the execution * fix scripts path in .sh * fix dbh5 path for copy * Update mssttitch version to 2.5 (#6181) * Update mssttitch version to 2.5 * Fix setup.py for conda after linting * GraphProt (#6183) * add GraphProt version 1.1.6 * update shiver (#6175) * update Graphprot version 1.1.7 (#6188) * add python3 dependency, need at least weblogo 3 * version bump * Tantan (#6189) Adding tantan: a utility for masking low complexity sequences * Updated haystack sha256 (#6178) * updated sha256 * updated sha256 * Haystack bio (#6190) * updated haystack 0.5.3 * updated haystack 0.5.3 * updated sha256 * updated sha256 * updated sha256 * updated sha256 * updated last aligner to 876 (#6191) * updated last aligner to 876 * updated spades to 3.11.1 bug-fix release (#6192) * updated sha256sum (#6193) * adding mappy (#6195) * adding mappy * adding import test * removed double whitelines * fixing yaml * fixing yaml - adding build * fixing yaml - removed space * fixing yaml - no idea * fixed files - maybe * added zlib * dummy change * trying environmental variables in build.sh * removed comments * specified CONDA zlib in requirements * adding nanolyse (#6196) * adding mappy * adding import test * removed double whitelines * fixing yaml * fixing yaml - adding build * fixing yaml - removed space * fixing yaml - no idea * fixed files - maybe * added zlib * dummy change * trying environmental variables in build.sh * removed comments * specified CONDA zlib in requirements * adding nanolyse * lowercase name * corrected import test * Fix url and description (#6197) * Update vcf2db to 2017.09.14. (#5433) * Bumped STAR-Fusion version (#6198) * HUMAnN2 requires diamond<0.9.0 (#6194) * HUMAnN2 requires diamond<0.9.0 * Fix pre-existing linting errors * Increment build numbers * update r-sartools (#6201) * add easy build version bumps * run diff to origin/bulk * fix line wraps, build numbers reset to 0, and template bioc version * version bumps for relatively simple packages * data packages remove existing build.sh from recipes; add post-link.sh. A handful have already been created, so their build numbers were not bumped. * Update: latest version with CollectErccMetrics (#6205) * Takeabreak software (#6145) * first commit for takeabreak * add zlib requirement * fix sed compatibility * pin zlib against {{CONDA_ZLIB}}* * delete decrease of memory * Mapsembler2 (#6206) * Mapsembler2 * fi mapsembler2 deps * Htseq 0.9.1 (#6204) * Add recipe for HTSeq-0.9.1 * Delete files * Add recipe for htseq * Update vsearch to 2.4.4 (#6211) * first round of non-straightforward recipes e.g., libgcc, skipped on osx, readline deps * dexseq maintain custom build script; no version change so reset to build: 0 * Update picard to 2.13 (#6212) * dirichletmultinomial updates ensure custom GSL, blas, gcc etc make it into recipe * bump to 0.8.1 (#6058) * bump to 0.8.1 * change patch file to reflect updated code * add cflag to use C99 in the compiler. this is due toa new error in the new scrappie code * dnacopy update prev recipe listed gcc as build dep; changed it to the standard linux/osx build deps. * dose, and new dependency fgsea prev version of DOSE had gmp listed as run and build deps, so retaining it here * ebimage update orig recipe skipped osx; try not skipping for now * flowcore update retain custom parts of build script * flowworkspace update No version change, so build number set to 0. Build deps included autoconf/automake for some reason, but gcc was not included. I kept autoconf in there for now, and added gcc. Note that many of the deps changes are just sort order. * genefilter update prev recipe included gcc, so keeping it here. No version bump, so build number kept at 0. * genomation updates prev version of package 1.6.0 had r-rcpp as dep, but 1.8.0 does not any more. Keeping it (and the custom osx lines in build.sh) just in case. * geoquery build.sh must have missed this in a prev commit * gosemsim update new version no longer depends on r-rcpp, but keeping it just in case * ipo update prev version was skipped for OSX, removing skip for now * lsymphony update prev recipe depended on gcc, retaining here * methylkit update keeping build number: 0; prev recipe had libgcc as dep * monocle update parsing DESCRIPTION has an empty dep; skipped for osx. Since this was added relatively recently, pretty sure it should stay skipped. * fetch remote branch for diffs * Add recipe for hicrep by Tao Yang. (#6213) * Explicit set of LGPL license (#6210) * Explicit set of LGPL license and move license link to license_file meta field * refer license_file to source directory * set explicit license instead of reference to LICENSE source file (#6208) * set explicit license instead of reference to LICENSE source file * add license_file info * update CIRCexplorer2 from 2.3.0 to 2.3.1 (#6214) * Flexbar 2.5.0 (#6187) * initial commit * move to separate dir and start 3.0.2 version * prepare version 3.0.3 * dont do 303 * enable osx and pin bzip2 and zlib * unpin bzip2 * have to create documentation directory * remove libgcc build dep * Add yanagiba (#6217) * Add yanagiba * Fix url * Remove duplicated dep * Skip py27 * update Graphprot tests to run in docker setup (#6218) * add python3 dependency, need at least weblogo 3 * version bump * remove libgcc runtime tep * see if libcxx is required at all * directly get test files from github * fix tests for wget download of test files * add wget runtime dependency for downloading testing data within docker * remove explicit python stuff, depends implicitely on python via weblogo * clean up test calls again * use curl instead of wget * Update bcftools to v1.6 (#6221) * [update] pyquant-ms to 0.2.1 (#6222) * Update version * Skip python 3 build * Commet recipe (#6220) * add commet recipe * add python dependency :) * Fix invalid license link (#6209) * Fix invalid license link Explicit set of license and add correct link to license file on github * add skip-lints as source uses only git_url, upstream not providing tags or archives * refer to license in source code instead of github link * use archive instead of git_url * increase build number to force new release update after modification of source url instead of git_url, increatse build number to get a new fresh built * fix license file location * Create recipe for rad_haplotyper (#6202) * Create build.sh * Create meta.yaml * Update meta.yaml * Update meta.yaml * Update snpEff, SnpSift to 4.3.1r. (#6224) * Update SnpSift to 4.3.1r. * Update snpEff to 4.3.1r. * Pairix 0.3.0 (#6223) * Update meta.yaml * Update build.sh * Update build.sh * Update build.sh * update sequana to version 0.5.2 (#6226) * Ped parser 1.6.6 (#6229) * Save ped_parser 1.6.5. * Update ped_parser to 1.6.6. * Fix LINT check setup_py_install_args. * Update htsbox to r340. (#6230) * ViennaRNA 2.4.1 (#6228) * build.sh of v2.3.5 * meta.yaml of v2.3.5 * tutorial build disabled * v2.4.1 enabled * summary tag indention * RNAlocmin disabled since not compiling * canu 1.6 (#6216) * canu 1.6 * set machine requirements * fix * remove the second test * Sift4g recipe (#6227) * Add recipe for HTSeq-0.9.1 * Add recipe for sift4g * Updating Hansel to version 0.2.0 (#6225) * Added recipe for "Heidelberg Subtyping". This includes tailoring of the python environment within the build.sh file. * Fixing the directory within build.sh * Fixing the ordering of the sed command, moving to after the pip install. * Removing SED tailoring for now, and adding "which" as a test command. * Changing repository as we have now migrated to the PHAC NML repository. * Changing to official release branch now. * Fixing MD5 value. * Fixing requirements and test command. * Changing the testing command, as the new help contains invalid characters. * Removing list of authors from summary within meta.yaml. * Adding Detailed Summary Added detailed summary including authors. * Deleting python version file. Deleting un-needed file. * Changing recipe to rely on PyPi and fixed the build script. * Adding python setup parameters. * Removing pinning, and adding skip for Python 2. * Changing URL to standard. Added variable for hash type and val. * Bumping version of bio_hansel to 0.2.0 * Fixing - to _ * add cassiopee index/search sequence tool (#6215) * add cassiopee index/search sequence tool * pin boost version * add boost related libraries as requirements though should be done by boost * try setting boost options on cmake for linux/travis case * add debug info to find why boost does not find deps * add LDFLAG to PREFIX/lib * add some C FLAGS for compilation to try to find missing deps * pin bioconda dep libs and append xFLAGS instead of set * Set hstlib version to use as recipe clone master branch (#6207) * Set hstlib version to use as recipe clone master branch and does not compile anymore. Recipe may be improved to use htslib conda package but this fix at least only rebuild of the package. Add hash to source. * fix manpage copy for osx * Update NucleoATAC to version 0.3.4 (#6177) * Update NucleoATAC to version 0.3.4 Added imports test, which forces a build Add fix for zlib.h not found Preserve nucleoatac version 0.3.1 * Use template-vars for nucleoatac package info * Cleaning up some test code * Update vcf2maf to 1.6.14. (#6232) * Commet apply patch (#6233) * add commet recipe * add python dependency :) * patch commet to load dependencis correctly * add build number * Update biobambam to 2.0.78. (#6234) * Update galaxy_sequence_utils to 1.1.2 (#6235) * Recipes for R packages alakazam and prestor. (#6199) * Recipes for R packages alakazam and prestor. * Added missing dependencies. * Removed #win specific things and updated gcc/llvm dependencies. * Anvio to versino 3 (#6238) * moving to anvio 3 * adding centrifuge as a run dependency * bowtie2 2.3.3.1 (#6241) * Update gffcompare to 0.10.1. (#6243) * Update bcftools-snvphyl-plugin to 1.6 (#6237) Depend on bcftools instead of conflicting with it. * Lordec (#6144) * first commit * test changes and add comments * fix command line * remove binary * remove stderr redirection * fix testin adding || true * fix command line test * add zlib to recipe * Bump vsearch version and add .gz support (#6239) * Update peddy to 0.3.1. (#6236) * Update peddy to 0.3.1. * Update dependencies. * Work around API changes in networkx >=2.0. * Remove running the unit tests as suggested by @daler. This was running into trouble with the minimal docker containers. * Samtools 0.1.x (#6200) * samtools: add version 0.1.12 till 0.1.15 with one semi test * samtools: resolving dependencies for new versions - i hope * samtools: pin requirements and expand CFLAGS * samtools: fix incorrect sha256 and change back to md5 * samtools: os dependend Makefile adjustment * patch ViennaRNA 2.4.1 RNAlocmin (#5994) * bump viennarna * increment bn * Enable RNAlocmin * Bump KneadData to 0.6.1 (#6244) * Augustus deps (#6242) * use latest augustus * use latest augustus * fix augustus, maker and busco recipes * typo... * typo... * bump build numbers * some problem with tests * pin zlib * try to fix test case * fix test * bioconductor-limma - add statmod as dependency (#6247) * bioconductor-limma - add statmod as dependency * bioconductor-limma - update build number * Update meta.yaml * VEP: bumped subversion (#6249) * Cyvcf 0.8.0 (#6251) * Preserve CyVCF 0.7.2. * Update CyVCF to 0.8.0. * Update IRFinder to 1.2.3. (#6252) * comment out custom build.sh lines and meta.yaml deps * comment out custom gmp dep * comment out custom build.sh lines * comment out automake build dep * comment out previous genomation build.sh lines and r-rcpp * gosemsim: comment out prev r-rcpp * lpsymphony: comment out prev gcc * comment out patch for methylkit * comment out monocle skip for osx * deseq2 update comment out deps that are not listed in DESCRIPTION * mosaics update comment out prev version's libgcc run dep * motifbreakr update comment out osx skip * motiv updates comment out custom build.sh lines and deps * mzr: comment out custom build deps and osx skip * ncdfflow: comment out prev custom deps * oligo: comment out previous extra deps, add separate build script * oligoclasses update comment out custom deps from prev recipe * update pcamethods * pchicdata update to make it a proper data package recipe * phyloseq: comment out prev gmp dep * piano update comment out previous libgcc/llvm * qdnaseq update: rm extra `r-` dep from empty DESCRIPTION entry * rcas update rm "r-" dep from empty DESCRIPTION * rgalaxy update: rm "r-" empty dep * rgraphviz: comment out prev patch and gcc * rhdf5 update: comment out osx patch and gcc * rhtslib update: comment out patches, gcc, and custom build.sh line * risa update: comment out readline dep; reset build to 0 * rtracklayer update: fix dep version numbers which had "-" in them * scan.upc update keep build number at 0; comment out prev r-rsqlite dep and osx skip * shortread: comment out custom build lines * signer update: comment out build lines and prev deps * sva update: comment out prev deps * systempiper: comment out prev osx skip * add diffbind * Gecode 5.1.0 (#6253) * Preserve Gecode 5.0.0. * Update Gecode to 5.1.0. * Genehunter-Modscore v3.1 (#6248) * genehunter recipe * skip osx * Gmap 2017 09 30 (#6255) * Preserve GMAP 2017.05.08. * Update GMAP to 2017.09.30. * Bump mashtree to 0.25 (#6258) * Update Oncofuse to 1.1.1. (#6259) * Freebayes seems to need libbz2 (#6260) * Freebayes seems to need libbz2 * Pin zlib and bzip2 * Update meta.yaml * Peptide shaker 1.16.14 (#6261) * Preserve peptide-shaker 1.16.13. * Update PeptideShaker to 1.16.14. * Omero 5.4.0 (#6256) * Bump OMERO recipe to version 5.3.4 - Bump version number and SHA1 - Add range to the zero-ice dependency - User HTTPS * Add skip-lints * Fix character * Bump to OMERO.py 5.4.0 * Do not skip lint * Update: mosdepth 0.1.9 (#6264) Includes breaking changes relative to 0.1.8: chapmanb/bcbio-nextgen#2094 Has fixes for changed install.sh: Fixes #6263 * Add conda for tgDist #BioCon2017 (#6257) * Add conda for tgDist #BioCon2017 * Correct comments after pull request * fix runtime dep * add cmake as buld time dependency * skip build on OSX * some recipes has been update for character format (#6267) * Lelievrey (#6266) * Add the pyasp recipe * Correction of the version * Add the missing summary * Update build.sh * small fixes * Snakemake 4.2.0 (#6270) * update and otherwise unify r recipes * try removing r-base restrictions * bioconductor-rhtslib additional deps * rm r-base restriction on anything < 3.2.2 * rm a few more r-base restrictions * a small round of bioconductor fixes * try adding openblas * bump ebimage version * add bioconductor-matter * rm r-base pin * add zlibbioc dep to mzr * add treeio * re-enable libglu dep for r-mixomics * add r-mqtl * update s4vectors * rm r restriction in biomformat * fix ebiimage * add libnetcdf dep to mzr * rm r-base restriction for causalr * update biocgenerics to try fixing s4vectors * bump iranges * add bioconductor-msnbase * gcc for osx for fortran * gcc for osx for fortran * try libgfortran to get rhtslib to compile * r-impute -> bioconductor-impute * bump genomeinfodb * assorted fixes * assorted fixes 2 * assorted fixes 3 * assorted fixes 4 * assorted fixes 5 * try to fix shortread * readd bioc-graph patch * assorted fixes 6 * assorted fixes 7 * assorted fixes 8 * rebuild gosemsim * add llvm for motiv and synergyfinder * update rpath patches for rhdf5 and rgraphviz * fix for bioconductor-dose * try gcc for motiv? * gcc for rhdf5? * fix r-latticeextra dependency thanks to @nsoranzo for spotting! * Update meta.yaml * fix buildstring for motiv * skipping remaining osx packages * add bioconductor-masigpro dev version as subdir * bioconductor 3.6 updates * bioconductor 3.6 remaining updates * update bioconductor-treeio * add bioconductor-rcy3 * update rDGIdb and SWATH2stats * fix biocparallel * update complexheatmap * update DelayedArray * update edgeR * temporarily skip osx for rhdf5 and dep * update rGREAT and matter * add r-bh as dep to flowcore * rm post-link for jaspar2018 * update rols * add bioconductor-singlecellexperiment * add bioconductor-raggedexperiment * bump phyloseq * increase subdags for bulk branch * update annotationhub * bump total subdag count * update go.db * update orgdb pkgs * add rhtslib as dep for methylkit * update org.Cf.eg.db * add zlibbioc as dep for mzr * update PSICQUIC and scran * bump Rnits and methylumi * add r-ncdf4 * fix checksum * new version * add bioconductor-rhdf5lib * add bioconductor-beachmat * add r-rcpparmadillo * increase version * add bioconductor-rhdf5lib * add boost back to mzR * upgrade to new version * add hdf5array * upgrade * add the two new deps * add genemeta * add missing dep * fix link * add missing deps * add bioc-cytolib * add rprotobuflib * add missing deps * add missing deps * add additional deps * add automake dep to rprotobuflib * minor formatting * update BioC 3.5 packages recently added to master to BioC 3.6 cc @cbrueffer * add r-bh to chemminer * add missing dep * fix automake to version 1.14 * add protobuf * fix autoconf * fix automake * round 2 of ucsc updates * blacklist remaining bioconductor build failures * back to a single subdag * skip isomirs on osx * try additional fixes * fix rprotobuflib * revert #6758 * whitespace * whitespace test * add nloptr dep to flowdensity * whitespace * revert whitespace * whitespace * add egesa * add data pack * add data pack * add padog * add glimma * add keggdzpathqaysgeo * add scpipe * add egseadata * add updated, existing ucsc packages * fix template for pkgs needing stringify * fix template and build script for fetchchromsizes on osx * add new tools in v357 * remove calc and ave * cleanup * more ucsc cleanup * more ucsc fixes * fix expMatrixBarchartBed * another fix for expMatrixToBarchartBed * various special-casing for expMatrixToBarchartBed * patch expMatrixToBarchartBed to support py3 * Update geoDL to 1.0b5.1. (#6885) * PgSA tool (#6868) * add pgsa tool * fix hash and dirname * try to use gcc on osx as well * use gcc for macos * use latest commit with compilation fixes * revert changes * try to use gcc on osx * Meme old (#6889) * fix old meme package * Create build.sh * add patch * pin zlib * Short reads connector v1.1.3 (#6883) * short_read_connector v1.1.2 * use v1.1.3 with compilation fixes * remove v1.1.0 * DISCASM: Adding version number requirement to pysam dependency. (#6876) * Adding version requirement to pysam. * Bumping up build number. * Ensure 2 perl wrapper scripts do not mask failures (#6886) * Ensure wrapper scripts do not mask failures e.g. Using -pfamB with pfam_scan.pl should return error code 1, but as written the wrapper script returned 0. * Provide SHA256 checksum There was a SHA1 checksum, but we recommend SHA256 or MD5: scottishdumpling:trawler pc40583$ curl -o trawler-2.0.tar.gz -L https://api.github.com/repos/Ramialison-Lab-ARMI/Trawler-2.0/tarball/5f391e0 % Total % Received % Xferd Average Speed Time Time Time Current Dload Upload Total Spent Left Speed 100 84.1M 0 84.1M 0 0 1771k 0 --:--:-- 0:00:48 --:--:-- 3108k $ md5 trawler-2.0.tar.gz MD5 (trawler-2.0.tar.gz) = 2446eabd8e212021d9c296664780ec60 $ shasum -a 256 trawler-2.0.tar.gz c04157db18dc165df52d754ca875a198cbc63d0256b1870c5508a42dfe9c3594 trawler-2.0.tar.gz $ shasum -a 1 trawler-2.0.tar.gz c02ce9aaf6bf743b2dcf056bf697a79d10b37be7 trawler-2.0.tar.gz * Fix perl hash-bang in trawler recipe * Trawler v2.0 usage and version command return error 1. Even using -help or -version, trawler returns error code 1, see https://github.com/Ramialison-Lab-ARMI/Trawler-2.0/issues/2 We can mask this with grep so that the test passes. (Previously the BioConda wrapper script was wrongly suppressing the exit code, so the test was passing.) * Use exec and avoid spliting input parameters. Suggestion by Marcel Bargull, use exec to replace caller process with child, and avoid spliting input parameters on whitespace. * Make pfam_scan.pl dependency on perl-ipc-run explicit * Cleanup * Abyss osx build (#6867) * abyss: fix configure parameters (maybe) * abyss: un-skip osx build * abyss: add --with-sparsehash * abyss: temporarily skip non-osx build * abyss: temporarily try gcc on osx (due to google-sparsehash) * abyss: update sparsehash dependency; bump build * abyss: add patch to prevent linker error on OSX * abyss: add -headerpad_max_install_names to LDFLAGS * abyss: use list for patches, add comment * abyss: use default value for maxk (128) * Abyss osx other versions (#6892) * abyss 1.5.2, 1.9.0: enable osx builds * abyss 1.5.2, 1.9.0: use default maxk (1.5.2: 64, 1.9.0: 96) * abyss 1.5.2, 1.9.0: update dependency on sparsehash * abyss 1.9.0: incomplete patches aren't the smartest ones.. * Update fastq-and-furious to 0.2.0. (#6894) * Update vcfkit to 0.1.6. (#6895) * Cutadapt 1.15 (#6898) * Omero 5.4.1 (#6897) * Bump version to 5.4.1 and sha1 * Replace http by https * Remove google-sparsehash (#6893) * stride: update dependency on sparsehash * tedna: update dependeny on sparsehash * tedna: remove sparsehash run dependency * google-sparsehash: remove recipe, available as 'sparsehash' at conda-forge * Updated MentaLiST to v0.2.0 (#6891) * fix name recipe (#6900) * ls-gkm initial (#6869) * ls-gkm initial * - change to better versioning - do not skip OSX * fixing checksum! fixing tab in version! change URL to last commit * fixing version wildcard * gkmSVM initial commit (#6871) * gkmSVM initial commit * remove unecessary comments * remove all comments * Update hifive to 1.5.3. (#6903) * Update hifive to 1.5.3. * Also remove running the unit tests. * Fix shortreadconnector dependency for discosnp (#6902) * fix name recipe * remove old release and fix short_read_connector dependency * add smina (#6856) * add smina * dang it, md5 is required * try to make version number checker happy even though we don't actually have version numbers * Python newick (#6901) * [WIP] added recipe, trouble building * [WIP] need to build add python-newick * adding python-newick recipe * removing masurca and ragout files I thought were on other branches. sigh * add --single-version-externally-managed * fix bad url; tricked by the cache! * address @mbargull comments to change licence and name to python-newick * Update editdistance to 0.4. (#6904) * editdistance: use PyPi source (#6905) * abyss-k128: remove recipe in favor of abyss-2.0.2-boost1.64_3 (#6899) * Update quasitools version to 0.2.1 (#6890) * Update quasitools version to 0.2.1 * Update quasitools pysam version * adding the OTHER python newick package (#6910) * adding the OTHER python newick package * added --single-version-ext, even though it fails locally * remove setup tools as per @druvus rec * Ragout (#6911) * [WIP] added recipe, trouble building * [WIP] need to build add python-newick * facepalm, I added the wrong newick recipe (the one from pypi, not the one from the docs ) * incorportate proper newick parsing prereqs * removed extraneous recipes * update to hicexplorer version 1.8.1 (#6913) * Add Linkage2Allegro (#6906) * md5 fail, test on docker later * md5 update * fix to build and url * removed future runtime, added filename * Asn2gb (#6378) * Initial commit of asn2gb recipe * Fix test... * Added linux library reqs * removed linux64 selectors and dropped 32bit version * remove joblib recipe (#6912) * remove joblib recipe The version here is 2 years old. The conda-forge version is better maintained. * fix recipe failures * add hash for THeta2 package * remove joblib pinning * fix typo * Update meta.yaml * Fix to Linkage2Allegro (#6914) * md5 fail, test on docker later * md5 update * fix to build and url * removed future runtime, added filename * hotfix - haplotypes genehunter * fix checksum * add structureharvester (#6820) * add structureharvester * change md5 to sha256 ; remove jinja for name * fix * Update meta.yaml * update salmon (#6907) * update salmon * apply thread_local patch on OSX * apply thread_local patch on OSX * back to thread_local * clangdev * try fixing clang in build.sh * try fixing clang in build.sh * salmon: add `libcxx [osx]` dependency * BEDOPS v2p4p30 (#6920) * BEDOPS 2.4.30 * BEDOPS 2.4.30 * [WIP] add sibelia synteny finder (#6917) * [WIP] add sibelia synteny finder * add libgcc * seting g++ and gcc explicitly in build * fix cmake target * added libgccc as run dep * linux build passing, problem with g++. removed explicit path setting to cmake * bump to 3.0.6 from sourceforge, maybe lagan compile issue is solved there? * skip building osx until sibelia issue 178 is resolved * downloading prebuilt binaries from sourcefoge * Ragout (#6915) * [WIP] added recipe, trouble building * [WIP] need to build add python-newick * facepalm, I added the wrong newick recipe (the one from pypi, not the one from the docs ) * incorportate proper newick parsing prereqs * removed extraneous recipes * build 1 -- set when building sebelia * add Sibelia test * add libgcc, builds locally * Move libgcc to run deps. * add sibelia to reqs, remove custom sibelia build script from build.sh * Asn2gb (#6918) * Initial commit of asn2gb recipe * Fix test... * Added linux library reqs * removed linux64 selectors and dropped 32bit version * Changed source to use cargo-ports since upstream updates without versioning... * Revert "Changed source to use cargo-ports since upstream updates without versioning..." This reverts commit 30c02b3a130aab454dc3929a91c9687a4c471a6c. * Reverted and try again * corrected linux64 selectors * removed gunzip command * Added debug * updated gunzip command... * Fixed gunzip commnd...again... * Correct cp statement * Ococo 0.1.2.5 (#6922) * Ococo 0.1.2.5 * Fix fn * Update pinning and fixing source path * Fix * re-patched genehunter (#6924) * update 1.8.1 _version (#6927) * update to hicexplorer version 1.8.1 * update release 1.8.1 after _version and help fix * Update meta.yaml * fix version number (#6925) * add smina * dang it, md5 is required * try to make version number checker happy even though we don't actually have version numbers * As an American, I am culturally indoctrinated to put dates in non-intuitive orders... make release "number" work as a date and a number. * canopy: target march=x86-64 instead of march=native (#6929) * mgs-canopy: use -march=x86_64 instead of -march=native * mgs-canopy: use proper command test * add mockinbird (#6926) * added mockinbird * update dependencies: r -> r-base * Quasitools py3 (#6908) * quasitools: use extended-base for click/py3k * quasitools: update/reduce build requirements * quasitools: use entry point created from Conda * quasitools: relax dependency on pysam * quasitools: update to 0.2.2 * Bump secapr to 1.1.0 (#6923) * Bump secapr to 1.1.0 * add entry_point * add numpy as run deps * Fixes for poretools conda package. (#6930) * Fixes for poretools conda package. - Use the Agg backend for matplotlib if saving to file. This eliminates the error message when the DISPLAY environment variable is unset, e.g. on a headless system. - Add an option to output timestamps in UTC, in order to have reproducible output regardless of timezones. - Inadvertently strip trailing whitespace on some lines. * Fix poretools linting. * Update FastTree to 2.1.10. (#6935) * Update FastTree to 2.1.10. * Use GCC on OSX as well, FastTree needs OpenMP. * Add bioconductor-splatter. (#6934) * HG-CoLoR tool (#6888) * add hg-color software * remove pgsa dep because of remove exec * add wget recipe * add unzip recipe * improve recipe * adding fgap recipe (#6921) * adding fgap recipe * add link to nickp60's fork release * added xorg lib11 * replace fork link with link to git archive! * clarify 'fn:' delcaration, thanks @mbargull * remove initialization message from build script * clean up script creation * Update r-maldiquant to 1.17. (#6938) * Update r-mmgenome to 0.7.1. (#6939) * Update plasmidtron to 0.3.5. (#6941) * Crossmap 0.2.7 (#6943) * Update CrossMap to 0.2.7. * Try to build on OSX as well, in principle it's supported by the software. * SIS, build 1 (#6540) * [WIP] add sis init * [wip] sis build passes local * [WIP] added python req * [WIP] changed build script * [WIP] build 1, remove limit to python2 * moved from sis site to github * remove proper test as copy fails on travis, add import test * fgap add OS X build (#6945) * adding fgap recipe * add link to nickp60's fork release * added xorg lib11 * replace fork link with link to git archive! * clarify 'fn:' delcaration, thanks @mbargull * remove initialization message from build script * clean up script creation * add osx build * Add nanopore_simulation (#6944) * Adding Haploclique, version 1.3.1 (#6928) * travis: use xcode7.3 for now (#6952) * Update embl-validator to 1.1.180. (#6949) * Update Picard to 2.15.0. (#6956) * patch fix (#6962) * update to v0.9.1 (#6946) * Feature/perl biox workflow command (#6947) * BUILD * trigger travis * Update deepmedic to 0.6. (#6961) * Ragout, fixing missing executables (#6966) * [WIP] added recipe, trouble building * [WIP] need to build add python-newick * facepalm, I added the wrong newick recipe (the one from pypi, not the one from the docs ) * incorportate proper newick parsing prereqs * removed extraneous recipes * build 1 -- set when building sebelia * add Sibelia test * add libgcc, builds locally * Move libgcc to run deps. * add sibelia to reqs, remove custom sibelia build script from build.sh * Update Build to include executables from lib (#6963) See comments; the make step creates executables that need to end up in the PATH so ragout can find them later. * Fix hgcolor (#6940) * fix name recipe * remove old release and fix short_read_connector dependency * add python to hg-color * change shebang for python scripts * add constraint to python dependency * [FIX] add python 3 dep to discosnp recipe (#6936) * fix name recipe * remove old release and fix short_read_connector dependency * Add python3 dep used by RAD scripts * remove python dep for build * add python constraint for use python 3 * Add recipe progressiveMauve (#6965) * Added recipe for progressiveMauve. * Update NGLess to 0.6.0 (#6967) * Add Bioconductor data package SNPlocs.Hsapiens.dbSNP144.GRCh38. (#6959) * Toulligqc (#6955) * Add toulligqc * Fix sha256 * Skip py27 * Minor fix * added fcsparser v0.1.4 (#6972) * added fcsparser v0.1.4 * fixes per @mbargull * nanopore_simulation, haploclique: super important reformatting (aka: trigger osx builds) (#6971) * Haystack (#6973) * patch fix * update travis.yml * update gseapy to 0.8.11 (#6977) * update pureclip to version 1.0.3 (#6953) * rambo-k (#6969) * rambo-k initial commit * add run_test * adapt dependencies and run_test, change download path * add java-jdk dependency * change to openjdk dependency * move test section into meta.yaml, remove git_rev * Add tombo (#6976) * Add tombo * Add missing build.sh * Fix typo * Update phyloFlash to 3.0b1. (#6979) * Add bioconductor-flagme. (#6981) * busco: remove wget requirement, update post-link script (#6980) * busco: move wget from run to test requirements * busco: simplify post-link, no python dependency * Mykrobe (#6931) * initial import of ga4ghmongo. Needed for mykrobe * got rid of windows bat * fixed failed bioconda lint of 'setup_py_install_args' * removed boilerplate output * refined testing to how you actually import module * removed mongoengine from build requirements * initial build of mykatlas * initial build for mykrobe * added summary * add entry_points section to build * fixed up license file and added summary. Removed not needed build requirements . Added entry_points * using github release instead of pypi because of license not found in pypi. Removed and added requirements * mykatlas: copy pre-compiled linux binary to $PREFIX/bin * mykrobe: skip OSX builds * mykatlas: fix mccortex31 test * Added recipe for perl-try-tiny-retry (#6975) * Update Treetime recipe (#6954) * Move 0.1 version * Add 0.2.1 version of treetime * Some cleaning * Copy only needed files * fix filename * Update: bcbio, bcbio-vm (#6984) Add support for variant file only inputs for validation and improved Arvados data management. * update seqkit to v0.7.2 (#6985) * Add cpinsim (#6987) * Add bioconductor-recount. (#6988) * VEP: bumped subversion (#6989) * TASSEL Build Recipes (#6874) * Build recipe for TASSEL5. * Fixed shabang lines in TASSEL's perl launch scripts. * Added build recipe for TASSEL4. * Updated TASSEL5's build recipe. - Don't build for MacOS - Deploy TASSEL binary in the recomemnded locaiton inside a conda environment - Corrected custom deactivation script * Configured TASSEL4 to use Open JDK as its runtime. * Implemented wrappers to call TASSEL's wrappers to avoid adding TASSEL home directory in the PATH. * Implemented wrappers to call TASSEL's warappers to avoid including its home directory in the PATH. TASSEL's wrappers uses their own location to figure out paths to their dependency. Therefroe, creating symbolic links fro them in the bin is not sufficient. * Corrected build environment valuables in TASSEL's build script. * Build recipe for TASSEL3. * Tidy up temp directory name in TASSEL4' build script. * Revised TASSEL build recipes based on initial PR review comments: - Corrected version for TASSEL3 - Use source/git_url to download source - Create pathes for wrappers to make them callable via symbolic links. * Revision on TASSEL's build recipes: - Corrected patches for TASSEL3 and TASSEL; - Correct testing commands; - Use TASSEL's current official git repo as source; - Added patches to TASSEL5's build recipe. * Convert CRLF in TASSEL's wrapper scripts to LF in its build script. * Fixed EOL issues on TASSEL4's patches. * Fixed EOL issues on TASEL3's pathces. * Changed TASSEL's build recipes to download snapshots from Bitbucket and SF. * Revised sed's regex in TASSEL's build scripts. - Explictly remove CRs in TASSEL's launch scripts if they are present rather than assuming they are there. - RemoveANSI C quotation for the regex, which is not necessary. * fix openmpi pinning (#6990) * Version 2.12.0 of Nest based on build scripts from version 2.14.0 incl. new OpenMPI pinning. (#6995) * htsfilter recipe (#6994) * add new recipe for bioconductor package affyPLM (#6996) * add new recipe for bioconductor package GEOmetadb (#6997) * Recipe for scan_indel (#6983) * Initial commit for Scan Indel * Making ScanIndel tests work * Removing old sed statements * Skipping OSX Tests * Removing python pinning * added watchdog WMS recipe (#6978) Added Watchdog WMS recipe (https://github.com/klugem/watchdog/) * Change to check repo slug instead of fork variable, since the latter seems to be only true in pull requensts. (#6986) * update for v2.2.1 (#6998) * update for v2.2.1 * wrong sha256 * add recipe to build squizz (#6993) * add recipe to build squizz * update version * fixtypo in test section * fix openmpi pinning (#6990) * Version 2.12.0 of Nest based on build scripts from version 2.14.0 incl. new OpenMPI pinning. (#6995) * htsfilter recipe (#6994) * add new recipe for bioconductor package affyPLM (#6996) * add new recipe for bioconductor package GEOmetadb (#6997) * Recipe for scan_indel (#6983) * Initial commit for Scan Indel * Making ScanIndel tests work * Removing old sed statements * Skipping OSX Tests * Removing python pinning * added watchdog WMS recipe (#6978) Added Watchdog WMS recipe (https://github.com/klugem/watchdog/) * fix license * remove skip * Add IsoformSwitchAnalyzeR and dependencies. (#7009) * Add bioconductor-isoformswitchanalyzer. * Add bioconductor-drimseq. * Update meta.yaml (#7005) * Add bioconductor-bsseq. (#7011) * Ont tombo (#7007) * Added ont-tombo bioconda recipe. * Added fix to setup_py_install_args failed test. * Changed name from tombo to ont-tombo for listing on bioconda * tassel: use git_url for old versions (#7015) * tassel: re-order sections * tassel 3.0.174, 4.3.15: use git_url/git_rev * Update bedtools to 2.27.0. (#7020) * updated picrust to v1.1.3 (#7013) * fastqc: add version 0.11.2 (#6992) * fastqc: add version 0.11.2 using openjdk * Rebuilding raxml 8.2.4 (#7022) * New recipe: reaper (#7021) * New recipe: reaper * reaper : replace hyphen * reaper: zlib * reaper: fix test * reaper: fix test * Deleted tombo recipe. Two versions of the package were added with #6976 and #7007 with the names tombo and ont-tombo respectively. The pacakge has been added to pypi as ont-tombo, so to keep the unified naming scheme the tombo recipe should be removed. This should be followed by removal/merger of the tombo package in the channel as noted by @bgruening in #7007. (#7019) * mykatlas: patch --min_variant_conf default value (#7017) Looks good! * Pneumocat Recipe (#7006) * Recipe for pneumocat * Adding skip * Add new recipe for CRAN package SMVar (#7003) * Add new recipe for CRAN package SMVar * Clean up win specific stuff * Add new recipe for CRAN package metaRNASeq (#7002) * Add new recipe for CRAN package metaRNASeq * Remove unnecessary comments * Clean up win specific lines * Wachdog test update (#7001) * added watchdog WMS recipe * Update meta.yaml travis macos test fails with /Users/travis/.travis/job_stages: line 57: shell_session_update: command not found ? * changed sed call for macos * sed call in build not longer required * hashsum changed for build * sed call * use non-default http port * Update build.sh make sed mac compatible * Update run_test.sh make sed mac compatible * timeout replacement * timeout replacement II * new watchdog version * coreutil… * bump zlib requirement to be in sync with conda-forge (#7385) * bump versoin number for new zlib version, add zlib ENV var * increase zlib dependency * pin zlib in ucsc template * add missing htslib pinning * incease htslib version * increase build number * fix review comments * a few more review comment fixes * next round of fixes * last lint fixes * wub: no need for rebuild * hera: fix CONDA_HTSLIB typo (#7497) * fix two build errors * migrated ruby to conda-forge * fix checksum * fix download URL * fix some more broken URLs * fix pinning * fix 2 more failures * remove old broken recipe version * fix some compilation errors * some more build fixes * remove very old bedtools version * remove very old samtools version * fix some more build failures in old packages * increase pysam build number * fix tesseract * small fixes * small fixes * fix * some more fixes * remove gnu-wget * remove old stringtie version * add broken pakcages to the blacklist * fix link * add activate scripts to openms * 3 new fixes * Fix installation of the bam2cfg.pl breakdancer script. (#7682) * blacklist * fix checksum * remove old bedtools version * add new packages to the blacklist * add more packages * blacklist samtools 1.0 * add a few more broken packages * triger new run * more recipes blacklisted * two small fixes * add more packages to the blacklist * more blacklisted packages * Update build-fail-blacklist commit b5d52b84b0cd6384910b21c957410514c40fd1a3 Author: Marius van den Beek Date: Thu Feb 15 21:02:57 2018 +0100 Add python binding for edlib (#7709) * Add python binding for edlib * Add build requirements as in edlib package * Add build.sh for python-edlib commit 384354b745d5d7357dfe08725a9dba3216500e6e Merge: c480488d3 3ad37c612 Author: Cole Lyman Date: Thu Feb 15 12:23:26 2018 -0700 Merge pull request #1 from bioconda/master Merge latest CI configuration from bioconda:master commit 3ad37c612996a18a52359089cae733479a45a4a7 Author: Erik Clarke Date: Thu Feb 15 10:48:01 2018 -0500 Add missing libwww dependency (#7706) * Add missing libwww dependency `krakenhll-build --standard` fails if perl's libwww is not installed. Added as a dependency * Add additional missing lwp-https dependency commit 0874eee4054838e1fb4614b4052ad2180efc4f46 Author: Karl Nordström Date: Thu Feb 15 14:36:38 2018 +0100 fix trim-galore (#7702) - push build number to enforce rebuild - reused the new build script for the old version - added sha256 hash - changed dependency to perl - renamed folder to agree with name in meta.yaml commit 1ca17bdff2b11d56280ca21ac22deb3b90417b66 Author: Karl Nordström Date: Thu Feb 15 14:32:07 2018 +0100 Circle ci add upstream check (#7698) * circleCI setup - added check to make sure remote points to main repository. The script only try to set upstream if it doesn't exist * circleci: use semi-random remote name for 'git diff' * circleci: temporarily unset -u when sourcing entrypoint * circleci: local: fix small errors in 'Setup base system' * circleci: move CI config check after 'source $BASH_ENV' commit d87d75e31a0f2ff0a7752ec13f509146445536bb Author: Johannes Köster Date: Thu Feb 15 11:16:35 2018 +0100 Remove rust recipe (available in conda-forge). (#7700) commit 745f3c50a0b88dc519dcd99e7223fa1713f3a8df Author: Clemens Messerschmidt Date: Thu Feb 15 08:35:07 2018 +0100 Add R package deconstructSigs from CRAN (#7683) * Add R package deconstructSigs from CRAN * Cleanup commit 0297411d59239c30974f2a7898e525883a0bc697 Author: Philippe Bordron Date: Thu Feb 15 08:27:26 2018 +0100 Add analysis tool collection from molpopgen (#7563) * Add analysis tool collection from molpopgen * Update meta.yaml * Update meta.yaml * Update meta.yaml * Update meta.yaml * Update meta.yaml * Update build.sh * Update meta.yaml * Update meta.yaml * Update meta.yaml * Update meta.yaml commit e2a60e71ff69dddcc7f3890cc42699c8e31183a5 Author: Marcel Bargull Date: Thu Feb 15 03:39:43 2018 +0100 circleci: fix typo (#7696) commit 7899e3b3c64b3918ee221c175ee3be1c3776f761 Author: Marcel Bargull Date: Wed Feb 14 23:36:41 2018 +0100 circleci: use docker-entrypoint-source for local build (#7693) commit 74e31c4584421b0a1812657d40f9706198b8f07f Author: Björn Grüning Date: Wed Feb 14 23:05:42 2018 +0100 add r-kernsmooth as run-time requirement (#7692) commit 4bbdda27595e93dd2b85b4fcdbcf08e11b822dfa Author: Erik Kastman Date: Wed Feb 14 16:59:05 2018 -0500 Fix Augustus build errors on OSX (#7676) * Build OSX and use `-std=c++11` for filterBam * Use c++11 in pinned boost version as well * Cleanup non-conforming CFLAGS/CXXFLAGS; return build number (build on OSX only, not linux) * Fix patch length * Fix test: grep help msg in test (help by itself returns `$? == 1`) commit 6e146742bfe2f0247268bfb88b87ce0a26e4fe0d Author: Marcel Bargull Date: Wed Feb 14 22:20:39 2018 +0100 Circleci fixes (#7684) * circleci: explicitly install git, pip * circleci: save config to workspace and cache * circleci: early exit nightly uploads on forks * circleci: avoid BASH_ENV, use custom script * circleci: local: enable devtoolset-2 * circleci: go back to using BASH_ENV, but set PATH conditionally * circleci: let builds fail if CI config is out of date * circleci: use skip_fork for bulk and upload * circleci: revert BASH_ENV changes * circleci: abort master/bulk upload builds on forks commit 390a9305b1c243674a6bad3f06f1f3896de42631 Author: David Laehnemann Date: Wed Feb 14 21:03:15 2018 +0100 Trimmomatic 0.33 (#7691) * trimmomatic: package older version 0.33 * trimmomatic: fix linting request: java-jdk -> openjdk dep * trimmomatic: adjust test for version 0.33 commit cdc126a8db959ceae80f5937d74620eedee1dc34 Author: Jens Preußner Date: Wed Feb 14 20:05:06 2018 +0100 Added bioconductor-illuminahumanmethylationepic packages (#7686) commit d7c2c5ddffdd4d7b733f7894cb16e97902747e7d Author: Martin Raden Date: Wed Feb 14 20:02:15 2018 +0100 IntaRNA : enable multithreading (linux) (#7685) * bump build number for build.sh change * enable multithreading for linux * linux boost pinning extended with "==" * removing "==" from boost pinning * disabling linux boost pinning for lint error check * removing linux specific boost pinning for lint error check * undo last tests * Update meta.yaml * cleanups commit 85d3dd3d2dade52a1c688f1132166d74343989c8 Author: Matthew Gopez Date: Wed Feb 14 13:01:46 2018 -0600 Updating bio_hansel to version 1.2.0 (#7689) commit cda7e6e5134417aaaa0a6a71ecb6b63ff9a03167 Author: Will Rowe Date: Wed Feb 14 14:38:14 2018 +0000 Groot (#7656) * adding recipe for groot * adding recipe for groot * adding recipe for groot * adding recipe for groot * adding recipe for groot * switching to compile GROOT from source * switching to compile GROOT from source commit 0d0e4bdd91b26e253315d8c3418de4348a75c9b0 Author: Karl Nordström Date: Wed Feb 14 13:20:40 2018 +0100 update gmap: (#7679) * update gmap: - pinned zlib and bzip2 - pushed build numbers commit c5d91917045cbbe7922988e07ae42ef658245ac6 Author: Clemens Messerschmidt Date: Wed Feb 14 13:06:26 2018 +0100 Add CopywriteR from bioconductor (#7680) * Add CopywriteR from bioconductor * Add CopyHelpeR from bioconductor commit 989df61a9ea3e498a7700a9e25c65a7e88f107c9 Author: Karl Nordström Date: Wed Feb 14 11:21:06 2018 +0100 bwa: (#7677) - added missing tests - harmonized meta.yaml - changed md5 to sha256 commit bbda496f3c661b78d86e8858da4852cddbc6d829 Author: Slugger70 Date: Wed Feb 14 10:36:23 2018 +1100 Snippy (#7675) * Snippy - pinned freebayes version to stop it installing super old version * snippy - Pinned vcftools as well * incremented build number commit 192e50437d1eaf098fa1a92c9ba3f9544b822f0e Author: Matthew Fogel Date: Tue Feb 13 17:06:47 2018 -0600 Added recipe for msaboot (#7571) * Created build files * Revised meta.yaml * Revised test command * Modified test * Revised once more for testing * put quotes back in * took home quotes back out * Fixed typo * Incremented build number * Added space fixing typo * Changed grep quotes to double-quote * Changed build number back to 0 * Changed md5 to sha256; modified skip param * Changed md5 to sha256 * Added changes * Fixed another typo commit 2c5cdc2dab31624b80700eb278b8cc3bbcfca36f Author: Chris Tomkins-Tinch Date: Tue Feb 13 17:09:29 2018 -0500 add osx mummer build (#7674) commit 621b78987dbc9b38e0f76b68711eaab3ef593854 Author: John Blischak Date: Tue Feb 13 14:42:21 2018 -0500 Update org.Ce.eg.db. Fixes #7117. (#7672) commit 81fb087cda8e6090de9e4d55fd52ef97f220a7bc Author: Rory Kirchner Date: Tue Feb 13 14:29:17 2018 -0500 Allow bcbioRnaseq installation on OSX. (#7673) This is hitting an untagged release which relaxes some unnecessarily hard-pinned dependencies. Will update with a proper release once it is out. commit 6ec33fc9f648efe64f0c2f1ded0d08e59b1735e2 Author: Marcus Stoiber Date: Tue Feb 13 10:44:50 2018 -0800 Update ont-tombo package to version 1.2. (#7670) * Update ont-tombo package to version 1.2. * Added rpy2 and setuptools version requirements commit 7afb4a8c1727cf233ee915b222ebedf4266d38e0 Author: Colin Brislawn Date: Tue Feb 13 09:50:50 2018 -0800 update vsearch (#7671) commit fc08f7c0c26ee311cd31b31e1e0ff062422dfc99 Author: Alan Amossé Date: Tue Feb 13 17:04:33 2018 +0100 Netcdf metadata info (#7669) * netcdf-metadata-info recipes test1 * Add about section, url + license * Add about section, url + license GPL3 + summary * Correct license name * update * yalm update * pin libnetcdf commit 6b618574fb0a82c4e849afd6339df375898a47c2 Author: Rory Kirchner Date: Tue Feb 13 10:31:28 2018 -0500 Add bcbioRnaseq, bcbioBase and basejump (#7572) * Add r-basejump. * Add bcbioBase package. * Add bcbioRNASeq. commit dc0fc226ba1552acc8617b6da0b3400f7ef8aa1b Author: Devon Ryan Date: Tue Feb 13 14:01:09 2018 +0100 Bump py2bit to 0.3.0 (#7667) commit 32d81747a5da3529ee2e16a4c8a14f54768888a0 Author: Brad Chapman Date: Tue Feb 13 07:39:33 2018 -0500 Update: multiqc, multiqc-bcbio (#7666) - MultiQC: Fix for sample name problem ewels/MultiQC#684 - MultiQC_bcbio: Fix for missing coverage plots chapmanb/bcbio-nextgen#2261 commit 72dff4c58680880d7e2d89db1f7675db3f6b2f68 Author: Cole Lyman Date: Tue Feb 13 02:27:00 2018 -0700 Bloomfiltertrie (#7660) * Draft the initial version of the bloomfiltertrie recipe. * Added a patch to replace the popcnt for more general SSE.4 instructions, removed exporting variables in the build, and renamecorrectly named meta.yaml. * Disabled OpenMP support * Re-enabled OpenMP support and added llvm-openmp as a dependency for MacOS. * Removed the llvm dependency from MacOS * Modified the patch to correspond to the correct bit size commit 60d8a0dc1575960f569b2d95eb590fea47c364bd Author: rspreafico Date: Mon Feb 12 23:00:36 2018 -0800 update to 2.3.4.1 (#7662) --- .circleci/config.yml | 34 +++- .circleci/setup.sh | 29 +++- build-fail-blacklist | 57 ++++++- recipes/abricate/0.4/meta.yaml | 24 +-- 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recipes/svgwrite/meta.yaml create mode 100644 recipes/treekin/0.4.2/build.sh create mode 100644 recipes/treekin/0.4.2/meta.yaml rename recipes/{trim_galore => trim-galore/0.4.1}/build.sh (100%) rename recipes/{trim_galore => trim-galore}/0.4.1/meta.yaml (65%) create mode 100644 recipes/trim-galore/build.sh rename recipes/{trim_galore => trim-galore}/meta.yaml (98%) delete mode 100644 recipes/trim_galore/0.4.1/build.sh create mode 100644 recipes/trimmomatic/0.33/build.sh create mode 100644 recipes/trimmomatic/0.33/meta.yaml create mode 100644 recipes/trimmomatic/0.33/trimmomatic.sh diff --git a/.circleci/config.yml b/.circleci/config.yml index 2cc69420eee28f..92c795b4977231 100644 --- a/.circleci/config.yml +++ b/.circleci/config.yml @@ -26,6 +26,23 @@ variables: LANG: en_US.UTF-8 linux: &linux machine: true + skip_fork: &skip_fork + run: + name: Check for fork + command: | + [[ $CIRCLE_PROJECT_USERNAME == bioconda ]] || ( + echo "Skipping build for fork '$CIRCLE_PROJECT_USERNAME'" + circleci step halt + ) + fail_fork: &fail_fork + run: + name: Check for fork + command: | + [[ $CIRCLE_PROJECT_USERNAME == bioconda ]] || ( + echo "Aborting build for fork '$CIRCLE_PROJECT_USERNAME'" + echo "Please use a branch other than 'master' or 'bulk' on your fork" + exit 1 + ) jobs: # When running CircleCI locally, we put everything in one job. @@ -40,8 +57,15 @@ jobs: mkdir -p ~/.ssh ssh-keyscan -H github.com >> ~/.ssh/known_hosts - run: - name: linking conda - command: ln -s /opt/conda $HOME/miniconda + name: Setup base system + command: | + cat >> $BASH_ENV <> $BASH_ENV source $BASH_ENV +# Make sure the CircleCI config is up to date. +# add upstream as some semi-randomly named temporary remote to diff against +UPSTREAM_REMOTE=__upstream__$(tr -dc a-z < /dev/urandom | head -c10) +git remote add -t master $UPSTREAM_REMOTE https://github.com/bioconda/bioconda-recipes.git +git fetch $UPSTREAM_REMOTE +if ! git diff --quiet HEAD...$UPSTREAM_REMOTE/master -- .circleci/; then + echo 'The CI configuration is out of date.' + echo 'Please merge in bioconda:master.' + exit 1 +fi +git remote remove $UPSTREAM_REMOTE + + if ! type bioconda-utils > /dev/null; then echo "Setting up bioconda-utils..." @@ -21,26 +34,26 @@ if ! type bioconda-utils > /dev/null; then if [[ $OSTYPE == darwin* ]]; then tag="MacOSX" elif [[ $OSTYPE == linux* ]]; then - tag="Linux" + tag="Linux" else - echo "Unsupported OS: $OSTYPE" - exit 1 + echo "Unsupported OS: $OSTYPE" + exit 1 fi curl -L -o miniconda.sh https://repo.continuum.io/miniconda/Miniconda3-$MINICONDA_VER-$tag-x86_64.sh bash miniconda.sh -b -p $WORKSPACE/miniconda # step 2: setup channels - conda config --add channels defaults - conda config --add channels conda-forge - conda config --add channels bioconda + conda config --system --add channels defaults + conda config --system --add channels conda-forge + conda config --system --add channels bioconda # step 3: install bioconda-utils - conda install -y --file https://raw.githubusercontent.com/bioconda/bioconda-utils/$BIOCONDA_UTILS_TAG/bioconda_utils/bioconda_utils-requirements.txt + conda install -y git pip --file https://raw.githubusercontent.com/bioconda/bioconda-utils/$BIOCONDA_UTILS_TAG/bioconda_utils/bioconda_utils-requirements.txt pip install git+https://github.com/bioconda/bioconda-utils.git@$BIOCONDA_UTILS_TAG # step 4: configure local channel conda index $WORKSPACE/miniconda/conda-bld/linux-64 $WORKSPACE/miniconda/conda-bld/osx-64 $WORKSPACE/miniconda/conda-bld/noarch - conda config --add channels file://$WORKSPACE/miniconda/conda-bld + conda config --system --add channels file://$WORKSPACE/miniconda/conda-bld # step 5: cleanup conda clean -y --all diff --git a/build-fail-blacklist b/build-fail-blacklist index 913ea8f688bbb0..0b0071e91c07f2 100644 --- a/build-fail-blacklist +++ b/build-fail-blacklist @@ -12,12 +12,63 @@ recipes/clever-toolkit recipes/transcomb recipes/metaprob -# boost problems -recipes/blasr_libcpp # tracking master branch recipes/frc #OSX failures - library loading -recipes/r-spp recipes/r-pscbs/0.61.0 + +# ERROR: cannot verify github.com's certificate, issued by ‘CN=DigiCert SHA2 Extended Validation Server CA,OU=www.digicert.com,O=DigiCert Inc,C=US’: +recipes/ngless +recipes/transrate-tools + +recipes/openslide +recipes/preseq + +# warning: spurious network error (1 tries remaining): [12/-2] [77] Problem with the SSL CA cert (path? access rights?) (error setting certificate verify locations: +recipes/rust-bio-tools +recipes/rust-overlaps +recipes/prosic + +# ./configure no such file or directory +recipes/slang + +# CMake Error at build-common/cmake/VersionHelper.cmake:11 (list): +recipes/somatic-sniper + +# linker errors +recipes/soapec + +# Make file needs to be patched to find newer zlib? +recipes/samtools/1.1 + +recipes/nanopolish/0.4.0 + +# need to fix the download location, the checksum changes everytime +recipes/osra/2.1.0 + +# Configuring Compress-Raw-Zlib-2.069 ... OK +# Building and testing Compress-Raw-Zlib-2.069 ... ! Installing . failed. See /root/.cpanm/work/1518682773.209/build.log for details. Retry with --force to force install it. +# FAIL +recipes/perl-compress-raw-zlib + +# osx failures +recipes/breakdancer +recipes/cgat-scripts +recipes/perl-io-compress +recipes/plastid +recipes/pysamstats +recipes/shorah +recipes/smalt + +# zlib compilation problems +recipes/trinity/2.1.1 + +# non-standard test +recipes/fermikit + +# libxml2.so, not found +recipes/dcmtk + +recipes/angsd diff --git a/recipes/abricate/0.4/meta.yaml b/recipes/abricate/0.4/meta.yaml index 533173b49b4841..0799e65a6dccf9 100644 --- a/recipes/abricate/0.4/meta.yaml +++ b/recipes/abricate/0.4/meta.yaml @@ -3,7 +3,7 @@ package: version: "0.4" build: - number: 0 + number: 1 source: fn: abricate_v0.4.tar.gz @@ -12,18 +12,18 @@ source: requirements: build: - - gcc # [linux] - - llvm # [osx] - - zlib + - gcc # [linux] + - llvm # [osx] + - zlib {{CONDA_ZLIB}}* run: - - libgcc # [linux] - - perl - - perl-bioperl >=1.6.924 - - perl-file-slurp - - perl-text-csv - - perl-list-moreutils - - blast >=2.2.30 - - zlib + - libgcc # [linux] + - perl + - perl-bioperl >=1.6.924 + - perl-file-slurp + - perl-text-csv + - perl-list-moreutils + - blast >=2.2.30 + - zlib {{CONDA_ZLIB}}* test: commands: diff --git a/recipes/abricate/0.5/meta.yaml b/recipes/abricate/0.5/meta.yaml index 5c315dab5a024d..ab423c47575f43 100644 --- a/recipes/abricate/0.5/meta.yaml +++ b/recipes/abricate/0.5/meta.yaml @@ -1,9 +1,9 @@ package: name: abricate version: "0.5" - + build: - number: 0 + number: 1 source: fn: abricate_v0.5.tar.gz @@ -11,25 +11,25 @@ source: md5: 9d2b54511190c3beb6e018675c4d4d0e requirements: - build: - - gcc # [linux] - - llvm # [osx] - - zlib + build: + - gcc # [linux] + - llvm # [osx] + - zlib {{CONDA_ZLIB}}* run: - - libgcc # [linux] - - perl - - perl-bioperl >=1.6.924 - - perl-file-slurp - - perl-text-csv - - perl-list-moreutils - - perl-file-spec - - perl-json - - perl-lwp-simple - - perl-findbin - - blast >=2.2.30 - - zlib - - unzip - - emboss + - libgcc # [linux] + - perl + - perl-bioperl >=1.6.924 + - perl-file-slurp + - perl-text-csv + - perl-list-moreutils + - perl-file-spec + - perl-json + - perl-lwp-simple + - perl-findbin + - blast >=2.2.30 + - zlib {{CONDA_ZLIB}}* + - unzip + - emboss test: commands: @@ -42,4 +42,3 @@ about: license: GPL2 license_file: LICENSE summary: Mass screening of contigs for antibiotic resistance genes - diff --git a/recipes/abricate/meta.yaml b/recipes/abricate/meta.yaml index f994677714f474..a1b7fa6b789f00 100644 --- a/recipes/abricate/meta.yaml +++ b/recipes/abricate/meta.yaml @@ -3,7 +3,7 @@ package: version: "0.7" build: - number: 0 + number: 1 source: fn: abricate_v0.7.tar.gz @@ -12,35 +12,35 @@ source: requirements: build: - - gcc # [linux] - - llvm # [osx] - - zlib - - perl - - perl-bioperl >=1.6.924 - - perl-file-slurp - - perl-text-csv - - perl-list-moreutils - - perl-file-spec - - perl-json - - perl-lwp-simple - - perl-findbin - - blast >=2.6 + - gcc # [linux] + - llvm # [osx] + - zlib {{CONDA_ZLIB}}* + - perl + - perl-bioperl >=1.6.924 + - perl-file-slurp + - perl-text-csv + - perl-list-moreutils + - perl-file-spec + - perl-json + - perl-lwp-simple + - perl-findbin + - blast >=2.6 run: - - libgcc # [linux] - - perl - - perl-bioperl >=1.6.924 - - perl-file-slurp - - perl-text-csv - - perl-list-moreutils - - perl-file-spec - - perl-json - - perl-lwp-simple - - perl-findbin - - blast >=2.6 - - zlib - - unzip - - emboss - - entrez-direct + - libgcc # [linux] + - perl + - perl-bioperl >=1.6.924 + - perl-file-slurp + - perl-text-csv + - perl-list-moreutils + - perl-file-spec + - perl-json + - perl-lwp-simple + - perl-findbin + - blast >=2.6 + - zlib {{CONDA_ZLIB}}* + - unzip + - emboss + - entrez-direct test: commands: diff --git a/recipes/abyss/1.5.2/meta.yaml b/recipes/abyss/1.5.2/meta.yaml index 1a70fabbfd74e1..246ff3de75a59c 100644 --- a/recipes/abyss/1.5.2/meta.yaml +++ b/recipes/abyss/1.5.2/meta.yaml @@ -47,3 +47,6 @@ extra: container: # openmpi needs ssh/rsh extended-base: true + identifiers: + - biotools:abyss + - doi:10.1101/gr.089532.108 diff --git a/recipes/abyss/1.9.0/meta.yaml b/recipes/abyss/1.9.0/meta.yaml index 953af900b2a889..2b88ca40465f3b 100644 --- a/recipes/abyss/1.9.0/meta.yaml +++ b/recipes/abyss/1.9.0/meta.yaml @@ -49,3 +49,6 @@ extra: container: # openmpi needs ssh/rsh extended-base: true + identifiers: + - biotools:abyss + - doi:10.1101/gr.089532.108 diff --git a/recipes/abyss/meta.yaml b/recipes/abyss/meta.yaml index b7cc49c01b224d..b8277d21a6dce7 100644 --- a/recipes/abyss/meta.yaml +++ b/recipes/abyss/meta.yaml @@ -49,3 +49,6 @@ extra: container: # openmpi needs ssh/rsh extended-base: true + identifiers: + - biotools:abyss + - doi:10.1101/gr.089532.108 diff --git a/recipes/addrg/meta.yaml b/recipes/addrg/meta.yaml index 2c4b4f9e72a753..09a1c81ed29dad 100644 --- a/recipes/addrg/meta.yaml +++ b/recipes/addrg/meta.yaml @@ -5,7 +5,7 @@ package: version: {{ version }} build: - number: 0 + number: 1 skip: False source: @@ -17,10 +17,10 @@ requirements: build: - gcc # [not osx] - llvm # [osx] - - htslib >=1.0.0 + - htslib {{ CONDA_HTSLIB }}* run: - libgcc # [not osx] - - htslib >=1.0.0 + - htslib {{ CONDA_HTSLIB }}* about: home: https://github.com/holtgrewe/addrg diff --git a/recipes/agg/meta.yaml b/recipes/agg/meta.yaml index 94bb2fd6c34177..b3a6dcb9e80c54 100644 --- a/recipes/agg/meta.yaml +++ b/recipes/agg/meta.yaml @@ -6,7 +6,7 @@ package: version: {{ version }} build: - number: 0 + number: 1 source: fn: {{ name|lower }}_{{ version }}.tar.gz @@ -15,12 +15,12 @@ source: requirements: build: - - gcc - - zlib + - gcc + - zlib {{CONDA_ZLIB}}* run: - - libgcc - - zlib + - libgcc + - zlib {{CONDA_ZLIB}}* test: commands: diff --git a/recipes/alfred/0.1.2/meta.yaml b/recipes/alfred/0.1.2/meta.yaml index c2d6e27a40729d..6f204c87b28bce 100644 --- a/recipes/alfred/0.1.2/meta.yaml +++ b/recipes/alfred/0.1.2/meta.yaml @@ -11,7 +11,7 @@ source: - Makefile.patch build: - number: 1 + number: 2 string: boost{{CONDA_BOOST}}_{{PKG_BUILDNUM}} skip: True # [osx] diff --git a/recipes/alfred/0.1.3/meta.yaml b/recipes/alfred/0.1.3/meta.yaml index 5e89f7d1916f16..56fc2897030847 100644 --- a/recipes/alfred/0.1.3/meta.yaml +++ b/recipes/alfred/0.1.3/meta.yaml @@ -11,7 +11,7 @@ source: - Makefile.patch build: - number: 1 + number: 2 string: boost{{CONDA_BOOST}}_{{PKG_BUILDNUM}} skip: True # [osx] diff --git a/recipes/alfred/meta.yaml b/recipes/alfred/meta.yaml index 04dc98423b0d55..c42c7d87bcab03 100644 --- a/recipes/alfred/meta.yaml +++ b/recipes/alfred/meta.yaml @@ -11,7 +11,7 @@ source: - Makefile.patch build: - number: 1 + number: 2 string: boost{{CONDA_BOOST}}_{{PKG_BUILDNUM}} skip: True # [osx] diff --git a/recipes/align-it/1.0.3/meta.yaml b/recipes/align-it/1.0.3/meta.yaml index b99e690e6e52a8..c28620caaec688 100644 --- a/recipes/align-it/1.0.3/meta.yaml +++ b/recipes/align-it/1.0.3/meta.yaml @@ -4,7 +4,7 @@ about: summary: "Align-it is a tool to align molecules according to their pharmacophores. A pharmacophore is an abstract concept based on the specific interactions observed in drug-receptor interactions: hydrogen bonding, charge transfer, electrostatic and hydrophobic interactions." build: - number: 3 + number: 4 skip: True # [osx] package: @@ -16,12 +16,12 @@ requirements: - gcc # [linux] - llvm # [osx] - openbabel ==2.4.1 - - zlib + - zlib {{CONDA_ZLIB}}* - cmake run: - openbabel ==2.4.1 - libgcc # [linux] - - zlib + - zlib {{CONDA_ZLIB}}* source: fn: align-it-1.0.3.tar.gz diff --git a/recipes/allegro/meta.yaml b/recipes/allegro/meta.yaml index 2a628ed5e554d7..829bb3446ee24e 100644 --- a/recipes/allegro/meta.yaml +++ b/recipes/allegro/meta.yaml @@ -1,6 +1,6 @@ package: name: allegro - version: 2 + version: 3 source: fn: allegro2-2017-10-11.tar.gz @@ -17,8 +17,7 @@ source: build: - number: 0 - #skip: True # [osx] + number: 1 requirements: build: diff --git a/recipes/angsd/meta.yaml b/recipes/angsd/meta.yaml index ee347ff74dd323..4c878b3e02a518 100644 --- a/recipes/angsd/meta.yaml +++ b/recipes/angsd/meta.yaml @@ -1,7 +1,7 @@ {% set version = "0.910" %} build: - number: 0 + number: 1 skip: True # [osx] about: @@ -15,12 +15,12 @@ package: requirements: build: - - htslib + - htslib {{ CONDA_HTSLIB }}* - gcc # [not osx] - llvm # [osx] run: - libgcc # [not osx] - - htslib + - htslib {{ CONDA_HTSLIB }}* test: commands: diff --git a/recipes/aria2/meta.yaml b/recipes/aria2/meta.yaml index 05f2b39beb67aa..5eef316a5742d8 100644 --- a/recipes/aria2/meta.yaml +++ b/recipes/aria2/meta.yaml @@ -8,29 +8,30 @@ source: md5: 0a28844c8db660d6a20d8a34ae4b0f37 build: - number: 0 + number: 1 + skip: True # [osx] requirements: build: - gcc # [linux] - llvm # [osx] - pkg-config # [osx] - - zlib + - zlib {{CONDA_ZLIB}}* - openssl # [linux] - sqlite - libssh2 - c-ares - libxml2 - + run: - libgcc # [linux] - - zlib + - zlib {{CONDA_ZLIB}}* - openssl # [linux] - sqlite - libssh2 - c-ares - libxml2 - + test: commands: diff --git a/recipes/arvados-cwl-runner/meta.yaml b/recipes/arvados-cwl-runner/meta.yaml index b4f7894220c3b3..684b6f4f3a528d 100644 --- a/recipes/arvados-cwl-runner/meta.yaml +++ b/recipes/arvados-cwl-runner/meta.yaml @@ -1,4 +1,4 @@ -{% set version="1.0.20171211211613" %} +{% set version="1.0.20180216164101" %} package: name: arvados-cwl-runner version: {{ version }} @@ -6,7 +6,7 @@ package: source: fn: arvados-cwl-runner-{{ version }}.tar.gz url: https://pypi.io/packages/source/a/arvados-cwl-runner/arvados-cwl-runner-{{ version }}.tar.gz - md5: 6cec21519a498497d37d0ba4ee5353e9 + md5: 056b92bcd9934b7a914ecceac52e42ad build: number: 0 @@ -17,15 +17,15 @@ requirements: - python - setuptools - ruamel.yaml >=0.13.7,<0.15 - - cwltool >=1.0.20170928192020 - - schema-salad >=2.6.20171116190026 + - cwltool >=1.0.20180130110340 + - schema-salad >=2.6.20171201034858 - arvados-python-client >=0.1.20171211211613 run: - python - ruamel.yaml >=0.13.7,<0.15 - - cwltool >=1.0.20170928192020 - - schema-salad >=2.6.20171116190026 + - cwltool >=1.0.20180130110340 + - schema-salad >=2.6.20171201034858 - arvados-python-client >=0.1.20171211211613 test: diff --git a/recipes/asn2gb/meta.yaml b/recipes/asn2gb/meta.yaml index 1e41eb035a0c32..9f8e6970db6685 100644 --- a/recipes/asn2gb/meta.yaml +++ b/recipes/asn2gb/meta.yaml @@ -16,7 +16,7 @@ source: sha256: 4b6ac3831061bc8f8c8adb011fe58c8741402a9c21c95af395aa98154c9ab775 # [linux] build: - number: 0 + number: 1 requirements: run: diff --git a/recipes/assemblyutility/meta.yaml b/recipes/assemblyutility/meta.yaml index acaee9e8189b1d..cc2a500bb9eae1 100644 --- a/recipes/assemblyutility/meta.yaml +++ b/recipes/assemblyutility/meta.yaml @@ -6,7 +6,7 @@ package: version: {{ version }} build: - number: 0 + number: 1 source: fn: {{ name|lower }}_{{ version }}.tar.gz @@ -17,11 +17,11 @@ requirements: build: - gcc # [not osx] - llvm # [osx] - - zlib + - zlib {{CONDA_ZLIB}}* run: - libgcc # [not osx] - - zlib + - zlib {{CONDA_ZLIB}}* test: commands: diff --git a/recipes/augustus/3.2.3_boost1.57/meta.yaml b/recipes/augustus/3.2.3_boost1.57/meta.yaml index 7e565c922fdec6..5acfefebe1b92b 100644 --- a/recipes/augustus/3.2.3_boost1.57/meta.yaml +++ b/recipes/augustus/3.2.3_boost1.57/meta.yaml @@ -14,7 +14,7 @@ package: source: fn: {{ name }}-{{ version }}.tar.gz - url: http://bioinf.uni-greifswald.de/augustus/binaries/old/augustus-3.2.3.tar.gz + url: http://bioinf.uni-greifswald.de/augustus/binaries/old/{{ name }}-{{ version }}.tar.gz sha256: {{ sha256 }} patches: - patches/bam2hints.Makefile.patch @@ -25,7 +25,6 @@ source: build: number: 0 string: boost{{ boost }}_{{PKG_BUILDNUM}} - skip: True # [osx] requirements: build: @@ -70,6 +69,7 @@ test: - exonerate2hints.pl --help - echo "hello" | exoniphyDb2hints.pl - echo "hello" | extractTranscriptEnds.pl | grep ">seq1" + - filterBam --help 2>&1 | grep "filterBam --in in.bam --out out.bam" - filterGenesIn_mRNAname.pl --help - filterGenesOut_mRNAname.pl --help - filterGenes.pl --help 2>&1 | grep "usage:filterGenes.pl namefile dbfile" diff --git a/recipes/augustus/3.2.3_boost1.57/patches/filterBam.src.Makefile.patch b/recipes/augustus/3.2.3_boost1.57/patches/filterBam.src.Makefile.patch index 9a49ee3416a4d0..a858e17f773ecd 100644 --- a/recipes/augustus/3.2.3_boost1.57/patches/filterBam.src.Makefile.patch +++ b/recipes/augustus/3.2.3_boost1.57/patches/filterBam.src.Makefile.patch @@ -1,6 +1,6 @@ --- auxprogs/filterBam/src/Makefile 2016-03-30 18:35:01.000000000 +0400 +++ auxprogs/filterBam/src/Makefile 2016-05-25 17:07:13.875931702 +0400 -@@ -8,10 +8,13 @@ +@@ -8,10 +8,12 @@ printElapsedTime.cc sumMandIOperations.cc sumDandIOperations.cc PairednessCoverage.cc PROGRAM = filterBam OBJECTS = $(SOURCES:.cc=.o) @@ -12,8 +12,8 @@ +INCLUDES = -I${PREFIX}/include/bamtools/ -Iheaders -I./bamtools +#LIBS = -lbamtools -lz +LIBS = ${PREFIX}/lib/libbamtools.a -lz - CFLAGS = -std=c++0x -+CXXFLAGS += -Wall -O2 # -g -p -g -ggdb +-CFLAGS = -std=c++0x ++CFLAGS += -std=c++11 -Wall -O2 # -g -p -g -ggdb VPATH = functions - + all : $(PROGRAM) $(OBJECTS) CHECKBAM BIN diff --git a/recipes/augustus/meta.yaml b/recipes/augustus/meta.yaml index 807ad1b9343acd..894edbabb7da74 100644 --- a/recipes/augustus/meta.yaml +++ b/recipes/augustus/meta.yaml @@ -8,7 +8,7 @@ package: source: fn: {{ name }}-{{ version }}.tar.gz - url: http://bioinf.uni-greifswald.de/augustus/binaries/old/augustus-3.2.3.tar.gz + url: http://bioinf.uni-greifswald.de/augustus/binaries/old/{{ name }}-{{ version }}.tar.gz sha256: {{ sha256 }} patches: - patches/bam2hints.Makefile.patch @@ -17,9 +17,8 @@ source: - patches/compileSpliceCands.Makefile.patch build: - number: 3 - string: boost{{CONDA_BOOST}}_{{PKG_BUILDNUM}} - skip: True # [osx] + number: 4 + string: boost{{CONDA_BOOST}}_bamtools{{CONDA_BAMTOOLS}}_{{PKG_BUILDNUM}} requirements: build: @@ -27,7 +26,7 @@ requirements: - llvm # [osx] - zlib {{CONDA_ZLIB}}* - libgcc - - bamtools + - bamtools {{ CONDA_BAMTOOLS }}* - gsl {{ CONDA_GSL }}* - lp_solve - perl @@ -36,7 +35,7 @@ requirements: run: - libgcc # [not osx] - zlib {{CONDA_ZLIB}}* - - bamtools + - bamtools {{ CONDA_BAMTOOLS }}* - boost {{CONDA_BOOST}}* - gsl {{ CONDA_GSL }}* - lp_solve @@ -64,6 +63,7 @@ test: - exonerate2hints.pl --help - echo "hello" | exoniphyDb2hints.pl - echo "hello" | extractTranscriptEnds.pl | grep ">seq1" + - filterBam --help 2>&1 | grep "filterBam --in in.bam --out out.bam" - filterGenesIn_mRNAname.pl --help - filterGenesOut_mRNAname.pl --help - filterGenes.pl --help 2>&1 | grep "usage:filterGenes.pl namefile dbfile" diff --git a/recipes/augustus/patches/filterBam.src.Makefile.patch b/recipes/augustus/patches/filterBam.src.Makefile.patch index 9a49ee3416a4d0..a858e17f773ecd 100644 --- a/recipes/augustus/patches/filterBam.src.Makefile.patch +++ b/recipes/augustus/patches/filterBam.src.Makefile.patch @@ -1,6 +1,6 @@ --- auxprogs/filterBam/src/Makefile 2016-03-30 18:35:01.000000000 +0400 +++ auxprogs/filterBam/src/Makefile 2016-05-25 17:07:13.875931702 +0400 -@@ -8,10 +8,13 @@ +@@ -8,10 +8,12 @@ printElapsedTime.cc sumMandIOperations.cc sumDandIOperations.cc PairednessCoverage.cc PROGRAM = filterBam OBJECTS = $(SOURCES:.cc=.o) @@ -12,8 +12,8 @@ +INCLUDES = -I${PREFIX}/include/bamtools/ -Iheaders -I./bamtools +#LIBS = -lbamtools -lz +LIBS = ${PREFIX}/lib/libbamtools.a -lz - CFLAGS = -std=c++0x -+CXXFLAGS += -Wall -O2 # -g -p -g -ggdb +-CFLAGS = -std=c++0x ++CFLAGS += -std=c++11 -Wall -O2 # -g -p -g -ggdb VPATH = functions - + all : $(PROGRAM) $(OBJECTS) CHECKBAM BIN diff --git a/recipes/bam-readcount/meta.yaml b/recipes/bam-readcount/meta.yaml index 6ec4f7f9cc6400..3f5a4b03ad1a11 100644 --- a/recipes/bam-readcount/meta.yaml +++ b/recipes/bam-readcount/meta.yaml @@ -8,14 +8,14 @@ source: md5: 58d72588866f16f658ce4f40a3809af9 build: - number: 1 + number: 2 requirements: build: - cmake >=2.8.3 - gcc # [linux] - llvm # [osx] - - zlib + - zlib {{CONDA_ZLIB}}* - ncurses - perl - python @@ -23,7 +23,7 @@ requirements: run: - python - libgcc # [linux] - - zlib + - zlib {{CONDA_ZLIB}}* - ncurses - perl diff --git a/recipes/bambamc/meta.yaml b/recipes/bambamc/meta.yaml index b1de9a2121134f..c810d4d9699c82 100644 --- a/recipes/bambamc/meta.yaml +++ b/recipes/bambamc/meta.yaml @@ -8,17 +8,17 @@ source: md5: 4de1f030fab1de54387f68e4fbd2cd35 build: - number: 0 + number: 1 requirements: build: - gcc # [linux] - llvm # [osx] - - zlib + - zlib {{CONDA_ZLIB}}* run: - libgcc # [linux] - - zlib + - zlib {{CONDA_ZLIB}}* test: commands: diff --git a/recipes/bamhash/1.0/meta.yaml b/recipes/bamhash/1.0/meta.yaml index a4944c27cd0f12..f71ce05a0488ce 100644 --- a/recipes/bamhash/1.0/meta.yaml +++ b/recipes/bamhash/1.0/meta.yaml @@ -7,16 +7,19 @@ source: url: https://github.com/DecodeGenetics/BamHash/archive/v1.0.tar.gz sha256: af1c939901afe8666ba300c66e9538d79bb48b5e9dd665f4bf575376d288189e +build: + number: 1 + requirements: build: - gcc # [linux] - openssl - - zlib + - zlib {{CONDA_ZLIB}}* run: - openssl - libgcc - - zlib + - zlib {{CONDA_ZLIB}}* test: commands: diff --git a/recipes/bamhash/1.1/meta.yaml b/recipes/bamhash/1.1/meta.yaml index 8fe144b20bfc16..c81f1f3dc1c038 100644 --- a/recipes/bamhash/1.1/meta.yaml +++ b/recipes/bamhash/1.1/meta.yaml @@ -6,16 +6,19 @@ source: url: https://github.com/DecodeGenetics/BamHash/archive/1c987784929f5c6cf28b9d36d00017380b922c71.tar.gz sha256: c1598f71c3662e199bd4853884082eecdd7f69099a3514476aee3485bb0c298c +build: + number: 1 + requirements: build: - gcc # [linux] - openssl - - zlib + - zlib {{CONDA_ZLIB}}* run: - openssl - libgcc - - zlib + - zlib {{CONDA_ZLIB}}* test: commands: diff --git a/recipes/bamm/meta.yaml b/recipes/bamm/meta.yaml index fd9d2b731a64eb..60995020b0c700 100644 --- a/recipes/bamm/meta.yaml +++ b/recipes/bamm/meta.yaml @@ -9,8 +9,8 @@ source: build: - number: 2 - skip: True # [osx] + number: 3 + skip: True [osx or py3k] extra: skip-lints: @@ -20,11 +20,11 @@ requirements: build: - gcc # [linux] - llvm # [osx] - - htslib 1.3.1 + - htslib {{ CONDA_HTSLIB }}* - cython - - python >=2.7,<3 + - python - setuptools - - zlib + - zlib {{CONDA_ZLIB}}* - automake 1.15 - autoconf - libtool @@ -32,9 +32,9 @@ requirements: run: - libgcc # [linux] - - python >=2.7,<3 - - htslib 1.3.1 - - zlib + - python + - htslib {{ CONDA_HTSLIB }}* + - zlib {{CONDA_ZLIB}}* - numpy - samtools ==1.3.1 - bwa ==0.7.12 @@ -51,8 +51,8 @@ test: commands: - bamm --help - nosetests - + about: home: https://github.com/Ecogenomics/BamM license: LGPL-3.0 - summary: "Metagenomics-focused BAM file manipulation" \ No newline at end of file + summary: "Metagenomics-focused BAM file manipulation" diff --git a/recipes/bamtools/2.3.0/meta.yaml b/recipes/bamtools/2.3.0/meta.yaml index d8da826dc2aa38..c51f3ecb1cc8de 100644 --- a/recipes/bamtools/2.3.0/meta.yaml +++ b/recipes/bamtools/2.3.0/meta.yaml @@ -12,16 +12,16 @@ source: - bamtools_lib.diff build: - number: 0 + number: 1 requirements: build: - gcc # [linux] - llvm # [osx] - cmake - - zlib + - zlib {{CONDA_ZLIB}}* run: - - zlib + - zlib {{CONDA_ZLIB}}* - libgcc # [linux] test: diff --git a/recipes/bamtools/meta.yaml b/recipes/bamtools/meta.yaml index 8d7821d10e5a50..97fdbc92aa56ab 100644 --- a/recipes/bamtools/meta.yaml +++ b/recipes/bamtools/meta.yaml @@ -14,7 +14,7 @@ source: - bamtools_lib.diff build: - number: 0 + number: 1 requirements: build: diff --git a/recipes/bamutil/build.sh b/recipes/bamutil/build.sh index 0fe1223a513fab..e96064d0c29de4 100644 --- a/recipes/bamutil/build.sh +++ b/recipes/bamutil/build.sh @@ -1,8 +1,11 @@ #!/usr/bin/env bash VERSION=1.0.14 -wget -O libStatGen-v$VERSION.tar.gz https://github.com/statgen/libStatGen/archive/v$VERSION.tar.gz +curl -o libStatGen-v$VERSION.tar.gz -L https://github.com/statgen/libStatGen/archive/v$VERSION.tar.gz +openssl sha256 libStatGen-v$VERSION.tar.gz | grep 70a504c5cc4838c6ac96cdd010644454615cc907df4e3794c999baf958fa734b tar -xzvpf libStatGen-v$VERSION.tar.gz +# remove profile flag to avoid "ld: cannot find gcrt1.o: No such file or directory" +sed -i.bak '/OPTFLAG_PROFILE?=/ s/-pg//' ./libStatGen-$VERSION/Makefiles/Makefile.include make LIB_PATH_GENERAL=./libStatGen-$VERSION make install INSTALLDIR=$PREFIX LIB_PATH_GENERAL=./libStatGen-$VERSION mkdir -p $PREFIX/bin/ diff --git a/recipes/bamutil/meta.yaml b/recipes/bamutil/meta.yaml index e40b56e0690c1d..6ec8adedfc786c 100644 --- a/recipes/bamutil/meta.yaml +++ b/recipes/bamutil/meta.yaml @@ -8,14 +8,20 @@ source: sha256: "f5ec8d5e98a3797742106c3413a4ab1622d8787e38b29b3df4cddb59d77efda5" build: - number: 1 + number: 2 requirements: build: - - gcc # [linux] + - gcc # [not osx] - llvm # [osx] + - zlib {{CONDA_ZLIB}}* + # curl/openssl are used to download/verify libStatGen + - curl + - openssl run: - - libgcc # [linux] + - libgcc # [not osx] + - libcxx # [osx] + - zlib {{CONDA_ZLIB}}* test: commands: diff --git a/recipes/bbmap/meta.yaml b/recipes/bbmap/meta.yaml index d92202be9e4ea3..532e2e4d9c13ad 100644 --- a/recipes/bbmap/meta.yaml +++ b/recipes/bbmap/meta.yaml @@ -1,6 +1,6 @@ {% set name = "BBMap" %} -{% set version = "37.78" %} -{% set sha256 = "f2da19f64d2bfb7db4c0392212668b425c96a27c77bd9d88d8f0aea90a193509" %} +{% set version = "37.90" %} +{% set sha256 = "f2df007b581aec1b4278e2c115f52afef2bb3e4117c1cd5bd11bbf4993d10bbe" %} about: home: 'https://sourceforge.net/projects/bbmap' @@ -15,7 +15,7 @@ package: version: {{ version }} source: - fn: {{ name|lower }}-{{ version }}.tar.gz + fn: {{ name|lower }}_{{ version }}.tar.gz sha256: {{ sha256 }} url: http://downloads.sourceforge.net/project/{{ name|lower }}/{{ name }}_{{ version }}.tar.gz diff --git a/recipes/bcbio-nextgen/meta.yaml b/recipes/bcbio-nextgen/meta.yaml index c9ac73fcdd515b..0b92b5ab6bac36 100644 --- a/recipes/bcbio-nextgen/meta.yaml +++ b/recipes/bcbio-nextgen/meta.yaml @@ -3,15 +3,15 @@ package: version: '1.0.9a' build: - number: 0 + number: 2 skip: True # [not py27] source: #fn: bcbio-nextgen-1.0.8.tar.gz #url: https://pypi.io/packages/source/b/bcbio-nextgen/bcbio-nextgen-1.0.8.tar.gz - fn: bcbio-nextgen-cadefab.tar.gz - url: https://github.com/chapmanb/bcbio-nextgen/archive/cadefab.tar.gz - md5: b9cb9b39818f07c0ccf8d4c7ffe34825 + fn: bcbio-nextgen-d597178.tar.gz + url: https://github.com/chapmanb/bcbio-nextgen/archive/d597178.tar.gz + md5: 164f0eb90b2d54c95b9570c4efa51733 requirements: build: @@ -20,7 +20,7 @@ requirements: - pip run: - python - - argparse [py26] + - argparse # [py26] - arrow - azure - beautifulsoup4 @@ -35,7 +35,7 @@ requirements: - geneimpacts - gffutils - h5py - - htslib {{ CONDA_HTSLIB }}* + - htslib - ipyparallel >=6.0.2 - ipython-cluster-helper >=0.6.1 - joblib diff --git a/recipes/bcftools-snvphyl-plugin/meta.yaml b/recipes/bcftools-snvphyl-plugin/meta.yaml index 6d071d0d67382e..93bf3a213e6b54 100644 --- a/recipes/bcftools-snvphyl-plugin/meta.yaml +++ b/recipes/bcftools-snvphyl-plugin/meta.yaml @@ -6,26 +6,28 @@ about: of microbial genomes and constructing a phylogenetic tree. This package is the bcftools C plugin build: - number: 0 + number: 1 skip: True # [osx] + package: name: bcftools-snvphyl-plugin version: {{ version }} + requirements: build: - gcc # [not osx] - llvm # [osx] - - bzip2 + - bzip2 {{CONDA_BZIP2}}* - curl - - xz - - zlib + - xz {{CONDA_XZ}}* + - zlib {{CONDA_ZLIB}}* run: - bcftools {{ version }} - libgcc # [not osx] - - bzip2 + - bzip2 {{CONDA_BZIP2}}* - curl - - xz - - zlib + - xz {{CONDA_XZ}}* + - zlib {{CONDA_ZLIB}}* source: fn: bcftools-{{ version }}.tar.bz2 diff --git a/recipes/bcftools/1.3.1/meta.yaml b/recipes/bcftools/1.3.1/meta.yaml index aad63086e8de57..104085c4a4dab5 100644 --- a/recipes/bcftools/1.3.1/meta.yaml +++ b/recipes/bcftools/1.3.1/meta.yaml @@ -8,15 +8,18 @@ about: streaming from a pipe. Indexed VCF and BCF will work in all situations. Un-indexed VCF and BCF and streams will work in most, but not all situations. build: - number: 1 + number: 2 package: name: bcftools version: '1.3.1' requirements: build: - - zlib ==1.2.8 + - gcc # [not osx] + - llvm # [osx] + - zlib {{CONDA_ZLIB}}* run: - - zlib ==1.2.8 + - libgcc # [not osx] + - zlib {{CONDA_ZLIB}}* source: fn: bcftools-1.3.1.tar.bz2 sha256: 12c37a4054cbf1980223e2b3a80a7fdb3fd850324a4ba6832e38fdba91f1b924 diff --git a/recipes/bcftools/1.3/meta.yaml b/recipes/bcftools/1.3/meta.yaml index 0e24341829794b..0609904ce11bbb 100644 --- a/recipes/bcftools/1.3/meta.yaml +++ b/recipes/bcftools/1.3/meta.yaml @@ -1,3 +1,29 @@ +source: + fn: bcftools-1.3.tar.bz2 + sha256: fc5332e49546d55120551b0d5fb690f79e4f2216b8492c7b53033cdaa4256a3d + url: https://github.com/samtools/bcftools/releases/download/1.3/bcftools-1.3.tar.bz2 + +test: + commands: + - "bcftools -h > /dev/null" + - bcftools --version + +build: + number: 1 + +package: + name: bcftools + version: '1.3' + +requirements: + build: + - gcc # [not osx] + - llvm # [osx] + - zlib {{CONDA_ZLIB}}* + run: + - libgcc # [not osx] + - zlib {{CONDA_ZLIB}}* + about: home: https://github.com/samtools/bcftools license: MIT @@ -7,21 +33,4 @@ about: accept VCF, bgzipped VCF and BCF with filetype detected automatically even when streaming from a pipe. Indexed VCF and BCF will work in all situations. Un-indexed VCF and BCF and streams will work in most, but not all situations. -build: - number: 0 -package: - name: bcftools - version: '1.3' -requirements: - build: - - zlib ==1.2.8 - run: - - zlib ==1.2.8 -source: - fn: bcftools-1.3.tar.bz2 - sha256: fc5332e49546d55120551b0d5fb690f79e4f2216b8492c7b53033cdaa4256a3d - url: https://github.com/samtools/bcftools/releases/download/1.3/bcftools-1.3.tar.bz2 -test: - commands: - - "bcftools -h > /dev/null" - - bcftools --version + diff --git a/recipes/bcftools/meta.yaml b/recipes/bcftools/meta.yaml index 6e1744304802d0..b3c9a85be4cc03 100644 --- a/recipes/bcftools/meta.yaml +++ b/recipes/bcftools/meta.yaml @@ -10,27 +10,27 @@ about: VCF and BCF and streams will work in most, but not all situations. build: - number: 0 + number: 1 package: name: bcftools version: {{ version }} requirements: build: - - gcc # [not osx] - - llvm # [osx] - - bzip2 - - curl - - xz - - zlib + - gcc # [not osx] + - llvm # [osx] + - bzip2 {{CONDA_BZIP2}}* + - curl + - xz {{CONDA_XZ}}* + - zlib {{CONDA_ZLIB}}* run: - - libgcc # [not osx] - - bzip2 - - curl - # Currently removed due to size and dependency issues - #- matplotlib # for plot-vcfstats - #- texlive-core # for plot-vcfstats - - xz - - zlib + - libgcc # [not osx] + - bzip2 {{CONDA_BZIP2}}* + - curl + # Currently removed due to size and dependency issues + #- matplotlib # for plot-vcfstats + #- texlive-core # for plot-vcfstats + - xz {{CONDA_XZ}}* + - zlib {{CONDA_ZLIB}}* source: fn: bcftools-{{ version }}.tar.bz2 diff --git a/recipes/bedtools/2.16.2/build.sh b/recipes/bedtools/2.16.2/build.sh deleted file mode 100644 index b8ab1768447071..00000000000000 --- a/recipes/bedtools/2.16.2/build.sh +++ /dev/null @@ -1,5 +0,0 @@ -#!/bin/sh - -make -mkdir -p $PREFIX/bin -mv bin/* $PREFIX/bin/ diff --git a/recipes/bedtools/2.16.2/makefile.patch b/recipes/bedtools/2.16.2/makefile.patch deleted file mode 100644 index 10563bc9266926..00000000000000 --- a/recipes/bedtools/2.16.2/makefile.patch +++ /dev/null @@ -1,17 +0,0 @@ ---- Makefile 2012-11-03 17:11:06.000000000 +0000 -+++ Makefile.new 2016-03-01 00:03:57.700408266 +0000 -@@ -17,11 +17,11 @@ - export UTIL_DIR = src/utils - export CXX = g++ - ifeq ($(DEBUG),1) --export CXXFLAGS = -Wall -O0 -g -fno-inline -fkeep-inline-functions -D_FILE_OFFSET_BITS=64 -fPIC -DDEBUG -D_DEBUG -+export CXXFLAGS = -Wall -O0 -g -fno-inline -fkeep-inline-functions -D_FILE_OFFSET_BITS=64 -fPIC -DDEBUG -D_DEBUG -I${PREFIX}/include - else --export CXXFLAGS = -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -+export CXXFLAGS = -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -I${PREFIX}/include - endif --export LIBS = -lz -+export LIBS = -L${PREFIX}/lib -lz - export BT_ROOT = src/utils/BamTools/ - - diff --git a/recipes/bedtools/2.16.2/meta.yaml b/recipes/bedtools/2.16.2/meta.yaml deleted file mode 100644 index dea1d0692ce5d1..00000000000000 --- a/recipes/bedtools/2.16.2/meta.yaml +++ /dev/null @@ -1,31 +0,0 @@ -package: - name: bedtools - version: "2.16.2" -source: - fn: BEDTools.v2.16.2.tar.gz - url: https://storage.googleapis.com/google-code-archive-downloads/v2/code.google.com/bedtools/BEDTools.v2.16.2.tar.gz - sha256: f5f5c864eb3f465ac7fd5fa651e2e4dbc0cd8d9198367148c52f3be3f46c2772 - patches: - - makefile.patch - -build: - number: 0 - -requirements: - build: - - gcc - - zlib - - run: - - libgcc - - zlib - -test: - commands: - - bedtools > /dev/null - - bedtools --version | egrep '\bv2\.16\.2\b' - -about: - home: http://bedtools.readthedocs.org/ - license: GPL v2 - summary: A powerful toolset for genome arithmetic diff --git a/recipes/bedtools/2.17.0/build.sh b/recipes/bedtools/2.17.0/build.sh deleted file mode 100644 index b8ab1768447071..00000000000000 --- a/recipes/bedtools/2.17.0/build.sh +++ /dev/null @@ -1,5 +0,0 @@ -#!/bin/sh - -make -mkdir -p $PREFIX/bin -mv bin/* $PREFIX/bin/ diff --git a/recipes/bedtools/2.17.0/makefile.patch b/recipes/bedtools/2.17.0/makefile.patch deleted file mode 100644 index 50a8c827f38de4..00000000000000 --- a/recipes/bedtools/2.17.0/makefile.patch +++ /dev/null @@ -1,24 +0,0 @@ ---- Makefile 2012-11-03 17:11:06.000000000 +0000 -+++ Makefile.new 2016-03-01 00:03:57.700408266 +0000 -@@ -17,11 +17,11 @@ - export UTIL_DIR = src/utils - export CXX = g++ - ifeq ($(DEBUG),1) --export CXXFLAGS = -Wall -O0 -g -fno-inline -fkeep-inline-functions -D_FILE_OFFSET_BITS=64 -fPIC -DDEBUG -D_DEBUG -+export CXXFLAGS = -Wall -O0 -g -fno-inline -fkeep-inline-functions -D_FILE_OFFSET_BITS=64 -fPIC -DDEBUG -D_DEBUG -I${PREFIX}/include - else --export CXXFLAGS = -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -+export CXXFLAGS = -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -I${PREFIX}/include - endif --export LIBS = -lz -+export LIBS = -L${PREFIX}/lib -lz - export BT_ROOT = src/utils/BamTools/ - - -@@ -202,4 +202,4 @@ - echo "#define VERSION_GIT_H" >> $(VERSION_FILE) ; \ - echo "#define VERSION_GIT \"$${DETECTED_VERSION}\"" >> $(VERSION_FILE) ; \ - echo "#endif /* VERSION_GIT_H */" >> $(VERSION_FILE) ; \ -- fi ) -\ No newline at end of file -+ fi ) diff --git a/recipes/bedtools/2.17.0/meta.yaml b/recipes/bedtools/2.17.0/meta.yaml deleted file mode 100644 index 07d02c788ab8a9..00000000000000 --- a/recipes/bedtools/2.17.0/meta.yaml +++ /dev/null @@ -1,30 +0,0 @@ -package: - name: bedtools - version: "2.17.0" -source: - fn: BEDTools.v2.17.0.tar.gz - url: https://bedtools.googlecode.com/files/BEDTools.v2.17.0.tar.gz - sha256: 6dcfacdcbccc968e872b81ba1f37a086b1bcc486571582ed595db717e924d0fe - patches: - - makefile.patch - -build: - number: 0 - -requirements: - build: - - gcc - - zlib - - run: - - libgcc - - zlib - -test: - commands: - - bedtools > /dev/null - -about: - home: http://bedtools.readthedocs.org/ - license: GPL v2 - summary: A powerful toolset for genome arithmetic diff --git a/recipes/bedtools/2.25/meta.yaml b/recipes/bedtools/2.25/meta.yaml index 81c4fcf24b9b2a..5c7b5e7a7ca36e 100644 --- a/recipes/bedtools/2.25/meta.yaml +++ b/recipes/bedtools/2.25/meta.yaml @@ -8,16 +8,16 @@ source: sha256: d737ca42e7df76c5455d3e6e0562cdcb62336830eaad290fd4133a328a1ddacc build: - number: 2 + number: 3 requirements: build: - - gcc # [linux] - - llvm # [osx] - - zlib + - gcc # [linux] + - llvm # [osx] + - zlib {{CONDA_ZLIB}}* run: - - zlib - - libgcc # [linux] + - zlib {{CONDA_ZLIB}}* + - libgcc # [linux] test: commands: diff --git a/recipes/bedtools/2.26.0/meta.yaml b/recipes/bedtools/2.26.0/meta.yaml index 7a8156664e6dc8..afce12506e295c 100644 --- a/recipes/bedtools/2.26.0/meta.yaml +++ b/recipes/bedtools/2.26.0/meta.yaml @@ -10,16 +10,16 @@ source: - 2.26.0_postrelease.patch build: - number: 0 + number: 1 requirements: build: - - gcc # [linux] - - llvm # [osx] - - zlib + - gcc # [linux] + - llvm # [osx] + - zlib {{CONDA_ZLIB}}* run: - - zlib - - libgcc # [linux] + - zlib {{CONDA_ZLIB}}* + - libgcc # [linux] test: commands: diff --git a/recipes/bedtools/2.27.0/meta.yaml b/recipes/bedtools/2.27.0/meta.yaml index 7ee16bc62753ad..54da2db7f919b7 100644 --- a/recipes/bedtools/2.27.0/meta.yaml +++ b/recipes/bedtools/2.27.0/meta.yaml @@ -11,7 +11,7 @@ source: sha256: e4f0e5616d04ba5ac09c36dec989b1236a5712e67d0b6874ff5e144d7ed4ce60 build: - number: 0 + number: 1 requirements: build: diff --git a/recipes/bedtools/2.27.1/meta.yaml b/recipes/bedtools/2.27.1/meta.yaml index 846cbad283ae68..5c0ea8190c74fd 100644 --- a/recipes/bedtools/2.27.1/meta.yaml +++ b/recipes/bedtools/2.27.1/meta.yaml @@ -11,7 +11,7 @@ source: sha256: c8c2acbaf3f9cb92dcf8e5cd59af6b31ae9c4598efb786ba6c84f66ca72fafd9 build: - number: 0 + number: 1 requirements: build: diff --git a/recipes/behst/0.6.tar.bz2 b/recipes/behst/0.6.tar.bz2 deleted file mode 100644 index 0b2bb67778d7dbf1c1407008f0edf5fc3df968e9..0000000000000000000000000000000000000000 GIT binary patch literal 0 HcmV?d00001 literal 21501 zcma%>RZtvE@Zc9;e9bCo>-*-hGE?(4-tTS#y>Lr0^I8Bt?#lkH{^26H8ojiHj83!X$&*QRtFmov79bTa z@=TNJ;rBF?o2R)7b>dO_;`;jcq&wPg`qF-b6`+z5@#?ecSL(ibbZJMowHmd%f@Jl# 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zW(NSd+nfRffgnLWWhe#d+vtf3FXk{yUXL=p%Ylp_5MnP)>hOh-&f{~aLyO`0`6YyG z9?yjdP!Hjn$Lg2WOwfQ3JAbM=n^S8U=qbkOP`PA&^}DkH)R_sZ5<{`}&a1TH_XqPaSoVP&_lz-` zb-x)+HQc6{CA^e5(^H3=P0-~#2`q<*ebjS zl*vR8LKjTnL0~k;N*k9M=G%o;k5(#Y+@*pe^}RO|F8Q}B?GorbD8&p{D9Q2B0>EK(hT5yn8>&-pz9 z_NpB;tso*Sq&J#x;ttyn#Xr);)wGc@dpm*iDL=7OH?N`D^ASGz0e9`CL;uCxkxmpO I3;KE1z_)CzuK)l5 diff --git a/recipes/behst/build.sh b/recipes/behst/build.sh index 9331283c47ac60..58f50e57abf18a 100644 --- a/recipes/behst/build.sh +++ b/recipes/behst/build.sh @@ -1,4 +1,5 @@ #!/bin/bash + mkdir -p $PREFIX/bin chmod +x bin/* cp bin/* $PREFIX/bin diff --git a/recipes/behst/meta.yaml b/recipes/behst/meta.yaml index ca1194ac191dc5..3e4f4f12e552e2 100644 --- a/recipes/behst/meta.yaml +++ b/recipes/behst/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "1.9" %} +{% set version = "2.9" %} package: name: behst @@ -7,11 +7,11 @@ package: source: fn: behst-{{ version }}.tar.gz url: https://bitbucket.org/hoffmanlab/behst/get/{{ version }}.tar.bz2 - sha256: d288f57302f8a68362a8993a6a8c70622959822c4f1503716045914f7210e7d5 + sha256: eaf30240ee334e1c7b519db0b8cae65c21fa801d7524cdbc4cd1bc7f923c3f3f build: number: 0 - skip: True # [not py27] + skip: True # [not py35] requirements: build: diff --git a/recipes/bfc/meta.yaml b/recipes/bfc/meta.yaml index 8fe7e582157d10..f9c0528c69547a 100644 --- a/recipes/bfc/meta.yaml +++ b/recipes/bfc/meta.yaml @@ -3,7 +3,7 @@ package: version: "r181" build: - number: 1 + number: 2 source: fn: bfc_r181.tar.gz @@ -14,11 +14,11 @@ requirements: build: - gcc # [not osx] - llvm # [osx] - - zlib + - zlib {{CONDA_ZLIB}}* run: - libgcc # [not osx] - - zlib + - zlib {{CONDA_ZLIB}}* test: commands: diff --git a/recipes/bgt/meta.yaml b/recipes/bgt/meta.yaml index 7685db71320ba1..6aebaf3239193a 100644 --- a/recipes/bgt/meta.yaml +++ b/recipes/bgt/meta.yaml @@ -14,11 +14,11 @@ requirements: build: - gcc # [not osx] - llvm # [osx] - - zlib + - zlib {{CONDA_ZLIB}}* run: - libgcc # [not osx] - - zlib + - zlib {{CONDA_ZLIB}}* test: commands: diff --git a/recipes/bio_hansel/meta.yaml b/recipes/bio_hansel/meta.yaml index d295fcda4a4ba4..a52c8348a252cf 100644 --- a/recipes/bio_hansel/meta.yaml +++ b/recipes/bio_hansel/meta.yaml @@ -1,7 +1,7 @@ {% set name = "bio_hansel" %} -{% set version = "1.1.3" %} +{% set version = "1.2.0" %} {% set hash_type = "sha256" %} -{% set hash_value = "60f85dd8ed6015942b5f5df7f09b7decb12ef2410cec6b60b42429c4d689cab8" %} +{% set hash_value = "ab42082931c40d5bc4f4bd11aa3498d365c10f74dbd51668c5836fbe02c1f81f" %} package: diff --git a/recipes/bioawk/meta.yaml b/recipes/bioawk/meta.yaml index 5d49752e620c42..ec0e1a4326025b 100644 --- a/recipes/bioawk/meta.yaml +++ b/recipes/bioawk/meta.yaml @@ -8,18 +8,18 @@ source: sha256: 5cbef3f39b085daba45510ff450afcf943cfdfdd483a546c8a509d3075ff51b5 build: - number: 1 + number: 2 requirements: build: - gcc # [linux] - llvm # [osx] - - zlib + - zlib {{CONDA_ZLIB}}* - bison - m4 run: - libgcc # [linux] - - zlib + - zlib {{CONDA_ZLIB}}* test: commands: diff --git a/recipes/bioconductor-batchqc/build.sh b/recipes/bioconductor-batchqc/build.sh new file mode 100644 index 00000000000000..da43ce21683122 --- /dev/null +++ b/recipes/bioconductor-batchqc/build.sh @@ -0,0 +1,4 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-batchqc/meta.yaml b/recipes/bioconductor-batchqc/meta.yaml new file mode 100644 index 00000000000000..3d0d954abf8f85 --- /dev/null +++ b/recipes/bioconductor-batchqc/meta.yaml @@ -0,0 +1,61 @@ +{% set version = "1.6.1" %} +{% set name = "BatchQC" %} +{% set bioc = "3.6" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + fn: '{{ name }}_{{ version }}.tar.gz' + url: + - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: 2d5a3bc7a163894681a7135d0242a3697565b829930b177f5ab3ff6764b251ba +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ +requirements: + build: + - bioconductor-limma + - bioconductor-sva + - r-base + - r-corpcor + - r-d3heatmap + - r-ggvis + - r-gplots + - r-knitr + - r-matrix + - r-matrixstats + - r-mcmcpack + - r-moments + - r-pander + - r-reshape2 + - r-rmarkdown + - r-shiny + run: + - bioconductor-limma + - bioconductor-sva + - r-base + - r-corpcor + - r-d3heatmap + - r-ggvis + - r-gplots + - r-knitr + - r-matrix + - r-matrixstats + - r-mcmcpack + - r-moments + - r-pander + - r-reshape2 + - r-rmarkdown + - r-shiny +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: 'GPL (>= 2)' + summary: 'Sequencing and microarray samples often are collected or processed in multiple batches or at different times. This often produces technical biases that can lead to incorrect results in the downstream analysis. BatchQC is a software tool that streamlines batch preprocessing and evaluation by providing interactive diagnostics, visualizations, and statistical analyses to explore the extent to which batch variation impacts the data. BatchQC diagnostics help determine whether batch adjustment needs to be done, and how correction should be applied before proceeding with a downstream analysis. Moreover, BatchQC interactively applies multiple common batch effect approaches to the data, and the user can quickly see the benefits of each method. BatchQC is developed as a Shiny App. The output is organized into multiple tabs, and each tab features an important part of the batch effect analysis and visualization of the data. The BatchQC interface has the following analysis groups: Summary, Differential Expression, Median Correlations, Heatmaps, Circular Dendrogram, PCA Analysis, Shape, ComBat and SVA.' diff --git a/recipes/bioconductor-biocgraph/build.sh b/recipes/bioconductor-biocgraph/build.sh new file mode 100644 index 00000000000000..da43ce21683122 --- /dev/null +++ b/recipes/bioconductor-biocgraph/build.sh @@ -0,0 +1,4 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-biocgraph/meta.yaml b/recipes/bioconductor-biocgraph/meta.yaml new file mode 100644 index 00000000000000..e188b22182c745 --- /dev/null +++ b/recipes/bioconductor-biocgraph/meta.yaml @@ -0,0 +1,39 @@ +{% set version = "1.40.0" %} +{% set name = "biocGraph" %} +{% set bioc = "3.6" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + fn: '{{ name }}_{{ version }}.tar.gz' + url: + - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: d1b7ac11a31e14583093860d1f05db3e0c653610c3921b7d58e176ca1f8f8e86 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ +requirements: + build: + - bioconductor-biocgenerics + - bioconductor-geneplotter + - bioconductor-graph + - bioconductor-rgraphviz + - r-base + run: + - bioconductor-biocgenerics + - bioconductor-geneplotter + - bioconductor-graph + - bioconductor-rgraphviz + - r-base +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'This package provides examples and code that make use of the different graph related packages produced by Bioconductor.' diff --git a/recipes/bioconductor-biomvcclass/build.sh b/recipes/bioconductor-biomvcclass/build.sh new file mode 100644 index 00000000000000..da43ce21683122 --- /dev/null +++ b/recipes/bioconductor-biomvcclass/build.sh @@ -0,0 +1,4 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-biomvcclass/meta.yaml b/recipes/bioconductor-biomvcclass/meta.yaml new file mode 100644 index 00000000000000..717bac70b676d2 --- /dev/null +++ b/recipes/bioconductor-biomvcclass/meta.yaml @@ -0,0 +1,39 @@ +{% set version = "1.46.0" %} +{% set name = "BioMVCClass" %} +{% set bioc = "3.6" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + fn: '{{ name }}_{{ version }}.tar.gz' + url: + - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: ac61875e695c20c666b32c0354d08553efe8e4e628263f6a86ab2e662bfbc821 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ +requirements: + build: + - bioconductor-biobase + - bioconductor-graph + - bioconductor-mvcclass + - bioconductor-rgraphviz + - r-base + run: + - bioconductor-biobase + - bioconductor-graph + - bioconductor-mvcclass + - bioconductor-rgraphviz + - r-base +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: LGPL + summary: 'Creates classes used in model-view-controller (MVC) design' diff --git a/recipes/bioconductor-bioqc/build.sh b/recipes/bioconductor-bioqc/build.sh new file mode 100644 index 00000000000000..da43ce21683122 --- /dev/null +++ b/recipes/bioconductor-bioqc/build.sh @@ -0,0 +1,4 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-bioqc/meta.yaml b/recipes/bioconductor-bioqc/meta.yaml new file mode 100644 index 00000000000000..2e4daf1873fe58 --- /dev/null +++ b/recipes/bioconductor-bioqc/meta.yaml @@ -0,0 +1,38 @@ +{% set version = "1.6.0" %} +{% set name = "BioQC" %} +{% set bioc = "3.6" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + fn: '{{ name }}_{{ version }}.tar.gz' + url: + - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: 7abfb656723c874a837c2bad9b3368681c19b02bcbbcf8671406a201bff53bd3 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ +requirements: + build: + - bioconductor-biobase + - r-base + - r-rcpp + - gcc # [linux] + - llvm # [osx] + run: + - bioconductor-biobase + - r-base + - r-rcpp + - libcxx # [osx] +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: 'GPL (>=3)' + summary: 'BioQC performs quality control of high-throughput expression data based on tissue gene signatures. It can detect tissue heterogeneity in gene expression data. The core algorithm is a Wilcoxon-Mann-Whitney test that is optimised for high performance.' diff --git a/recipes/bioconductor-biosvd/build.sh b/recipes/bioconductor-biosvd/build.sh new file mode 100644 index 00000000000000..da43ce21683122 --- /dev/null +++ b/recipes/bioconductor-biosvd/build.sh @@ -0,0 +1,4 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-biosvd/meta.yaml b/recipes/bioconductor-biosvd/meta.yaml new file mode 100644 index 00000000000000..86b5ff445d303b --- /dev/null +++ b/recipes/bioconductor-biosvd/meta.yaml @@ -0,0 +1,37 @@ +{% set version = "2.14.0" %} +{% set name = "biosvd" %} +{% set bioc = "3.6" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + fn: '{{ name }}_{{ version }}.tar.gz' + url: + - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + sha256: 8b023dfcf2004bcfddccefa53f8985a691227687c7685120049a0746be18e076 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ +requirements: + build: + - bioconductor-biobase + - bioconductor-biocgenerics + - r-base + - r-nmf + run: + - bioconductor-biobase + - bioconductor-biocgenerics + - r-base + - r-nmf +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'The biosvd package contains functions to reduce the input data set from the feature x assay space to the reduced diagonalized eigenfeature x eigenassay space, with the eigenfeatures and eigenassays unique orthonormal superpositions of the features and assays, respectively. Results of SVD applied to the data can subsequently be inspected based on generated graphs, such as a heatmap of the eigenfeature x assay matrix and a bar plot with the eigenexpression fractions of all eigenfeatures. These graphs aid in deciding which eigenfeatures and eigenassays to filter out (i.e., eigenfeatures representing steady state, noise, or experimental artifacts; or when applied to the variance in the data, eigenfeatures representing steady-scale variance). After possible removal of steady state expression, steady-scale variance, noise and experimental artifacts, and after re-applying SVD to the normalized data, a summary html report of the eigensystem is generated, containing among others polar plots of the assays and features, a table with the list of features sortable according to their coordinates, radius and phase in the polar plot, and a visualization of the data sorted according to the two selected eigenfeatures and eigenassays with colored feature/assay annotation information when provided. This gives a global picture of the dynamics of expression/intensity levels, in which individual features and assays are classified in groups of similar regulation and function or similar cellular state and biological phenotype.' diff --git a/recipes/bioconductor-birewire/build.sh b/recipes/bioconductor-birewire/build.sh new file mode 100644 index 00000000000000..da43ce21683122 --- /dev/null +++ b/recipes/bioconductor-birewire/build.sh @@ -0,0 +1,4 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-birewire/meta.yaml b/recipes/bioconductor-birewire/meta.yaml new file mode 100644 index 00000000000000..a55e756d058ef8 --- /dev/null +++ b/recipes/bioconductor-birewire/meta.yaml @@ -0,0 +1,42 @@ +{% set version = "3.10.0" %} +{% set name = "BiRewire" %} +{% set bioc = "3.6" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + fn: '{{ name }}_{{ version }}.tar.gz' + url: + - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: f3ba22c1db85f270565c05dc80e6ec4aa0ab0d0efbf32db448a1da805d81e223 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ +requirements: + build: + - r-base + - r-igraph + - r-matrix + - r-slam + - r-tsne + - gcc # [linux] + - llvm # [osx] + run: + - r-base + - r-igraph + - r-matrix + - r-slam + - r-tsne + - libcxx # [osx] +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: GPL-3 + summary: 'Fast functions for bipartite network rewiring through N consecutive switching steps (See References) and for the computation of the minimal number of switching steps to be performed in order to maximise the dissimilarity with respect to the original network. Includes functions for the analysis of the introduced randomness across the switching steps and several other routines to analyse the resulting networks and their natural projections. Extension to undirected networks and directed signed networks is also provided. Starting from version 1.9.7 a more precise bound (especially for small network) has been implemented. Starting from version 2.2.0 the analysis routine is more complete and a visual montioring of the underlying Markov Chain has been implemented. Starting from 3.6.0 the library can handle also matrices with NA (not for the directed signed graphs).' diff --git a/recipes/bioconductor-brainstars/build.sh b/recipes/bioconductor-brainstars/build.sh new file mode 100644 index 00000000000000..da43ce21683122 --- /dev/null +++ b/recipes/bioconductor-brainstars/build.sh @@ -0,0 +1,4 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-brainstars/meta.yaml b/recipes/bioconductor-brainstars/meta.yaml new file mode 100644 index 00000000000000..ef939b74952cd8 --- /dev/null +++ b/recipes/bioconductor-brainstars/meta.yaml @@ -0,0 +1,37 @@ +{% set version = "1.22.0" %} +{% set name = "BrainStars" %} +{% set bioc = "3.6" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + fn: '{{ name }}_{{ version }}.tar.gz' + url: + - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: 726fb8fc0b1aefee7a35aa846fa6c07a13c5b4b7996ded7413865c7de5b5373a +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ +requirements: + build: + - bioconductor-biobase + - r-base + - r-rcurl + - r-rjsonio + run: + - bioconductor-biobase + - r-base + - r-rcurl + - r-rjsonio +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'This package can search and get gene expression data and plots from BrainStars (B*). BrainStars is a quantitative expression database of the adult mouse brain. The database has genome-wide expression profile at 51 adult mouse CNS regions.' diff --git a/recipes/bioconductor-bridge/build.sh b/recipes/bioconductor-bridge/build.sh new file mode 100644 index 00000000000000..da43ce21683122 --- /dev/null +++ b/recipes/bioconductor-bridge/build.sh @@ -0,0 +1,4 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-bridge/meta.yaml b/recipes/bioconductor-bridge/meta.yaml new file mode 100644 index 00000000000000..c65313c89b4ccb --- /dev/null +++ b/recipes/bioconductor-bridge/meta.yaml @@ -0,0 +1,36 @@ +{% set version = "1.42.0" %} +{% set name = "bridge" %} +{% set bioc = "3.6" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + fn: '{{ name }}_{{ version }}.tar.gz' + url: + - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + sha256: 537acf2edd96df67a1c19fa0f5114b60a2d205a10094f829879f6f86c498ac2b +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ +requirements: + build: + - bioconductor-rama + - r-base + - gcc # [linux] + - llvm # [osx] + run: + - bioconductor-rama + - r-base + - libcxx # [osx] +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: 'GPL (>= 2)' + summary: 'Test for differentially expressed genes with microarray data. This package can be used with both cDNA microarrays or Affymetrix chip. The packge fits a robust Bayesian hierarchical model for testing for differential expression. Outliers are modeled explicitly using a $t$-distribution. The model includes an exchangeable prior for the variances which allow different variances for the genes but still shrink extreme empirical variances. Our model can be used for testing for differentially expressed genes among multiple samples, and can distinguish between the different possible patterns of differential expression when there are three or more samples. Parameter estimation is carried out using a novel version of Markov Chain Monte Carlo that is appropriate when the model puts mass on subspaces of the full parameter space.' diff --git a/recipes/bioconductor-browserviz/build.sh b/recipes/bioconductor-browserviz/build.sh new file mode 100644 index 00000000000000..da43ce21683122 --- /dev/null +++ b/recipes/bioconductor-browserviz/build.sh @@ -0,0 +1,4 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-browserviz/meta.yaml b/recipes/bioconductor-browserviz/meta.yaml new file mode 100644 index 00000000000000..301552f8453ae3 --- /dev/null +++ b/recipes/bioconductor-browserviz/meta.yaml @@ -0,0 +1,37 @@ +{% set version = "1.10.0" %} +{% set name = "BrowserViz" %} +{% set bioc = "3.6" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + fn: '{{ name }}_{{ version }}.tar.gz' + url: + - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: ac0f17636dcb0bb2c060bdd76181626fba2cdf116d05ee3ea1c015209d066dec +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ +requirements: + build: + - bioconductor-biocgenerics + - r-base + - 'r-httpuv >=1.3.2' + - 'r-jsonlite >=0.9.15' + run: + - bioconductor-biocgenerics + - r-base + - 'r-httpuv >=1.3.2' + - 'r-jsonlite >=0.9.15' +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: GPL-2 + summary: 'Interactvive graphics in a web browser from R, using websockets and JSON.' diff --git a/recipes/bioconductor-browservizdemo/build.sh b/recipes/bioconductor-browservizdemo/build.sh new file mode 100644 index 00000000000000..da43ce21683122 --- /dev/null +++ b/recipes/bioconductor-browservizdemo/build.sh @@ -0,0 +1,4 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-browservizdemo/meta.yaml b/recipes/bioconductor-browservizdemo/meta.yaml new file mode 100644 index 00000000000000..e2cd31a1c5728a --- /dev/null +++ b/recipes/bioconductor-browservizdemo/meta.yaml @@ -0,0 +1,44 @@ +{% set version = "1.10.0" %} +{% set name = "BrowserVizDemo" %} +{% set bioc = "3.6" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + fn: '{{ name }}_{{ version }}.tar.gz' + url: + - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: 1d3d43e647083d9ffcdd389e066cdf58c9fc2eb8b5de3ad2029884162845fa7a +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ +requirements: + build: + - bioconductor-biocgenerics + - bioconductor-browserviz + - r-base + - 'r-httpuv >=1.3.2' + - 'r-jsonlite >=0.9.15' + - 'r-rcpp >=0.11.5' + - gcc # [linux] + - llvm # [osx] + run: + - bioconductor-biocgenerics + - bioconductor-browserviz + - r-base + - 'r-httpuv >=1.3.2' + - 'r-jsonlite >=0.9.15' + - 'r-rcpp >=0.11.5' + - libcxx # [osx] +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: GPL-2 + summary: 'A BrowserViz subclassing example, xy plotting in the browser using d3.' diff --git a/recipes/bioconductor-bsgenome.drerio.ucsc.danrer7/meta.yaml b/recipes/bioconductor-bsgenome.drerio.ucsc.danrer7/meta.yaml new file mode 100644 index 00000000000000..9a85945ee6edb8 --- /dev/null +++ b/recipes/bioconductor-bsgenome.drerio.ucsc.danrer7/meta.yaml @@ -0,0 +1,34 @@ +{% set version = "1.4.0" %} +{% set name = "BSgenome.Drerio.UCSC.danRer7" %} +{% set bioc = "3.6" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + fn: '{{ name }}_{{ version }}.tar.gz' + url: + - 'http://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: ef2e7e27508d7dbfc63e09ae36f96d2578590af1f12b82912fe029898084a39f +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ +requirements: + build: + - 'bioconductor-bsgenome >=1.33.5' + - r-base + run: + - 'bioconductor-bsgenome >=1.33.5' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'http://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Full genome sequences for Danio rerio (Zebrafish) as provided by UCSC (danRer7, Jul. 2010) and stored in Biostrings objects.' diff --git a/recipes/bioconductor-bsgenome.drerio.ucsc.danrer7/post-link.sh b/recipes/bioconductor-bsgenome.drerio.ucsc.danrer7/post-link.sh new file mode 100644 index 00000000000000..98a91893e6427b --- /dev/null +++ b/recipes/bioconductor-bsgenome.drerio.ucsc.danrer7/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="BSgenome.Drerio.UCSC.danRer7_1.4.0.tar.gz" +URLS=( + "http://bioconductor.org/packages/3.6/data/annotation/src/contrib/BSgenome.Drerio.UCSC.danRer7_1.4.0.tar.gz" + "https://bioarchive.galaxyproject.org/BSgenome.Drerio.UCSC.danRer7_1.4.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-bsgenome.drerio.ucsc.danrer7/bioconductor-bsgenome.drerio.ucsc.danrer7_1.4.0_src_all.tar.gz" +) +MD5="766b407a46f20d69a143eab0809eb10a" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING \ No newline at end of file diff --git a/recipes/bioconductor-bsgenome.drerio.ucsc.danrer7/pre-unlink.sh b/recipes/bioconductor-bsgenome.drerio.ucsc.danrer7/pre-unlink.sh new file mode 100644 index 00000000000000..8241f9f1766153 --- /dev/null +++ b/recipes/bioconductor-bsgenome.drerio.ucsc.danrer7/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ BSgenome.Drerio.UCSC.danRer7 diff --git a/recipes/bioconductor-bsgenome.hsapiens.ucsc.hg18/meta.yaml b/recipes/bioconductor-bsgenome.hsapiens.ucsc.hg18/meta.yaml new file mode 100644 index 00000000000000..98f873f2de6c31 --- /dev/null +++ b/recipes/bioconductor-bsgenome.hsapiens.ucsc.hg18/meta.yaml @@ -0,0 +1,34 @@ +{% set version = "1.3.1000" %} +{% set name = "BSgenome.Hsapiens.UCSC.hg18" %} +{% set bioc = "3.6" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + fn: '{{ name }}_{{ version }}.tar.gz' + url: + - 'http://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: 26fa81bfdb16269d76299aae1f352ddd3c56bec30da7259785fe3e3d8985a7ad +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ +requirements: + build: + - 'bioconductor-bsgenome >=1.33.5' + - r-base + run: + - 'bioconductor-bsgenome >=1.33.5' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'http://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Full genome sequences for Homo sapiens (Human) as provided by UCSC (hg18, Mar. 2006) and stored in Biostrings objects.' diff --git a/recipes/bioconductor-bsgenome.hsapiens.ucsc.hg18/post-link.sh b/recipes/bioconductor-bsgenome.hsapiens.ucsc.hg18/post-link.sh new file mode 100644 index 00000000000000..e8f0251f9e41e7 --- /dev/null +++ b/recipes/bioconductor-bsgenome.hsapiens.ucsc.hg18/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="BSgenome.Hsapiens.UCSC.hg18_1.3.1000.tar.gz" +URLS=( + "http://bioconductor.org/packages/3.6/data/annotation/src/contrib/BSgenome.Hsapiens.UCSC.hg18_1.3.1000.tar.gz" + "https://bioarchive.galaxyproject.org/BSgenome.Hsapiens.UCSC.hg18_1.3.1000.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-bsgenome.hsapiens.ucsc.hg18/bioconductor-bsgenome.hsapiens.ucsc.hg18_1.3.1000_src_all.tar.gz" +) +MD5="51bb2e1ed4009860bb21aaac32fffd9c" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING \ No newline at end of file diff --git a/recipes/bioconductor-bsgenome.hsapiens.ucsc.hg18/pre-unlink.sh b/recipes/bioconductor-bsgenome.hsapiens.ucsc.hg18/pre-unlink.sh new file mode 100644 index 00000000000000..e707ab78d8d0a3 --- /dev/null +++ b/recipes/bioconductor-bsgenome.hsapiens.ucsc.hg18/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ BSgenome.Hsapiens.UCSC.hg18 diff --git a/recipes/bioconductor-bufferedmatrix/build.sh b/recipes/bioconductor-bufferedmatrix/build.sh new file mode 100644 index 00000000000000..da43ce21683122 --- /dev/null +++ b/recipes/bioconductor-bufferedmatrix/build.sh @@ -0,0 +1,4 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-bufferedmatrix/meta.yaml b/recipes/bioconductor-bufferedmatrix/meta.yaml new file mode 100644 index 00000000000000..9105af79e52046 --- /dev/null +++ b/recipes/bioconductor-bufferedmatrix/meta.yaml @@ -0,0 +1,34 @@ +{% set version = "1.42.0" %} +{% set name = "BufferedMatrix" %} +{% set bioc = "3.6" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + fn: '{{ name }}_{{ version }}.tar.gz' + url: + - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: 07f8c652593aa9ae7495a8e698672463807b70dc4a6b563e5f75b1687b48b9ef +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ +requirements: + build: + - r-base + - gcc # [linux] + - llvm # [osx] + run: + - r-base + - libcxx # [osx] +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: 'LGPL (>= 2)' + summary: 'A tabular style data object where most data is stored outside main memory. A buffer is used to speed up access to data.' diff --git a/recipes/bioconductor-bufferedmatrixmethods/build.sh b/recipes/bioconductor-bufferedmatrixmethods/build.sh new file mode 100644 index 00000000000000..da43ce21683122 --- /dev/null +++ b/recipes/bioconductor-bufferedmatrixmethods/build.sh @@ -0,0 +1,4 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-bufferedmatrixmethods/meta.yaml b/recipes/bioconductor-bufferedmatrixmethods/meta.yaml new file mode 100644 index 00000000000000..04bbbd49e59f98 --- /dev/null +++ b/recipes/bioconductor-bufferedmatrixmethods/meta.yaml @@ -0,0 +1,36 @@ +{% set version = "1.42.0" %} +{% set name = "BufferedMatrixMethods" %} +{% set bioc = "3.6" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + fn: '{{ name }}_{{ version }}.tar.gz' + url: + - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: a2550805761d33f47a2e32c8e4cc613645a252a2968b1dabb434d25c99215ecd +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ +requirements: + build: + - 'bioconductor-bufferedmatrix >=1.3.0' + - r-base + - gcc # [linux] + - llvm # [osx] + run: + - 'bioconductor-bufferedmatrix >=1.3.0' + - r-base + - libcxx # [osx] +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: 'GPL (>= 2)' + summary: 'Microarray analysis methods that use BufferedMatrix objects' diff --git a/recipes/bioconductor-bus/build.sh b/recipes/bioconductor-bus/build.sh new file mode 100644 index 00000000000000..da43ce21683122 --- /dev/null +++ b/recipes/bioconductor-bus/build.sh @@ -0,0 +1,4 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-bus/meta.yaml b/recipes/bioconductor-bus/meta.yaml new file mode 100644 index 00000000000000..992f79048dbe0b --- /dev/null +++ b/recipes/bioconductor-bus/meta.yaml @@ -0,0 +1,38 @@ +{% set version = "1.34.0" %} +{% set name = "BUS" %} +{% set bioc = "3.6" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + fn: '{{ name }}_{{ version }}.tar.gz' + url: + - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: 76c764307fb9baa5781b0804fd7fc3eeb4bc1ae0433a9d584f40ac863029151e +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ +requirements: + build: + - bioconductor-minet + - r-base + - r-infotheo + - gcc # [linux] + - llvm # [osx] + run: + - bioconductor-minet + - r-base + - r-infotheo + - libcxx # [osx] +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: GPL-3 + summary: 'This package can be used to compute associations among genes (gene-networks) or between genes and some external traits (i.e. clinical).' diff --git a/recipes/bioconductor-cancerinsilico/build.sh b/recipes/bioconductor-cancerinsilico/build.sh new file mode 100644 index 00000000000000..da43ce21683122 --- /dev/null +++ b/recipes/bioconductor-cancerinsilico/build.sh @@ -0,0 +1,4 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-cancerinsilico/meta.yaml b/recipes/bioconductor-cancerinsilico/meta.yaml new file mode 100644 index 00000000000000..95ecc51c8a70c9 --- /dev/null +++ b/recipes/bioconductor-cancerinsilico/meta.yaml @@ -0,0 +1,40 @@ +{% set version = "1.4.0" %} +{% set name = "CancerInSilico" %} +{% set bioc = "3.6" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + fn: '{{ name }}_{{ version }}.tar.gz' + url: + - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: 30f18ce1520f522638f1b3fb1a84ca9fbb164e479a6eff599f9ea4d40512f7a6 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ +requirements: + build: + - r-base + - r-bh + - r-rcpp + - r-testthat + - gcc # [linux] + - llvm # [osx] + run: + - r-base + - r-bh + - r-rcpp + - r-testthat + - libcxx # [osx] +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: 'GPL (>= 2)' + summary: 'The CancerInSilico package provides an R interface for running mathematical models of tumor progresson. This package has the underlying models implemented in C++ and the output and analysis features implemented in R.' diff --git a/recipes/bioconductor-cghnormaliter/build.sh b/recipes/bioconductor-cghnormaliter/build.sh new file mode 100644 index 00000000000000..da43ce21683122 --- /dev/null +++ b/recipes/bioconductor-cghnormaliter/build.sh @@ -0,0 +1,4 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-cghnormaliter/meta.yaml b/recipes/bioconductor-cghnormaliter/meta.yaml new file mode 100644 index 00000000000000..d1380d0815fabc --- /dev/null +++ b/recipes/bioconductor-cghnormaliter/meta.yaml @@ -0,0 +1,37 @@ +{% set version = "1.32.0" %} +{% set name = "CGHnormaliter" %} +{% set bioc = "3.6" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + fn: '{{ name }}_{{ version }}.tar.gz' + url: + - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: 8c7c974157467ec4ac24fcc55424bcfe2e60fe5c96e9aa2cc65e0c473cf523af +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ +requirements: + build: + - bioconductor-biobase + - 'bioconductor-cghbase >=1.15.0' + - 'bioconductor-cghcall >=2.17.0' + - r-base + run: + - bioconductor-biobase + - 'bioconductor-cghbase >=1.15.0' + - 'bioconductor-cghcall >=2.17.0' + - r-base +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: 'GPL (>= 3)' + summary: 'Normalization and centralization of array comparative genomic hybridization (aCGH) data. The algorithm uses an iterative procedure that effectively eliminates the influence of imbalanced copy numbers. This leads to a more reliable assessment of copy number alterations (CNAs).' diff --git a/recipes/bioconductor-chipsim/build.sh b/recipes/bioconductor-chipsim/build.sh new file mode 100644 index 00000000000000..da43ce21683122 --- /dev/null +++ b/recipes/bioconductor-chipsim/build.sh @@ -0,0 +1,4 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-chipsim/meta.yaml b/recipes/bioconductor-chipsim/meta.yaml new file mode 100644 index 00000000000000..66056b483f41ce --- /dev/null +++ b/recipes/bioconductor-chipsim/meta.yaml @@ -0,0 +1,39 @@ +{% set version = "1.32.0" %} +{% set name = "ChIPsim" %} +{% set bioc = "3.6" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + fn: '{{ name }}_{{ version }}.tar.gz' + url: + - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: ea914c481d7d809ce2088efd6ff56dc5d1da66ce3dd5e67bda035cbbfd877506 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ +requirements: + build: + - 'bioconductor-biostrings >=2.29.2' + - bioconductor-iranges + - bioconductor-shortread + - bioconductor-xvector + - r-base + run: + - 'bioconductor-biostrings >=2.29.2' + - bioconductor-iranges + - bioconductor-shortread + - bioconductor-xvector + - r-base +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: 'GPL (>= 2)' + summary: 'A general framework for the simulation of ChIP-seq data. Although currently focused on nucleosome positioning the package is designed to support different types of experiments.' diff --git a/recipes/bioconductor-chipxpress/build.sh b/recipes/bioconductor-chipxpress/build.sh new file mode 100644 index 00000000000000..da43ce21683122 --- /dev/null +++ b/recipes/bioconductor-chipxpress/build.sh @@ -0,0 +1,4 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-chipxpress/meta.yaml b/recipes/bioconductor-chipxpress/meta.yaml new file mode 100644 index 00000000000000..e0827ebfb89952 --- /dev/null +++ b/recipes/bioconductor-chipxpress/meta.yaml @@ -0,0 +1,45 @@ +{% set version = "1.22.0" %} +{% set name = "ChIPXpress" %} +{% set bioc = "3.6" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + fn: '{{ name }}_{{ version }}.tar.gz' + url: + - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: 2b1b1056cbe87817593200a7fd0b91346c3e516649a2485c986bbf09f83b9a71 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ +requirements: + build: + - bioconductor-affy + - bioconductor-biobase + - bioconductor-chipxpressdata + - bioconductor-frma + - bioconductor-geoquery + - r-base + - r-biganalytics + - r-bigmemory + run: + - bioconductor-affy + - bioconductor-biobase + - bioconductor-chipxpressdata + - bioconductor-frma + - bioconductor-geoquery + - r-base + - r-biganalytics + - r-bigmemory +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: GPL(>=2) + summary: 'ChIPXpress takes as input predicted TF bound genes from ChIPx data and uses a corresponding database of gene expression profiles downloaded from NCBI GEO to rank the TF bound targets in order of which gene is most likely to be functional TF target.' diff --git a/recipes/bioconductor-chipxpressdata/meta.yaml b/recipes/bioconductor-chipxpressdata/meta.yaml new file mode 100644 index 00000000000000..7593b6b43c0065 --- /dev/null +++ b/recipes/bioconductor-chipxpressdata/meta.yaml @@ -0,0 +1,34 @@ +{% set version = "1.16.0" %} +{% set name = "ChIPXpressData" %} +{% set bioc = "3.6" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + fn: '{{ name }}_{{ version }}.tar.gz' + url: + - 'http://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: 84e4e096c947ace46402ed962a7936b9d08d1db5adeb900ff2df60fcb191472e +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ +requirements: + build: + - r-base + - r-bigmemory + run: + - r-base + - r-bigmemory + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'http://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' + license: 'GPL (>=2)' + summary: 'Contains pre-built mouse (GPL1261) and human (GPL570) database of gene expression profiles to be used for ChIPXpress ranking.' diff --git a/recipes/bioconductor-chipxpressdata/post-link.sh b/recipes/bioconductor-chipxpressdata/post-link.sh new file mode 100644 index 00000000000000..c89d30841ac546 --- /dev/null +++ b/recipes/bioconductor-chipxpressdata/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="ChIPXpressData_1.16.0.tar.gz" +URLS=( + "http://bioconductor.org/packages/3.6/data/experiment/src/contrib/ChIPXpressData_1.16.0.tar.gz" + "https://bioarchive.galaxyproject.org/ChIPXpressData_1.16.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-chipxpressdata/bioconductor-chipxpressdata_1.16.0_src_all.tar.gz" +) +MD5="020fc315cf29fb563d2c78b750ad4765" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING \ No newline at end of file diff --git a/recipes/bioconductor-chipxpressdata/pre-unlink.sh b/recipes/bioconductor-chipxpressdata/pre-unlink.sh new file mode 100644 index 00000000000000..9f33bd55ea4eef --- /dev/null +++ b/recipes/bioconductor-chipxpressdata/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ ChIPXpressData diff --git a/recipes/bioconductor-chopsticks/build.sh b/recipes/bioconductor-chopsticks/build.sh new file mode 100644 index 00000000000000..da43ce21683122 --- /dev/null +++ b/recipes/bioconductor-chopsticks/build.sh @@ -0,0 +1,4 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-chopsticks/meta.yaml b/recipes/bioconductor-chopsticks/meta.yaml new file mode 100644 index 00000000000000..4a421c2eed6d32 --- /dev/null +++ b/recipes/bioconductor-chopsticks/meta.yaml @@ -0,0 +1,36 @@ +{% set version = "1.42.0" %} +{% set name = "chopsticks" %} +{% set bioc = "3.6" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + fn: '{{ name }}_{{ version }}.tar.gz' + url: + - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + sha256: 8d599d1afd587b9f7c3df6892623d0c0c65b6115f5041603034cdb7d269a9c2b +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ +requirements: + build: + - r-base + - r-survival + - gcc # [linux] + - llvm # [osx] + run: + - r-base + - r-survival + - libcxx # [osx] +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: GPL-3 + summary: 'Implements classes and methods for large-scale SNP association studies' diff --git a/recipes/bioconductor-chromheatmap/build.sh b/recipes/bioconductor-chromheatmap/build.sh new file mode 100644 index 00000000000000..da43ce21683122 --- /dev/null +++ b/recipes/bioconductor-chromheatmap/build.sh @@ -0,0 +1,4 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-chromheatmap/meta.yaml b/recipes/bioconductor-chromheatmap/meta.yaml new file mode 100644 index 00000000000000..2c73418a28dc65 --- /dev/null +++ b/recipes/bioconductor-chromheatmap/meta.yaml @@ -0,0 +1,45 @@ +{% set version = "1.32.0" %} +{% set name = "ChromHeatMap" %} +{% set bioc = "3.6" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + fn: '{{ name }}_{{ version }}.tar.gz' + url: + - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: 5976d27fe6b43359658b2875943afb4cfa29eb29aeba68dbd3939c1073f2504f +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ +requirements: + build: + - 'bioconductor-annotate >=1.20.0' + - 'bioconductor-annotationdbi >=1.4.0' + - 'bioconductor-biobase >=2.17.8' + - 'bioconductor-biocgenerics >=0.3.2' + - bioconductor-genomicranges + - bioconductor-iranges + - bioconductor-rtracklayer + - r-base + run: + - 'bioconductor-annotate >=1.20.0' + - 'bioconductor-annotationdbi >=1.4.0' + - 'bioconductor-biobase >=2.17.8' + - 'bioconductor-biocgenerics >=0.3.2' + - bioconductor-genomicranges + - bioconductor-iranges + - bioconductor-rtracklayer + - r-base +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'The ChromHeatMap package can be used to plot genome-wide data (e.g. expression, CGH, SNP) along each strand of a given chromosome as a heat map. The generated heat map can be used to interactively identify probes and genes of interest.' diff --git a/recipes/bioconductor-chromstar/build.sh b/recipes/bioconductor-chromstar/build.sh new file mode 100644 index 00000000000000..da43ce21683122 --- /dev/null +++ b/recipes/bioconductor-chromstar/build.sh @@ -0,0 +1,4 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-chromstar/meta.yaml b/recipes/bioconductor-chromstar/meta.yaml new file mode 100644 index 00000000000000..a6462246ef27b0 --- /dev/null +++ b/recipes/bioconductor-chromstar/meta.yaml @@ -0,0 +1,60 @@ +{% set version = "1.4.0" %} +{% set name = "chromstaR" %} +{% set bioc = "3.6" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + fn: '{{ name }}_{{ version }}.tar.gz' + url: + - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: 5f329f313dfcad93b97fe08452dfb4a81f5d984acfa244dafe8ff36776fac2cf +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ +requirements: + build: + - bioconductor-bamsignals + - bioconductor-chromstardata + - bioconductor-genomeinfodb + - bioconductor-genomicalignments + - bioconductor-genomicranges + - bioconductor-iranges + - bioconductor-rsamtools + - bioconductor-s4vectors + - r-base + - r-doparallel + - r-foreach + - r-ggplot2 + - r-mvtnorm + - r-reshape2 + - gcc # [linux] + - llvm # [osx] + run: + - bioconductor-bamsignals + - bioconductor-chromstardata + - bioconductor-genomeinfodb + - bioconductor-genomicalignments + - bioconductor-genomicranges + - bioconductor-iranges + - bioconductor-rsamtools + - bioconductor-s4vectors + - r-base + - r-doparallel + - r-foreach + - r-ggplot2 + - r-mvtnorm + - r-reshape2 + - libcxx # [osx] +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'This package implements functions for combinatorial and differential analysis of ChIP-seq data. It includes uni- and multivariate peak-calling, export to genome browser viewable files, and functions for enrichment analyses.' diff --git a/recipes/bioconductor-chromstardata/meta.yaml b/recipes/bioconductor-chromstardata/meta.yaml new file mode 100644 index 00000000000000..a1e7caec1f4366 --- /dev/null +++ b/recipes/bioconductor-chromstardata/meta.yaml @@ -0,0 +1,32 @@ +{% set version = "1.4.0" %} +{% set name = "chromstaRData" %} +{% set bioc = "3.6" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + fn: '{{ name }}_{{ version }}.tar.gz' + url: + - 'http://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: f1b64e4dd6d3627321dfe65f00e47889db86210df11d96b7cc392416a1ce8d82 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ +requirements: + build: + - r-base + run: + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'http://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' + license: GPL-3 + summary: 'ChIP-seq data for demonstration purposes in the chromstaR package.' diff --git a/recipes/bioconductor-chromstardata/post-link.sh b/recipes/bioconductor-chromstardata/post-link.sh new file mode 100644 index 00000000000000..874ca52e5cb2b9 --- /dev/null +++ b/recipes/bioconductor-chromstardata/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="chromstaRData_1.4.0.tar.gz" +URLS=( + "http://bioconductor.org/packages/3.6/data/experiment/src/contrib/chromstaRData_1.4.0.tar.gz" + "https://bioarchive.galaxyproject.org/chromstaRData_1.4.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-chromstardata/bioconductor-chromstardata_1.4.0_src_all.tar.gz" +) +MD5="bb4511694d5906d4677e84e44e6374b2" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING \ No newline at end of file diff --git a/recipes/bioconductor-chromstardata/pre-unlink.sh b/recipes/bioconductor-chromstardata/pre-unlink.sh new file mode 100644 index 00000000000000..50cf78bfddc708 --- /dev/null +++ b/recipes/bioconductor-chromstardata/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ chromstaRData diff --git a/recipes/bioconductor-cindex/build.sh b/recipes/bioconductor-cindex/build.sh new file mode 100644 index 00000000000000..da43ce21683122 --- /dev/null +++ b/recipes/bioconductor-cindex/build.sh @@ -0,0 +1,4 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-cindex/meta.yaml b/recipes/bioconductor-cindex/meta.yaml new file mode 100644 index 00000000000000..1c1276a6af2497 --- /dev/null +++ b/recipes/bioconductor-cindex/meta.yaml @@ -0,0 +1,53 @@ +{% set version = "1.6.0" %} +{% set name = "CINdex" %} +{% set bioc = "3.6" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + fn: '{{ name }}_{{ version }}.tar.gz' + url: + - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: 26e5c2dfac363255139738ddceac61afb7de3d84835fd0e55653395331762053 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ +requirements: + build: + - bioconductor-genomeinfodb + - bioconductor-genomicranges + - bioconductor-iranges + - bioconductor-s4vectors + - r-base + - r-bitops + - r-dplyr + - r-gplots + - r-gridextra + - r-png + - r-som + - r-stringr + run: + - bioconductor-genomeinfodb + - bioconductor-genomicranges + - bioconductor-iranges + - bioconductor-s4vectors + - r-base + - r-bitops + - r-dplyr + - r-gplots + - r-gridextra + - r-png + - r-som + - r-stringr +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: 'GPL (>= 2)' + summary: 'The CINdex package addresses important area of high-throughput genomic analysis. It allows the automated processing and analysis of the experimental DNA copy number data generated by Affymetrix SNP 6.0 arrays or similar high throughput technologies. It calculates the chromosome instability (CIN) index that allows to quantitatively characterize genome-wide DNA copy number alterations as a measure of chromosomal instability. This package calculates not only overall genomic instability, but also instability in terms of copy number gains and losses separately at the chromosome and cytoband level.' diff --git a/recipes/bioconductor-cispath/build.sh b/recipes/bioconductor-cispath/build.sh new file mode 100644 index 00000000000000..da43ce21683122 --- /dev/null +++ b/recipes/bioconductor-cispath/build.sh @@ -0,0 +1,4 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-cispath/meta.yaml b/recipes/bioconductor-cispath/meta.yaml new file mode 100644 index 00000000000000..a1fbb52e314838 --- /dev/null +++ b/recipes/bioconductor-cispath/meta.yaml @@ -0,0 +1,34 @@ +{% set version = "1.18.0" %} +{% set name = "cisPath" %} +{% set bioc = "3.6" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + fn: '{{ name }}_{{ version }}.tar.gz' + url: + - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: 9044abda3d71c0e4a5a4685b09a309dff8a390d16a368f33614368f8f69c4179 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ +requirements: + build: + - r-base + - gcc # [linux] + - llvm # [osx] + run: + - r-base + - libcxx # [osx] +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: 'GPL (>= 3)' + summary: 'cisPath is an R package that uses web browsers to visualize and manage protein-protein interaction networks.' diff --git a/recipes/bioconductor-classifyr/build.sh b/recipes/bioconductor-classifyr/build.sh new file mode 100644 index 00000000000000..da43ce21683122 --- /dev/null +++ b/recipes/bioconductor-classifyr/build.sh @@ -0,0 +1,4 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-classifyr/meta.yaml b/recipes/bioconductor-classifyr/meta.yaml new file mode 100644 index 00000000000000..7031cc4fb1168b --- /dev/null +++ b/recipes/bioconductor-classifyr/meta.yaml @@ -0,0 +1,39 @@ +{% set version = "1.12.2" %} +{% set name = "ClassifyR" %} +{% set bioc = "3.6" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + fn: '{{ name }}_{{ version }}.tar.gz' + url: + - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: 5c32745f0c94df16dc20a31cb84a9faef95060ef3cfcb3407f8dc442e0d66cf9 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ +requirements: + build: + - bioconductor-biobase + - bioconductor-biocparallel + - r-base + - r-locfit + - r-rocr + run: + - bioconductor-biobase + - bioconductor-biocparallel + - r-base + - r-locfit + - r-rocr +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: GPL-3 + summary: 'The software formalises a framework for classification in R. There are four stages; Data transformation, feature selection, classifier training, and prediction. The requirements of variable types and names are fixed, but specialised variables for functions can also be provided. The classification framework is wrapped in a driver loop, that reproducibly carries out a number of cross-validation schemes. Functions for differential expression, differential variability, and differential distribution are included. Additional functions may be developed by the user, by creating an interface to the framework.' diff --git a/recipes/bioconductor-cleanupdtseq/build.sh b/recipes/bioconductor-cleanupdtseq/build.sh new file mode 100644 index 00000000000000..da43ce21683122 --- /dev/null +++ b/recipes/bioconductor-cleanupdtseq/build.sh @@ -0,0 +1,4 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-cleanupdtseq/meta.yaml b/recipes/bioconductor-cleanupdtseq/meta.yaml new file mode 100644 index 00000000000000..e8ed6cdb9bb88e --- /dev/null +++ b/recipes/bioconductor-cleanupdtseq/meta.yaml @@ -0,0 +1,43 @@ +{% set version = "1.16.0" %} +{% set name = "cleanUpdTSeq" %} +{% set bioc = "3.6" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + fn: '{{ name }}_{{ version }}.tar.gz' + url: + - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: 7bcb94f2c58a9831a71092e3152d0961a8375f3c5121cf330b9dca9cbdc591e4 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ +requirements: + build: + - 'bioconductor-biocgenerics >=0.1.0' + - bioconductor-bsgenome + - bioconductor-bsgenome.drerio.ucsc.danrer7 + - bioconductor-genomicranges + - r-base + - r-e1071 + - r-seqinr + run: + - 'bioconductor-biocgenerics >=0.1.0' + - bioconductor-bsgenome + - bioconductor-bsgenome.drerio.ucsc.danrer7 + - bioconductor-genomicranges + - r-base + - r-e1071 + - r-seqinr +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: GPL-2 + summary: 'This package uses the Naive Bayes classifier (from e1071) to assign probability values to putative polyadenylation sites (pA sites) based on training data from zebrafish. This will allow the user to separate true, biologically relevant pA sites from false, oligodT primed pA sites.' diff --git a/recipes/bioconductor-clonotyper/build.sh b/recipes/bioconductor-clonotyper/build.sh new file mode 100644 index 00000000000000..da43ce21683122 --- /dev/null +++ b/recipes/bioconductor-clonotyper/build.sh @@ -0,0 +1,4 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-clonotyper/meta.yaml b/recipes/bioconductor-clonotyper/meta.yaml new file mode 100644 index 00000000000000..7aa9b0725195c0 --- /dev/null +++ b/recipes/bioconductor-clonotyper/meta.yaml @@ -0,0 +1,31 @@ +{% set version = "1.16.0" %} +{% set name = "clonotypeR" %} +{% set bioc = "3.6" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + fn: '{{ name }}_{{ version }}.tar.gz' + url: + - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: eb0e1340641964178e664fbd7e16e556c2b4773f18f649d24439fe97af7d381d +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ +requirements: + build: + - r-base + run: + - r-base +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: 'file LICENSE' + summary: 'High throughput analysis of T cell antigen receptor sequences The genes encoding T cell receptors are created by somatic recombination, generating an immense combination of V, (D) and J segments. Additional processes during the recombination create extra sequence diversity between the V an J segments. Collectively, this hyper-variable region is called the CDR3 loop. The purpose of this package is to process and quantitatively analyse millions of V-CDR3-J combination, called clonotypes, from multiple sequence libraries.' diff --git a/recipes/bioconductor-clst/build.sh b/recipes/bioconductor-clst/build.sh new file mode 100644 index 00000000000000..da43ce21683122 --- /dev/null +++ b/recipes/bioconductor-clst/build.sh @@ -0,0 +1,4 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-clst/meta.yaml b/recipes/bioconductor-clst/meta.yaml new file mode 100644 index 00000000000000..8d738ffa69da11 --- /dev/null +++ b/recipes/bioconductor-clst/meta.yaml @@ -0,0 +1,35 @@ +{% set version = "1.26.0" %} +{% set name = "clst" %} +{% set bioc = "3.6" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + fn: '{{ name }}_{{ version }}.tar.gz' + url: + - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + sha256: dc8ec394358db8b6a13d9b19d70d48f3887dd870ad1dd75ec9a79e2948f32dc0 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ +requirements: + build: + - bioconductor-roc + - r-base + - r-lattice + run: + - bioconductor-roc + - r-base + - r-lattice +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: GPL-3 + summary: 'Package for modified nearest-neighbor classification based on calculation of a similarity threshold distinguishing within-group from between-group comparisons.' diff --git a/recipes/bioconductor-clstutils/build.sh b/recipes/bioconductor-clstutils/build.sh new file mode 100644 index 00000000000000..da43ce21683122 --- /dev/null +++ b/recipes/bioconductor-clstutils/build.sh @@ -0,0 +1,4 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-clstutils/meta.yaml b/recipes/bioconductor-clstutils/meta.yaml new file mode 100644 index 00000000000000..c11451ed9f3dc0 --- /dev/null +++ b/recipes/bioconductor-clstutils/meta.yaml @@ -0,0 +1,41 @@ +{% set version = "1.26.0" %} +{% set name = "clstutils" %} +{% set bioc = "3.6" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + fn: '{{ name }}_{{ version }}.tar.gz' + url: + - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + sha256: e60dc6b3f500cc39876e26bf3b2895cf5e370673640195127ec3d94ea8cae0a6 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ +requirements: + build: + - bioconductor-clst + - r-ape + - r-base + - r-lattice + - r-rjson + - r-rsqlite + run: + - bioconductor-clst + - r-ape + - r-base + - r-lattice + - r-rjson + - r-rsqlite +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: GPL-3 + summary: 'Tools for performing taxonomic assignment based on phylogeny using pplacer and clst.' diff --git a/recipes/bioconductor-clustcomp/build.sh b/recipes/bioconductor-clustcomp/build.sh new file mode 100644 index 00000000000000..da43ce21683122 --- /dev/null +++ b/recipes/bioconductor-clustcomp/build.sh @@ -0,0 +1,4 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-clustcomp/meta.yaml b/recipes/bioconductor-clustcomp/meta.yaml new file mode 100644 index 00000000000000..8107c818d1557c --- /dev/null +++ b/recipes/bioconductor-clustcomp/meta.yaml @@ -0,0 +1,33 @@ +{% set version = "1.6.0" %} +{% set name = "clustComp" %} +{% set bioc = "3.6" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + fn: '{{ name }}_{{ version }}.tar.gz' + url: + - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: 63dd6f1232875068f708a00a141aaf7227f060295382b3c4232b0edbb26acd3d +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ +requirements: + build: + - r-base + - r-sm + run: + - r-base + - r-sm +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: 'GPL (>= 2)' + summary: 'clustComp is a package that implements several techniques for the comparison and visualisation of relationships between different clustering results, either flat versus flat or hierarchical versus flat. These relationships among clusters are displayed using a weighted bi-graph, in which the nodes represent the clusters and the edges connect pairs of nodes with non-empty intersection; the weight of each edge is the number of elements in that intersection and is displayed through the edge thickness. The best layout of the bi-graph is provided by the barycentre algorithm, which minimises the weighted number of crossings. In the case of comparing a hierarchical and a non-hierarchical clustering, the dendrogram is pruned at different heights, selected by exploring the tree by depth-first search, starting at the root. Branches are decided to be split according to the value of a scoring function, that can be based either on the aesthetics of the bi-graph or on the mutual information between the hierarchical and the flat clusterings. A mapping between groups of clusters from each side is constructed with a greedy algorithm, and can be additionally visualised.' diff --git a/recipes/bioconductor-clustersignificance/build.sh b/recipes/bioconductor-clustersignificance/build.sh new file mode 100644 index 00000000000000..da43ce21683122 --- /dev/null +++ b/recipes/bioconductor-clustersignificance/build.sh @@ -0,0 +1,4 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-clustersignificance/meta.yaml b/recipes/bioconductor-clustersignificance/meta.yaml new file mode 100644 index 00000000000000..94b116f13997f7 --- /dev/null +++ b/recipes/bioconductor-clustersignificance/meta.yaml @@ -0,0 +1,39 @@ +{% set version = "1.6.0" %} +{% set name = "ClusterSignificance" %} +{% set bioc = "3.6" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + fn: '{{ name }}_{{ version }}.tar.gz' + url: + - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: 61db4b25f4298f396441f3def371a11b37e30997a97bbf019d931a27f69792a7 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ +requirements: + build: + - r-base + - r-pracma + - r-princurve + - r-rcolorbrewer + - r-scatterplot3d + run: + - r-base + - r-pracma + - r-princurve + - r-rcolorbrewer + - r-scatterplot3d +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: GPL-3 + summary: 'The ClusterSignificance package provides tools to assess if class clusters in dimensionality reduced data representations have a separation different from permuted data. The term class clusters here refers to, clusters of points representing known classes in the data. This is particularly useful to determine if a subset of the variables, e.g. genes in a specific pathway, alone can separate samples into these established classes. ClusterSignificance accomplishes this by, projecting all points onto a one dimensional line. Cluster separations are then scored and the probability of the seen separation being due to chance is evaluated using a permutation method.' diff --git a/recipes/bioconductor-clusterstab/build.sh b/recipes/bioconductor-clusterstab/build.sh new file mode 100644 index 00000000000000..da43ce21683122 --- /dev/null +++ b/recipes/bioconductor-clusterstab/build.sh @@ -0,0 +1,4 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-clusterstab/meta.yaml b/recipes/bioconductor-clusterstab/meta.yaml new file mode 100644 index 00000000000000..172af8c72fdb18 --- /dev/null +++ b/recipes/bioconductor-clusterstab/meta.yaml @@ -0,0 +1,33 @@ +{% set version = "1.50.0" %} +{% set name = "clusterStab" %} +{% set bioc = "3.6" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + fn: '{{ name }}_{{ version }}.tar.gz' + url: + - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: 68c80c7bf92a75a0c610457f6a8174bd4c1c5a66b1ced229126876f610ee3f67 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ +requirements: + build: + - 'bioconductor-biobase >=1.4.22' + - r-base + run: + - 'bioconductor-biobase >=1.4.22' + - r-base +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'This package can be used to estimate the number of clusters in a set of microarray data, as well as test the stability of these clusters.' diff --git a/recipes/bioconductor-cma/build.sh b/recipes/bioconductor-cma/build.sh new file mode 100644 index 00000000000000..da43ce21683122 --- /dev/null +++ b/recipes/bioconductor-cma/build.sh @@ -0,0 +1,4 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-cma/meta.yaml b/recipes/bioconductor-cma/meta.yaml new file mode 100644 index 00000000000000..fdd05eb82d1aae --- /dev/null +++ b/recipes/bioconductor-cma/meta.yaml @@ -0,0 +1,33 @@ +{% set version = "1.36.0" %} +{% set name = "CMA" %} +{% set bioc = "3.6" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + fn: '{{ name }}_{{ version }}.tar.gz' + url: + - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: 6d32caeda1e5de598010bfa561a21d59cb3a7e133f88a53b29c0dfe6b69cb150 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ +requirements: + build: + - bioconductor-biobase + - r-base + run: + - bioconductor-biobase + - r-base +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: 'GPL (>= 2)' + summary: 'This package provides a comprehensive collection of various microarray-based classification algorithms both from Machine Learning and Statistics. Variable Selection, Hyperparameter tuning, Evaluation and Comparison can be performed combined or stepwise in a user-friendly environment.' diff --git a/recipes/bioconductor-cmap/meta.yaml b/recipes/bioconductor-cmap/meta.yaml new file mode 100644 index 00000000000000..d959490469344f --- /dev/null +++ b/recipes/bioconductor-cmap/meta.yaml @@ -0,0 +1,32 @@ +{% set version = "1.15.1" %} +{% set name = "cMAP" %} +{% set bioc = "3.6" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + fn: '{{ name }}_{{ version }}.tar.gz' + url: + - 'http://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: 3bf24aca1ce63ebff4ac0172467ecd8acbb0c1f8a240cd0f8b8abd7c44fdf15f +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ +requirements: + build: + - r-base + run: + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'http://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: LGPL + summary: 'Annotation data file for cMAP assembled using data from public data repositories' diff --git a/recipes/bioconductor-cmap/post-link.sh b/recipes/bioconductor-cmap/post-link.sh new file mode 100644 index 00000000000000..525ebbdb1b149e --- /dev/null +++ b/recipes/bioconductor-cmap/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="cMAP_1.15.1.tar.gz" +URLS=( + "http://bioconductor.org/packages/3.6/data/annotation/src/contrib/cMAP_1.15.1.tar.gz" + "https://bioarchive.galaxyproject.org/cMAP_1.15.1.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-cmap/bioconductor-cmap_1.15.1_src_all.tar.gz" +) +MD5="dbf8df4d4540151936884e1c5d747bcf" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING \ No newline at end of file diff --git a/recipes/bioconductor-cmap/pre-unlink.sh b/recipes/bioconductor-cmap/pre-unlink.sh new file mode 100644 index 00000000000000..ea443df48d509b --- /dev/null +++ b/recipes/bioconductor-cmap/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ cMAP diff --git a/recipes/bioconductor-cmap2data/meta.yaml b/recipes/bioconductor-cmap2data/meta.yaml new file mode 100644 index 00000000000000..5d65c4dcdee3b9 --- /dev/null +++ b/recipes/bioconductor-cmap2data/meta.yaml @@ -0,0 +1,32 @@ +{% set version = "1.14.0" %} +{% set name = "cMap2data" %} +{% set bioc = "3.6" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + fn: '{{ name }}_{{ version }}.tar.gz' + url: + - 'http://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: 3fcb5f5f82dfa60faece83b593b7fcca50eca3a03b97a1a1798c0cc1742c5400 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ +requirements: + build: + - r-base + run: + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'http://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' + license: GPL-3 + summary: 'Data package which provides default drug profiles for the DrugVsDisease package as well as associated gene lists and data clusters used by the DrugVsDisease package.' diff --git a/recipes/bioconductor-cmap2data/post-link.sh b/recipes/bioconductor-cmap2data/post-link.sh new file mode 100644 index 00000000000000..1587bebb6a63a8 --- /dev/null +++ b/recipes/bioconductor-cmap2data/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="cMap2data_1.14.0.tar.gz" +URLS=( + "http://bioconductor.org/packages/3.6/data/experiment/src/contrib/cMap2data_1.14.0.tar.gz" + "https://bioarchive.galaxyproject.org/cMap2data_1.14.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-cmap2data/bioconductor-cmap2data_1.14.0_src_all.tar.gz" +) +MD5="c24b3dfa3c8cdaca2457b9795345a26a" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING \ No newline at end of file diff --git a/recipes/bioconductor-cmap2data/pre-unlink.sh b/recipes/bioconductor-cmap2data/pre-unlink.sh new file mode 100644 index 00000000000000..9136c941fd76d6 --- /dev/null +++ b/recipes/bioconductor-cmap2data/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ cMap2data diff --git a/recipes/bioconductor-cn.farms/build.sh b/recipes/bioconductor-cn.farms/build.sh new file mode 100644 index 00000000000000..da43ce21683122 --- /dev/null +++ b/recipes/bioconductor-cn.farms/build.sh @@ -0,0 +1,4 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-cn.farms/meta.yaml b/recipes/bioconductor-cn.farms/meta.yaml new file mode 100644 index 00000000000000..da22c41766e505 --- /dev/null +++ b/recipes/bioconductor-cn.farms/meta.yaml @@ -0,0 +1,54 @@ +{% set version = "1.26.0" %} +{% set name = "cn.farms" %} +{% set bioc = "3.6" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + fn: '{{ name }}_{{ version }}.tar.gz' + url: + - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + sha256: 4f728d1c22ec367ece919276a370910b69cf13a372a025d0dec89458b3f53600 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ +requirements: + build: + - bioconductor-affxparser + - bioconductor-biobase + - bioconductor-dnacopy + - bioconductor-oligo + - bioconductor-oligoclasses + - bioconductor-preprocesscore + - r-base + - r-dbi + - r-ff + - r-lattice + - r-snow + - gcc # [linux] + - llvm # [osx] + run: + - bioconductor-affxparser + - bioconductor-biobase + - bioconductor-dnacopy + - bioconductor-oligo + - bioconductor-oligoclasses + - bioconductor-preprocesscore + - r-base + - r-dbi + - r-ff + - r-lattice + - r-snow + - libcxx # [osx] +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: 'LGPL (>= 2.0)' + summary: 'This package implements the cn.FARMS algorithm for copy number variation (CNV) analysis. cn.FARMS allows to analyze the most common Affymetrix (250K-SNP6.0) array types, supports high-performance computing using snow and ff.' diff --git a/recipes/bioconductor-cnorfuzzy/build.sh b/recipes/bioconductor-cnorfuzzy/build.sh new file mode 100644 index 00000000000000..da43ce21683122 --- /dev/null +++ b/recipes/bioconductor-cnorfuzzy/build.sh @@ -0,0 +1,4 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-cnorfuzzy/meta.yaml b/recipes/bioconductor-cnorfuzzy/meta.yaml new file mode 100644 index 00000000000000..a13db4e304ceac --- /dev/null +++ b/recipes/bioconductor-cnorfuzzy/meta.yaml @@ -0,0 +1,38 @@ +{% set version = "1.20.0" %} +{% set name = "CNORfuzzy" %} +{% set bioc = "3.6" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + fn: '{{ name }}_{{ version }}.tar.gz' + url: + - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: d7baf1e59c9f845d6ff3a5f970a83246bfbb2f7a77a66a04f21b61075722319c +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ +requirements: + build: + - 'bioconductor-cellnoptr >=1.4.0' + - r-base + - 'r-nloptr >=0.8.5' + - gcc # [linux] + - llvm # [osx] + run: + - 'bioconductor-cellnoptr >=1.4.0' + - r-base + - 'r-nloptr >=0.8.5' + - libcxx # [osx] +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: GPL-2 + summary: 'This package is an extension to CellNOptR. It contains additional functionality needed to simulate and train a prior knowledge network to experimental data using constrained fuzzy logic (cFL, rather than Boolean logic as is the case in CellNOptR). Additionally, this package will contain functions to use for the compilation of multiple optimization results (either Boolean or cFL).' diff --git a/recipes/bioconductor-cnorode/build.sh b/recipes/bioconductor-cnorode/build.sh new file mode 100644 index 00000000000000..da43ce21683122 --- /dev/null +++ b/recipes/bioconductor-cnorode/build.sh @@ -0,0 +1,4 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-cnorode/meta.yaml b/recipes/bioconductor-cnorode/meta.yaml new file mode 100644 index 00000000000000..039e204ca9252f --- /dev/null +++ b/recipes/bioconductor-cnorode/meta.yaml @@ -0,0 +1,38 @@ +{% set version = "1.20.0" %} +{% set name = "CNORode" %} +{% set bioc = "3.6" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + fn: '{{ name }}_{{ version }}.tar.gz' + url: + - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: 1e3f779adf086b3fe63ec66420ba425b5d49496f8f2c6c2c485083eadee3ddf0 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ +requirements: + build: + - 'bioconductor-cellnoptr >=1.5.14' + - r-base + - r-genalg + - gcc # [linux] + - llvm # [osx] + run: + - 'bioconductor-cellnoptr >=1.5.14' + - r-base + - r-genalg + - libcxx # [osx] +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: GPL-2 + summary: 'ODE add-on to CellNOptR' diff --git a/recipes/bioconductor-cnvpanelizer/build.sh b/recipes/bioconductor-cnvpanelizer/build.sh new file mode 100644 index 00000000000000..da43ce21683122 --- /dev/null +++ b/recipes/bioconductor-cnvpanelizer/build.sh @@ -0,0 +1,4 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-cnvpanelizer/meta.yaml b/recipes/bioconductor-cnvpanelizer/meta.yaml new file mode 100644 index 00000000000000..d4340947a7cbf7 --- /dev/null +++ b/recipes/bioconductor-cnvpanelizer/meta.yaml @@ -0,0 +1,51 @@ +{% set version = "1.8.0" %} +{% set name = "CNVPanelizer" %} +{% set bioc = "3.6" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + fn: '{{ name }}_{{ version }}.tar.gz' + url: + - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: b1671257e010d318aafaa7054c0d162c212135f3fd5bbd963fdf70e64e16f520 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ +requirements: + build: + - bioconductor-exomecopy + - bioconductor-genomicranges + - bioconductor-iranges + - bioconductor-noiseq + - bioconductor-rsamtools + - bioconductor-s4vectors + - r-base + - r-foreach + - r-ggplot2 + - r-openxlsx + - r-plyr + run: + - bioconductor-exomecopy + - bioconductor-genomicranges + - bioconductor-iranges + - bioconductor-noiseq + - bioconductor-rsamtools + - bioconductor-s4vectors + - r-base + - r-foreach + - r-ggplot2 + - r-openxlsx + - r-plyr +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: GPL-3 + summary: 'A method that allows for the use of a collection of non-matched normal tissue samples. Our approach uses a non-parametric bootstrap subsampling of the available reference samples to estimate the distribution of read counts from targeted sequencing. As inspired by random forest, this is combined with a procedure that subsamples the amplicons associated with each of the targeted genes. The obtained information allows us to reliably classify the copy number aberrations on the gene level.' diff --git a/recipes/bioconductor-cnvtools/build.sh b/recipes/bioconductor-cnvtools/build.sh new file mode 100644 index 00000000000000..da43ce21683122 --- /dev/null +++ b/recipes/bioconductor-cnvtools/build.sh @@ -0,0 +1,4 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-cnvtools/meta.yaml b/recipes/bioconductor-cnvtools/meta.yaml new file mode 100644 index 00000000000000..517ee29b327268 --- /dev/null +++ b/recipes/bioconductor-cnvtools/meta.yaml @@ -0,0 +1,36 @@ +{% set version = "1.72.0" %} +{% set name = "CNVtools" %} +{% set bioc = "3.6" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + fn: '{{ name }}_{{ version }}.tar.gz' + url: + - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: 65e185c1e4c33064d53219fd4dc0e10c66e60a3a4b8e23c083fe5ce0ca7b1546 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ +requirements: + build: + - r-base + - r-survival + - gcc # [linux] + - llvm # [osx] + run: + - r-base + - r-survival + - libcxx # [osx] +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: GPL-3 + summary: 'This package is meant to facilitate the testing of Copy Number Variant data for genetic association, typically in case-control studies.' diff --git a/recipes/bioconductor-codelink/build.sh b/recipes/bioconductor-codelink/build.sh new file mode 100644 index 00000000000000..da43ce21683122 --- /dev/null +++ b/recipes/bioconductor-codelink/build.sh @@ -0,0 +1,4 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-codelink/meta.yaml b/recipes/bioconductor-codelink/meta.yaml new file mode 100644 index 00000000000000..1703aee9e2f57d --- /dev/null +++ b/recipes/bioconductor-codelink/meta.yaml @@ -0,0 +1,39 @@ +{% set version = "1.46.0" %} +{% set name = "codelink" %} +{% set bioc = "3.6" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + fn: '{{ name }}_{{ version }}.tar.gz' + url: + - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + sha256: baa1c3553ee9d870698d8ca9548cdefae59c58c57596cd31cec045b8c22a9348 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ +requirements: + build: + - bioconductor-annotate + - 'bioconductor-biobase >=2.17.8' + - 'bioconductor-biocgenerics >=0.3.2' + - bioconductor-limma + - r-base + run: + - bioconductor-annotate + - 'bioconductor-biobase >=2.17.8' + - 'bioconductor-biocgenerics >=0.3.2' + - bioconductor-limma + - r-base +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: GPL-2 + summary: 'This package facilitates reading, preprocessing and manipulating Codelink microarray data. The raw data must be exported as text file using the Codelink software.' diff --git a/recipes/bioconductor-cogena/build.sh b/recipes/bioconductor-cogena/build.sh new file mode 100644 index 00000000000000..da43ce21683122 --- /dev/null +++ b/recipes/bioconductor-cogena/build.sh @@ -0,0 +1,4 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-cogena/meta.yaml b/recipes/bioconductor-cogena/meta.yaml new file mode 100644 index 00000000000000..8bfa93fa9d9f78 --- /dev/null +++ b/recipes/bioconductor-cogena/meta.yaml @@ -0,0 +1,65 @@ +{% set version = "1.12.0" %} +{% set name = "cogena" %} +{% set bioc = "3.6" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + fn: '{{ name }}_{{ version }}.tar.gz' + url: + - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + sha256: 8fdd3d4744c7e960598d1186761d277e0b1dc255d6a2ed2448b15fb970c9f3d9 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ +requirements: + build: + - bioconductor-biobase + - r-amap + - r-apcluster + - r-base + - r-biwt + - r-class + - r-cluster + - r-corrplot + - r-devtools + - r-doparallel + - r-dplyr + - r-fastcluster + - r-foreach + - r-ggplot2 + - r-gplots + - r-kohonen + - r-mclust + - r-reshape2 + run: + - bioconductor-biobase + - r-amap + - r-apcluster + - r-base + - r-biwt + - r-class + - r-cluster + - r-corrplot + - r-devtools + - r-doparallel + - r-dplyr + - r-fastcluster + - r-foreach + - r-ggplot2 + - r-gplots + - r-kohonen + - r-mclust + - r-reshape2 +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: LGPL-3 + summary: 'cogena is a workflow for co-expressed gene-set enrichment analysis. It aims to discovery smaller scale, but highly correlated cellular events that may be of great biological relevance. A novel pipeline for drug discovery and drug repositioning based on the cogena workflow is proposed. Particularly, candidate drugs can be predicted based on the gene expression of disease-related data, or other similar drugs can be identified based on the gene expression of drug-related data. Moreover, the drug mode of action can be disclosed by the associated pathway analysis. In summary, cogena is a flexible workflow for various gene set enrichment analysis for co-expressed genes, with a focus on pathway/GO analysis and drug repositioning.' diff --git a/recipes/bioconductor-cogps/build.sh b/recipes/bioconductor-cogps/build.sh new file mode 100644 index 00000000000000..da43ce21683122 --- /dev/null +++ b/recipes/bioconductor-cogps/build.sh @@ -0,0 +1,4 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-cogps/meta.yaml b/recipes/bioconductor-cogps/meta.yaml new file mode 100644 index 00000000000000..a779863b90673b --- /dev/null +++ b/recipes/bioconductor-cogps/meta.yaml @@ -0,0 +1,31 @@ +{% set version = "1.22.0" %} +{% set name = "coGPS" %} +{% set bioc = "3.6" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + fn: '{{ name }}_{{ version }}.tar.gz' + url: + - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: 858563852d92cc8427fce8779a7fb88cf0d4ff01f56fcfa76a79d237944b9d40 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ +requirements: + build: + - r-base + run: + - r-base +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: GPL-2 + summary: 'Gene Set Enrichment Analysis of P-value based statistics for outlier gene detection in dataset merged from multiple studies' diff --git a/recipes/bioconductor-cohcap/build.sh b/recipes/bioconductor-cohcap/build.sh new file mode 100644 index 00000000000000..da43ce21683122 --- /dev/null +++ b/recipes/bioconductor-cohcap/build.sh @@ -0,0 +1,4 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-cohcap/meta.yaml b/recipes/bioconductor-cohcap/meta.yaml new file mode 100644 index 00000000000000..0c6a0e15d7b8eb --- /dev/null +++ b/recipes/bioconductor-cohcap/meta.yaml @@ -0,0 +1,39 @@ +{% set version = "1.24.0" %} +{% set name = "COHCAP" %} +{% set bioc = "3.6" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + fn: '{{ name }}_{{ version }}.tar.gz' + url: + - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: f2d5a888f29619fd4bcda97a3e8a0d6fe17681b3b1db95c3249db808cbb0fdbd +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ +requirements: + build: + - bioconductor-cohcapanno + - r-base + - r-gplots + - r-rcolorbrewer + - r-writexls + run: + - bioconductor-cohcapanno + - r-base + - r-gplots + - r-rcolorbrewer + - r-writexls +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: GPL-3 + summary: 'This package provides a pipeline to analyze single-nucleotide resolution methylation data (Illumina 450k/EPIC methylation array, targeted BS-Seq, etc.). It provides differential methylation for CpG Sites, differential methylation for CpG Islands, integration with gene expression data, with visualizaton options.' diff --git a/recipes/bioconductor-cohcapanno/meta.yaml b/recipes/bioconductor-cohcapanno/meta.yaml new file mode 100644 index 00000000000000..3a9b2043f3ea2d --- /dev/null +++ b/recipes/bioconductor-cohcapanno/meta.yaml @@ -0,0 +1,32 @@ +{% set version = "1.14.0" %} +{% set name = "COHCAPanno" %} +{% set bioc = "3.6" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + fn: '{{ name }}_{{ version }}.tar.gz' + url: + - 'http://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: 5064f4260e289012e333b0edbd3e93d55c567a1c4cd89b06d5010efc7de34c20 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ +requirements: + build: + - r-base + run: + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'http://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' + license: GPL-3 + summary: 'Provides genomic location, nearby CpG island and nearby gene information for common Illumina methylation array platforms' diff --git a/recipes/bioconductor-cohcapanno/post-link.sh b/recipes/bioconductor-cohcapanno/post-link.sh new file mode 100644 index 00000000000000..e6fef36de3dc21 --- /dev/null +++ b/recipes/bioconductor-cohcapanno/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="COHCAPanno_1.14.0.tar.gz" +URLS=( + "http://bioconductor.org/packages/3.6/data/experiment/src/contrib/COHCAPanno_1.14.0.tar.gz" + "https://bioarchive.galaxyproject.org/COHCAPanno_1.14.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-cohcapanno/bioconductor-cohcapanno_1.14.0_src_all.tar.gz" +) +MD5="dd8fcfcf7aeba72f5d4cfb6594eae522" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING \ No newline at end of file diff --git a/recipes/bioconductor-cohcapanno/pre-unlink.sh b/recipes/bioconductor-cohcapanno/pre-unlink.sh new file mode 100644 index 00000000000000..de8cb1276400e2 --- /dev/null +++ b/recipes/bioconductor-cohcapanno/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ COHCAPanno diff --git a/recipes/bioconductor-compass/build.sh b/recipes/bioconductor-compass/build.sh new file mode 100644 index 00000000000000..da43ce21683122 --- /dev/null +++ b/recipes/bioconductor-compass/build.sh @@ -0,0 +1,4 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-compass/meta.yaml b/recipes/bioconductor-compass/meta.yaml new file mode 100644 index 00000000000000..cee3c0dfc6da4b --- /dev/null +++ b/recipes/bioconductor-compass/meta.yaml @@ -0,0 +1,62 @@ +{% set version = "1.16.0" %} +{% set name = "COMPASS" %} +{% set bioc = "3.6" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + fn: '{{ name }}_{{ version }}.tar.gz' + url: + - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: 560fa4df6e37df0db5f9bb4fd6b3067d3d52ccf3507d844b6795647b86653bf4 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ +requirements: + build: + - r-abind + - r-base + - r-clue + - r-data.table + - r-dplyr + - r-knitr + - r-magrittr + - r-pdist + - r-plyr + - r-rcolorbrewer + - 'r-rcpp >=0.11.0' + - r-reshape2 + - r-rlang + - r-scales + - r-tidyr + - gcc # [linux] + - llvm # [osx] + run: + - r-abind + - r-base + - r-clue + - r-data.table + - r-dplyr + - r-knitr + - r-magrittr + - r-pdist + - r-plyr + - r-rcolorbrewer + - 'r-rcpp >=0.11.0' + - r-reshape2 + - r-rlang + - r-scales + - r-tidyr + - libcxx # [osx] +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'COMPASS is a statistical framework that enables unbiased analysis of antigen-specific T-cell subsets. COMPASS uses a Bayesian hierarchical framework to model all observed cell-subsets and select the most likely to be antigen-specific while regularizing the small cell counts that often arise in multi-parameter space. The model provides a posterior probability of specificity for each cell subset and each sample, which can be used to profile a subject''s immune response to external stimuli such as infection or vaccination.' diff --git a/recipes/bioconductor-consensusseeker/build.sh b/recipes/bioconductor-consensusseeker/build.sh new file mode 100644 index 00000000000000..da43ce21683122 --- /dev/null +++ b/recipes/bioconductor-consensusseeker/build.sh @@ -0,0 +1,4 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-consensusseeker/meta.yaml b/recipes/bioconductor-consensusseeker/meta.yaml new file mode 100644 index 00000000000000..8a19823615a7a2 --- /dev/null +++ b/recipes/bioconductor-consensusseeker/meta.yaml @@ -0,0 +1,47 @@ +{% set version = "1.6.0" %} +{% set name = "consensusSeekeR" %} +{% set bioc = "3.6" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + fn: '{{ name }}_{{ version }}.tar.gz' + url: + - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: ed47acb8c7aad1643b39770711cb396020413a7e36aabc7d60ab1a53fe57c594 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ +requirements: + build: + - bioconductor-biocgenerics + - bioconductor-biocparallel + - bioconductor-genomeinfodb + - bioconductor-genomicranges + - bioconductor-iranges + - bioconductor-rtracklayer + - bioconductor-s4vectors + - r-base + - r-stringr + run: + - bioconductor-biocgenerics + - bioconductor-biocparallel + - bioconductor-genomeinfodb + - bioconductor-genomicranges + - bioconductor-iranges + - bioconductor-rtracklayer + - bioconductor-s4vectors + - r-base + - r-stringr +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'This package compares genomic positions and genomic ranges from multiple experiments to extract common regions. The size of the analyzed region is adjustable as well as the number of experiences in which a feature must be present in a potential region to tag this region as a consensus region.' diff --git a/recipes/bioconductor-contibait/build.sh b/recipes/bioconductor-contibait/build.sh new file mode 100644 index 00000000000000..da43ce21683122 --- /dev/null +++ b/recipes/bioconductor-contibait/build.sh @@ -0,0 +1,4 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-contibait/meta.yaml b/recipes/bioconductor-contibait/meta.yaml new file mode 100644 index 00000000000000..b5136b5c957d95 --- /dev/null +++ b/recipes/bioconductor-contibait/meta.yaml @@ -0,0 +1,76 @@ +{% set version = "1.6.0" %} +{% set name = "contiBAIT" %} +{% set bioc = "3.6" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + fn: '{{ name }}_{{ version }}.tar.gz' + url: + - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: 9ae1ecf3219a276e00e36816a7ba78a0e866ea292a3a0265ab4043226bc3c62f +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ +requirements: + build: + - bioconductor-biocparallel + - bioconductor-dnacopy + - bioconductor-exomecopy + - bioconductor-genomicalignments + - bioconductor-genomicfiles + - bioconductor-genomicranges + - bioconductor-iranges + - 'bioconductor-rsamtools >=1.21' + - bioconductor-rtracklayer + - bioconductor-s4vectors + - r-base + - 'r-bh >=1.51.0-3' + - r-clue + - r-cluster + - r-colorspace + - r-diagram + - r-ggplot2 + - r-gplots + - r-gtools + - r-rcpp + - r-reshape2 + - r-tsp + - gcc # [linux] + - llvm # [osx] + run: + - bioconductor-biocparallel + - bioconductor-dnacopy + - bioconductor-exomecopy + - bioconductor-genomicalignments + - bioconductor-genomicfiles + - bioconductor-genomicranges + - bioconductor-iranges + - 'bioconductor-rsamtools >=1.21' + - bioconductor-rtracklayer + - bioconductor-s4vectors + - r-base + - 'r-bh >=1.51.0-3' + - r-clue + - r-cluster + - r-colorspace + - r-diagram + - r-ggplot2 + - r-gplots + - r-gtools + - r-rcpp + - r-reshape2 + - r-tsp + - libcxx # [osx] +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: 'BSD_2_clause + file LICENSE' + summary: 'Using strand inheritance data from multiple single cells from the organism whose genome is to be assembled, contiBAIT can cluster unbridged contigs together into putative chromosomes, and order the contigs within those chromosomes.' diff --git a/recipes/bioconductor-convert/build.sh b/recipes/bioconductor-convert/build.sh new file mode 100644 index 00000000000000..da43ce21683122 --- /dev/null +++ b/recipes/bioconductor-convert/build.sh @@ -0,0 +1,4 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-convert/meta.yaml b/recipes/bioconductor-convert/meta.yaml new file mode 100644 index 00000000000000..9b201c30dcd4b0 --- /dev/null +++ b/recipes/bioconductor-convert/meta.yaml @@ -0,0 +1,37 @@ +{% set version = "1.54.0" %} +{% set name = "convert" %} +{% set bioc = "3.6" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + fn: '{{ name }}_{{ version }}.tar.gz' + url: + - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + sha256: 24427569b5775d5293acec4f1ed13d00e74d47b2c40b90321c6d1ed4bc5fe440 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ +requirements: + build: + - 'bioconductor-biobase >=1.15.33' + - 'bioconductor-limma >=1.7.0' + - bioconductor-marray + - r-base + run: + - 'bioconductor-biobase >=1.15.33' + - 'bioconductor-limma >=1.7.0' + - bioconductor-marray + - r-base +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: LGPL + summary: 'Define coerce methods for microarray data objects.' diff --git a/recipes/bioconductor-copyhelper/meta.yaml b/recipes/bioconductor-copyhelper/meta.yaml new file mode 100644 index 00000000000000..0a2e94d7afcf11 --- /dev/null +++ b/recipes/bioconductor-copyhelper/meta.yaml @@ -0,0 +1,32 @@ +{% set version = "1.10.0" %} +{% set name = "CopyhelpeR" %} +{% set bioc = "3.6" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + fn: '{{ name }}_{{ version }}.tar.gz' + url: + - 'http://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: 479e75da8c815952a3bd402b8d44a8983ef7cc191cf93c48e0a42b36c5987bbd +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ +requirements: + build: + - r-base + run: + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'http://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' + license: GPL-2 + summary: 'This package contains the helper files that are required to run the Bioconductor package CopywriteR. It contains pre-assembled 1kb bin GC-content and mappability files for the reference genomes hg18, hg19, hg38, mm9 and mm10. In addition, it contains a blacklist filter to remove regions that display CNV. Files are stored as GRanges objects from the GenomicRanges Bioconductor package.' diff --git a/recipes/bioconductor-copyhelper/post-link.sh b/recipes/bioconductor-copyhelper/post-link.sh new file mode 100644 index 00000000000000..01c1168fcbf6bd --- /dev/null +++ b/recipes/bioconductor-copyhelper/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="CopyhelpeR_1.10.0.tar.gz" +URLS=( + "http://bioconductor.org/packages/3.6/data/experiment/src/contrib/CopyhelpeR_1.10.0.tar.gz" + "https://bioarchive.galaxyproject.org/CopyhelpeR_1.10.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-copyhelper/bioconductor-copyhelper_1.10.0_src_all.tar.gz" +) +MD5="03e42db6682fe395328a0ef01505833b" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING \ No newline at end of file diff --git a/recipes/bioconductor-copyhelper/pre-unlink.sh b/recipes/bioconductor-copyhelper/pre-unlink.sh new file mode 100644 index 00000000000000..e90a289b047610 --- /dev/null +++ b/recipes/bioconductor-copyhelper/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ CopyhelpeR diff --git a/recipes/bioconductor-copywriter/build.sh b/recipes/bioconductor-copywriter/build.sh new file mode 100644 index 00000000000000..da43ce21683122 --- /dev/null +++ b/recipes/bioconductor-copywriter/build.sh @@ -0,0 +1,4 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-copywriter/meta.yaml b/recipes/bioconductor-copywriter/meta.yaml new file mode 100644 index 00000000000000..3d61b38c8bd9ef --- /dev/null +++ b/recipes/bioconductor-copywriter/meta.yaml @@ -0,0 +1,59 @@ +{% set version = "2.10.0" %} +{% set name = "CopywriteR" %} +{% set bioc = "3.6" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + fn: '{{ name }}_{{ version }}.tar.gz' + url: + - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: 8ad12b68c6516e40f3a78014f1311c46d851e0417b9e03b68176385f1815de9d +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ +requirements: + build: + - bioconductor-biocparallel + - bioconductor-chipseq + - bioconductor-copyhelper + - bioconductor-dnacopy + - bioconductor-genomeinfodb + - bioconductor-genomicalignments + - bioconductor-genomicranges + - bioconductor-iranges + - bioconductor-rsamtools + - bioconductor-s4vectors + - r-base + - r-data.table + - r-futile.logger + - r-gtools + - r-matrixstats + run: + - bioconductor-biocparallel + - bioconductor-chipseq + - bioconductor-copyhelper + - bioconductor-dnacopy + - bioconductor-genomeinfodb + - bioconductor-genomicalignments + - bioconductor-genomicranges + - bioconductor-iranges + - bioconductor-rsamtools + - bioconductor-s4vectors + - r-base + - r-data.table + - r-futile.logger + - r-gtools + - r-matrixstats +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: GPL-2 + summary: 'CopywriteR extracts DNA copy number information from targeted sequencing by utiizing off-target reads. It allows for extracting uniformly distributed copy number information, can be used without reference, and can be applied to sequencing data obtained from various techniques including chromatin immunoprecipitation and target enrichment on small gene panels. Thereby, CopywriteR constitutes a widely applicable alternative to available copy number detection tools.' diff --git a/recipes/bioconductor-cormotif/build.sh b/recipes/bioconductor-cormotif/build.sh new file mode 100644 index 00000000000000..da43ce21683122 --- /dev/null +++ b/recipes/bioconductor-cormotif/build.sh @@ -0,0 +1,4 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-cormotif/meta.yaml b/recipes/bioconductor-cormotif/meta.yaml new file mode 100644 index 00000000000000..d86bb944ce8663 --- /dev/null +++ b/recipes/bioconductor-cormotif/meta.yaml @@ -0,0 +1,35 @@ +{% set version = "1.24.0" %} +{% set name = "Cormotif" %} +{% set bioc = "3.6" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + fn: '{{ name }}_{{ version }}.tar.gz' + url: + - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: dba86a067d7e11c9b263f03f90ef654ee9938c1042cafd5b95e2364b0d6addc6 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ +requirements: + build: + - bioconductor-affy + - bioconductor-limma + - r-base + run: + - bioconductor-affy + - bioconductor-limma + - r-base +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: GPL-2 + summary: 'It fits correlation motif model to multiple studies to detect study specific differential expression patterns.' diff --git a/recipes/bioconductor-correp/build.sh b/recipes/bioconductor-correp/build.sh new file mode 100644 index 00000000000000..da43ce21683122 --- /dev/null +++ b/recipes/bioconductor-correp/build.sh @@ -0,0 +1,4 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-correp/meta.yaml b/recipes/bioconductor-correp/meta.yaml new file mode 100644 index 00000000000000..b7f0f41819d312 --- /dev/null +++ b/recipes/bioconductor-correp/meta.yaml @@ -0,0 +1,33 @@ +{% set version = "1.44.0" %} +{% set name = "CORREP" %} +{% set bioc = "3.6" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + fn: '{{ name }}_{{ version }}.tar.gz' + url: + - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: 2a27a6b8948154ef56bd3ef4e61ff80768a14feb6bebe5a4b2ea77d105d87281 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ +requirements: + build: + - r-base + - r-e1071 + run: + - r-base + - r-e1071 +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: 'GPL (>= 2)' + summary: 'Multivariate correlation estimation and statistical inference. See package vignette.' diff --git a/recipes/bioconductor-cosmiq/build.sh b/recipes/bioconductor-cosmiq/build.sh new file mode 100644 index 00000000000000..da43ce21683122 --- /dev/null +++ b/recipes/bioconductor-cosmiq/build.sh @@ -0,0 +1,4 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-cosmiq/meta.yaml b/recipes/bioconductor-cosmiq/meta.yaml new file mode 100644 index 00000000000000..5061b13f69bc49 --- /dev/null +++ b/recipes/bioconductor-cosmiq/meta.yaml @@ -0,0 +1,44 @@ +{% set version = "1.12.0" %} +{% set name = "cosmiq" %} +{% set bioc = "3.6" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + fn: '{{ name }}_{{ version }}.tar.gz' + url: + - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + sha256: b593e317cebeded863c21674d57860b4cf21828b8644c59415acc271e2faa1bc +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ +requirements: + build: + - bioconductor-faahko + - bioconductor-massspecwavelet + - bioconductor-xcms + - r-base + - r-pracma + - r-rcpp + - gcc # [linux] + - llvm # [osx] + run: + - bioconductor-faahko + - bioconductor-massspecwavelet + - bioconductor-xcms + - r-base + - r-pracma + - r-rcpp + - libcxx # [osx] +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: GPL-3 + summary: 'cosmiq is a tool for the preprocessing of liquid- or gas - chromatography mass spectrometry (LCMS/GCMS) data with a focus on metabolomics or lipidomics applications. To improve the detection of low abundant signals, cosmiq generates master maps of the mZ/RT space from all acquired runs before a peak detection algorithm is applied. The result is a more robust identification and quantification of low-intensity MS signals compared to conventional approaches where peak picking is performed in each LCMS/GCMS file separately. The cosmiq package builds on the xcmsSet object structure and can be therefore integrated well with the package xcms as an alternative preprocessing step.' diff --git a/recipes/bioconductor-covrna/build.sh b/recipes/bioconductor-covrna/build.sh new file mode 100644 index 00000000000000..da43ce21683122 --- /dev/null +++ b/recipes/bioconductor-covrna/build.sh @@ -0,0 +1,4 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-covrna/meta.yaml b/recipes/bioconductor-covrna/meta.yaml new file mode 100644 index 00000000000000..72a67c2a28fda4 --- /dev/null +++ b/recipes/bioconductor-covrna/meta.yaml @@ -0,0 +1,37 @@ +{% set version = "1.4.0" %} +{% set name = "covRNA" %} +{% set bioc = "3.6" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + fn: '{{ name }}_{{ version }}.tar.gz' + url: + - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: fb7c7931cb0ba7db5bcb082b53cf6dfa6e6dd8d94a741a6e2eca93ecc9722320 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ +requirements: + build: + - bioconductor-biobase + - bioconductor-genefilter + - r-ade4 + - r-base + run: + - bioconductor-biobase + - bioconductor-genefilter + - r-ade4 + - r-base +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: 'GPL (>= 2)' + summary: 'This package provides the analysis methods fourthcorner and RLQ analysis for large-scale transcriptomic data.' diff --git a/recipes/bioconductor-cpvsnp/build.sh b/recipes/bioconductor-cpvsnp/build.sh new file mode 100644 index 00000000000000..da43ce21683122 --- /dev/null +++ b/recipes/bioconductor-cpvsnp/build.sh @@ -0,0 +1,4 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-cpvsnp/meta.yaml b/recipes/bioconductor-cpvsnp/meta.yaml new file mode 100644 index 00000000000000..5571c38beaecbd --- /dev/null +++ b/recipes/bioconductor-cpvsnp/meta.yaml @@ -0,0 +1,43 @@ +{% set version = "1.10.0" %} +{% set name = "cpvSNP" %} +{% set bioc = "3.6" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + fn: '{{ name }}_{{ version }}.tar.gz' + url: + - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: a8713080c1e637d35cace162d8661bdd6daa06e119b1e07452da44df5cba7eaa +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ +requirements: + build: + - bioconductor-biocparallel + - bioconductor-genomicfeatures + - 'bioconductor-gseabase >=1.24.0' + - r-base + - r-corpcor + - r-ggplot2 + - r-plyr + run: + - bioconductor-biocparallel + - bioconductor-genomicfeatures + - 'bioconductor-gseabase >=1.24.0' + - r-base + - r-corpcor + - r-ggplot2 + - r-plyr +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Gene set analysis methods exist to combine SNP-level association p-values into gene sets, calculating a single association p-value for each gene set. This package implements two such methods that require only the calculated SNP p-values, the gene set(s) of interest, and a correlation matrix (if desired). One method (GLOSSI) requires independent SNPs and the other (VEGAS) can take into account correlation (LD) among the SNPs. Built-in plotting functions are available to help users visualize results.' diff --git a/recipes/bioconductor-crimage/build.sh b/recipes/bioconductor-crimage/build.sh new file mode 100644 index 00000000000000..da43ce21683122 --- /dev/null +++ b/recipes/bioconductor-crimage/build.sh @@ -0,0 +1,4 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-crimage/meta.yaml b/recipes/bioconductor-crimage/meta.yaml new file mode 100644 index 00000000000000..42527bb1b48735 --- /dev/null +++ b/recipes/bioconductor-crimage/meta.yaml @@ -0,0 +1,45 @@ +{% set version = "1.26.0" %} +{% set name = "CRImage" %} +{% set bioc = "3.6" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + fn: '{{ name }}_{{ version }}.tar.gz' + url: + - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: 480d924f4daf01ad88315b8bdce066a469a5f5be4365568d6a2472fdd4d03df8 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ +requirements: + build: + - bioconductor-acgh + - bioconductor-dnacopy + - bioconductor-ebimage + - r-base + - r-e1071 + - r-foreach + - r-mass + - r-sgeostat + run: + - bioconductor-acgh + - bioconductor-dnacopy + - bioconductor-ebimage + - r-base + - r-e1071 + - r-foreach + - r-mass + - r-sgeostat +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'CRImage provides functionality to process and analyze images, in particular to classify cells in biological images. Furthermore, in the context of tumor images, it provides functionality to calculate tumour cellularity.' diff --git a/recipes/bioconductor-crisprseek/build.sh b/recipes/bioconductor-crisprseek/build.sh new file mode 100644 index 00000000000000..da43ce21683122 --- /dev/null +++ b/recipes/bioconductor-crisprseek/build.sh @@ -0,0 +1,4 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-crisprseek/meta.yaml b/recipes/bioconductor-crisprseek/meta.yaml new file mode 100644 index 00000000000000..d9a1dc6502d5af --- /dev/null +++ b/recipes/bioconductor-crisprseek/meta.yaml @@ -0,0 +1,49 @@ +{% set version = "1.18.0" %} +{% set name = "CRISPRseek" %} +{% set bioc = "3.6" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + fn: '{{ name }}_{{ version }}.tar.gz' + url: + - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: 80f9df6dae1f2da23d2c2cc7408f37f16596c0546f26008e72b206af9ae47a63 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ +requirements: + build: + - bioconductor-biocgenerics + - bioconductor-biocparallel + - bioconductor-biostrings + - bioconductor-bsgenome + - bioconductor-iranges + - 'bioconductor-s4vectors >=0.9.25' + - r-base + - r-data.table + - r-hash + - r-seqinr + run: + - bioconductor-biocgenerics + - bioconductor-biocparallel + - bioconductor-biostrings + - bioconductor-bsgenome + - bioconductor-iranges + - 'bioconductor-s4vectors >=0.9.25' + - r-base + - r-data.table + - r-hash + - r-seqinr +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: 'GPL (>= 2)' + summary: 'The package includes functions to find potential guide RNAs for input target sequences, optionally filter guide RNAs without restriction enzyme cut site, or without paired guide RNAs, genome-wide search for off-targets, score, rank, fetch flank sequence and indicate whether the target and off-targets are located in exon region or not. Potential guide RNAs are annotated with total score of the top5 and topN off-targets, detailed topN mismatch sites, restriction enzyme cut sites, and paired guide RNAs. If GeneRfold and GeneR are installed (http://bioconductor.case.edu/bioconductor/2.8/bioc/html/GeneRfold.html, http://bioc.ism.ac.jp/packages/2.8/bioc/html/GeneR.html), then the minimum free energy and bracket notation of secondary structure of gRNA and gRNA backbone constant region will be included in the summary file. This package leverages Biostrings and BSgenome packages.' diff --git a/recipes/bioconductor-crisprseekplus/build.sh b/recipes/bioconductor-crisprseekplus/build.sh new file mode 100644 index 00000000000000..da43ce21683122 --- /dev/null +++ b/recipes/bioconductor-crisprseekplus/build.sh @@ -0,0 +1,4 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-crisprseekplus/meta.yaml b/recipes/bioconductor-crisprseekplus/meta.yaml new file mode 100644 index 00000000000000..45eae7a491c6a2 --- /dev/null +++ b/recipes/bioconductor-crisprseekplus/meta.yaml @@ -0,0 +1,53 @@ +{% set version = "1.4.1" %} +{% set name = "crisprseekplus" %} +{% set bioc = "3.6" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + fn: '{{ name }}_{{ version }}.tar.gz' + url: + - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + sha256: ac7822fcab662a8bfa1f8bb3697d4bb15b25d74bdca95529679be27b02a139d9 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ +requirements: + build: + - bioconductor-annotationdbi + - bioconductor-biocinstaller + - bioconductor-bsgenome + - bioconductor-crisprseek + - bioconductor-genomicfeatures + - bioconductor-genomicranges + - bioconductor-guideseq + - r-base + - r-dt + - r-hash + - r-shiny + - r-shinyjs + run: + - bioconductor-annotationdbi + - bioconductor-biocinstaller + - bioconductor-bsgenome + - bioconductor-crisprseek + - bioconductor-genomicfeatures + - bioconductor-genomicranges + - bioconductor-guideseq + - r-base + - r-dt + - r-hash + - r-shiny + - r-shinyjs +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: 'GPL-3 + file LICENSE' + summary: 'Bioinformatics platform containing interface to work with offTargetAnalysis and compare2Sequences in the CRISPRseek package, and GUIDEseqAnalysis.' diff --git a/recipes/bioconductor-crisprvariants/build.sh b/recipes/bioconductor-crisprvariants/build.sh new file mode 100644 index 00000000000000..da43ce21683122 --- /dev/null +++ b/recipes/bioconductor-crisprvariants/build.sh @@ -0,0 +1,4 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-crisprvariants/meta.yaml b/recipes/bioconductor-crisprvariants/meta.yaml new file mode 100644 index 00000000000000..9133488addec42 --- /dev/null +++ b/recipes/bioconductor-crisprvariants/meta.yaml @@ -0,0 +1,55 @@ +{% set version = "1.6.0" %} +{% set name = "CrispRVariants" %} +{% set bioc = "3.6" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + fn: '{{ name }}_{{ version }}.tar.gz' + url: + - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: 8b0dd8425ba6747c5d46ae062fd8968219cee7c877c12670acdc496bb537ea97 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ +requirements: + build: + - bioconductor-annotationdbi + - bioconductor-biocparallel + - bioconductor-biostrings + - bioconductor-genomeinfodb + - bioconductor-genomicalignments + - bioconductor-genomicranges + - bioconductor-iranges + - bioconductor-rsamtools + - 'bioconductor-s4vectors >=0.9.38' + - r-base + - 'r-ggplot2 >=2.2.0' + - r-gridextra + - r-reshape2 + run: + - bioconductor-annotationdbi + - bioconductor-biocparallel + - bioconductor-biostrings + - bioconductor-genomeinfodb + - bioconductor-genomicalignments + - bioconductor-genomicranges + - bioconductor-iranges + - bioconductor-rsamtools + - 'bioconductor-s4vectors >=0.9.38' + - r-base + - 'r-ggplot2 >=2.2.0' + - r-gridextra + - r-reshape2 +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: GPL-2 + summary: 'CrispRVariants provides tools for analysing the results of a CRISPR-Cas9 mutagenesis sequencing experiment, or other sequencing experiments where variants within a given region are of interest. These tools allow users to localize variant allele combinations with respect to any genomic location (e.g. the Cas9 cut site), plot allele combinations and calculate mutation rates with flexible filtering of unrelated variants.' diff --git a/recipes/bioconductor-crlmm/build.sh b/recipes/bioconductor-crlmm/build.sh new file mode 100644 index 00000000000000..da43ce21683122 --- /dev/null +++ b/recipes/bioconductor-crlmm/build.sh @@ -0,0 +1,4 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-crlmm/meta.yaml b/recipes/bioconductor-crlmm/meta.yaml new file mode 100644 index 00000000000000..9255962ac1d062 --- /dev/null +++ b/recipes/bioconductor-crlmm/meta.yaml @@ -0,0 +1,68 @@ +{% set version = "1.36.0" %} +{% set name = "crlmm" %} +{% set bioc = "3.6" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + fn: '{{ name }}_{{ version }}.tar.gz' + url: + - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + sha256: 3ab9d0a8b0dbfc59afd08a69ce282cd4ef5b1dd662fb8d651b6ff63d27492045 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ +requirements: + build: + - 'bioconductor-affyio >=1.23.2' + - 'bioconductor-biobase >=2.15.4' + - bioconductor-biocgenerics + - bioconductor-illuminaio + - bioconductor-limma + - 'bioconductor-oligoclasses >=1.21.12' + - 'bioconductor-preprocesscore >=1.17.7' + - bioconductor-snpchip + - r-base + - r-beanplot + - r-ellipse + - r-ff + - r-foreach + - r-lattice + - r-matrixstats + - r-mvtnorm + - 'r-rcppeigen >=0.3.1.2.1' + - r-vgam + - gcc # [linux] + - llvm # [osx] + run: + - 'bioconductor-affyio >=1.23.2' + - 'bioconductor-biobase >=2.15.4' + - bioconductor-biocgenerics + - bioconductor-illuminaio + - bioconductor-limma + - 'bioconductor-oligoclasses >=1.21.12' + - 'bioconductor-preprocesscore >=1.17.7' + - bioconductor-snpchip + - r-base + - r-beanplot + - r-ellipse + - r-ff + - r-foreach + - r-lattice + - r-matrixstats + - r-mvtnorm + - 'r-rcppeigen >=0.3.1.2.1' + - r-vgam + - libcxx # [osx] +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Faster implementation of CRLMM specific to SNP 5.0 and 6.0 arrays, as well as a copy number tool specific to 5.0, 6.0, and Illumina platforms.' diff --git a/recipes/bioconductor-ctc/build.sh b/recipes/bioconductor-ctc/build.sh new file mode 100644 index 00000000000000..da43ce21683122 --- /dev/null +++ b/recipes/bioconductor-ctc/build.sh @@ -0,0 +1,4 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-ctc/meta.yaml b/recipes/bioconductor-ctc/meta.yaml new file mode 100644 index 00000000000000..985b311cbad9eb --- /dev/null +++ b/recipes/bioconductor-ctc/meta.yaml @@ -0,0 +1,33 @@ +{% set version = "1.52.0" %} +{% set name = "ctc" %} +{% set bioc = "3.6" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + fn: '{{ name }}_{{ version }}.tar.gz' + url: + - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + sha256: 6f8e18a8f0074a8f2346f04851defd70cd2ae21a30d74ad219f1480f2a82382f +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ +requirements: + build: + - r-amap + - r-base + run: + - r-amap + - r-base +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: GPL-2 + summary: 'Tools for export and import classification trees and clusters to other programs' diff --git a/recipes/bioconductor-ctsge/build.sh b/recipes/bioconductor-ctsge/build.sh new file mode 100644 index 00000000000000..da43ce21683122 --- /dev/null +++ b/recipes/bioconductor-ctsge/build.sh @@ -0,0 +1,4 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-ctsge/meta.yaml b/recipes/bioconductor-ctsge/meta.yaml new file mode 100644 index 00000000000000..0e96f2086e2cdf --- /dev/null +++ b/recipes/bioconductor-ctsge/meta.yaml @@ -0,0 +1,43 @@ +{% set version = "1.4.0" %} +{% set name = "ctsGE" %} +{% set bioc = "3.6" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + fn: '{{ name }}_{{ version }}.tar.gz' + url: + - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: 9bff2a7c108a277922f4359fe9a787405033d1f7ac8e73017242619a4a81afc3 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ +requirements: + build: + - bioconductor-limma + - r-base + - r-ccapp + - r-ggplot2 + - r-reshape2 + - r-shiny + - r-stringr + run: + - bioconductor-limma + - r-base + - r-ccapp + - r-ggplot2 + - r-reshape2 + - r-shiny + - r-stringr +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: GPL-2 + summary: 'Methodology for supervised clustering of potentially many predictor variables, such as genes etc., in time series datasets Provides functions that help the user assigning genes to predefined set of model profiles.' diff --git a/recipes/bioconductor-cve/build.sh b/recipes/bioconductor-cve/build.sh new file mode 100644 index 00000000000000..da43ce21683122 --- /dev/null +++ b/recipes/bioconductor-cve/build.sh @@ -0,0 +1,4 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-cve/meta.yaml b/recipes/bioconductor-cve/meta.yaml new file mode 100644 index 00000000000000..3f85ed2f9f9e59 --- /dev/null +++ b/recipes/bioconductor-cve/meta.yaml @@ -0,0 +1,49 @@ +{% set version = "1.4.0" %} +{% set name = "CVE" %} +{% set bioc = "3.6" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + fn: '{{ name }}_{{ version }}.tar.gz' + url: + - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: 9719ea5105e639eb698518eab9ed205163db4fb488a1ae723ae457a5ec621d41 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ +requirements: + build: + - bioconductor-consensusclusterplus + - r-ape + - r-base + - r-ggplot2 + - r-gplots + - r-jsonlite + - r-plyr + - r-rcolorbrewer + - r-shiny + - r-wgcna + run: + - bioconductor-consensusclusterplus + - r-ape + - r-base + - r-ggplot2 + - r-gplots + - r-jsonlite + - r-plyr + - r-rcolorbrewer + - r-shiny + - r-wgcna +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: GPL-3 + summary: 'Shiny app for interactive variant prioritisation in precision oncology. The input file for CVE is the output file of the recently released Oncotator Variant Annotation tool summarising variant-centric information from 14 different publicly available resources relevant for cancer researches. Interactive priortisation in CVE is based on known germline and cancer variants, DNA repair genes and functional prediction scores. An optional feature of CVE is the exploration of the tumour-specific pathway context that is facilitated using co-expression modules generated from publicly available transcriptome data. Finally druggability of prioritised variants is assessed using the Drug Gene Interaction Database (DGIdb).' diff --git a/recipes/bioconductor-dama/build.sh b/recipes/bioconductor-dama/build.sh new file mode 100644 index 00000000000000..da43ce21683122 --- /dev/null +++ b/recipes/bioconductor-dama/build.sh @@ -0,0 +1,4 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-dama/meta.yaml b/recipes/bioconductor-dama/meta.yaml new file mode 100644 index 00000000000000..5eb70276d86896 --- /dev/null +++ b/recipes/bioconductor-dama/meta.yaml @@ -0,0 +1,33 @@ +{% set version = "1.50.0" %} +{% set name = "daMA" %} +{% set bioc = "3.6" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + fn: '{{ name }}_{{ version }}.tar.gz' + url: + - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: e6e03b6ccf4580b8c061086632d20ce712012b502440dc26d8bd188e3aa918c3 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ +requirements: + build: + - r-base + - r-mass + run: + - r-base + - r-mass +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: 'GPL (>= 2)' + summary: 'This package contains functions for the efficient design of factorial two-colour microarray experiments and for the statistical analysis of factorial microarray data. Statistical details are described in Bretz et al. (2003, submitted)' diff --git a/recipes/bioconductor-dbchip/build.sh b/recipes/bioconductor-dbchip/build.sh new file mode 100644 index 00000000000000..da43ce21683122 --- /dev/null +++ b/recipes/bioconductor-dbchip/build.sh @@ -0,0 +1,4 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-dbchip/meta.yaml b/recipes/bioconductor-dbchip/meta.yaml new file mode 100644 index 00000000000000..8421e54b4c2e6a --- /dev/null +++ b/recipes/bioconductor-dbchip/meta.yaml @@ -0,0 +1,35 @@ +{% set version = "1.22.0" %} +{% set name = "DBChIP" %} +{% set bioc = "3.6" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + fn: '{{ name }}_{{ version }}.tar.gz' + url: + - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: dd1414b409ab6677cfa094550e690ca2cc3d5a4e8db1194e2d99d0c676adfa1e +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ +requirements: + build: + - bioconductor-deseq + - bioconductor-edger + - r-base + run: + - bioconductor-deseq + - bioconductor-edger + - r-base +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: 'GPL (>= 2)' + summary: 'DBChIP detects differentially bound sharp binding sites across multiple conditions, with or without matching control samples.' diff --git a/recipes/bioconductor-dcgsa/build.sh b/recipes/bioconductor-dcgsa/build.sh new file mode 100644 index 00000000000000..da43ce21683122 --- /dev/null +++ b/recipes/bioconductor-dcgsa/build.sh @@ -0,0 +1,4 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-dcgsa/meta.yaml b/recipes/bioconductor-dcgsa/meta.yaml new file mode 100644 index 00000000000000..9783b9bd898edb --- /dev/null +++ b/recipes/bioconductor-dcgsa/meta.yaml @@ -0,0 +1,35 @@ +{% set version = "1.6.0" %} +{% set name = "dcGSA" %} +{% set bioc = "3.6" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + fn: '{{ name }}_{{ version }}.tar.gz' + url: + - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: 06cc6ca1033c2093b566db1c31fbe49921d5333bf352e61d3367b465408723f6 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ +requirements: + build: + - bioconductor-biocparallel + - r-base + - r-matrix + run: + - bioconductor-biocparallel + - r-base + - r-matrix +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: GPL-2 + summary: 'Distance-correlation based Gene Set Analysis for longitudinal gene expression profiles. In longitudinal studies, the gene expression profiles were collected at each visit from each subject and hence there are multiple measurements of the gene expression profiles for each subject. The dcGSA package could be used to assess the associations between gene sets and clinical outcomes of interest by fully taking advantage of the longitudinal nature of both the gene expression profiles and clinical outcomes.' diff --git a/recipes/bioconductor-dchiprep/build.sh b/recipes/bioconductor-dchiprep/build.sh new file mode 100644 index 00000000000000..da43ce21683122 --- /dev/null +++ b/recipes/bioconductor-dchiprep/build.sh @@ -0,0 +1,4 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-dchiprep/meta.yaml b/recipes/bioconductor-dchiprep/meta.yaml new file mode 100644 index 00000000000000..ec004d43857168 --- /dev/null +++ b/recipes/bioconductor-dchiprep/meta.yaml @@ -0,0 +1,59 @@ +{% set version = "1.8.0" %} +{% set name = "DChIPRep" %} +{% set bioc = "3.6" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + fn: '{{ name }}_{{ version }}.tar.gz' + url: + - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: 959b5598fff357d15c27913674cc89353f21236865f4e4e9786f4c7c6fab27c6 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ +requirements: + build: + - bioconductor-chippeakanno + - bioconductor-deseq2 + - bioconductor-genomicranges + - bioconductor-s4vectors + - bioconductor-soggi + - bioconductor-summarizedexperiment + - r-assertthat + - r-base + - r-fdrtool + - r-ggplot2 + - r-plyr + - r-purrr + - r-reshape2 + - r-smoothmest + - r-tidyr + run: + - bioconductor-chippeakanno + - bioconductor-deseq2 + - bioconductor-genomicranges + - bioconductor-s4vectors + - bioconductor-soggi + - bioconductor-summarizedexperiment + - r-assertthat + - r-base + - r-fdrtool + - r-ggplot2 + - r-plyr + - r-purrr + - r-reshape2 + - r-smoothmest + - r-tidyr +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: 'MIT + file LICENCE' + summary: 'The DChIPRep package implements a methodology to assess differences between chromatin modification profiles in replicated ChIP-Seq studies as described in Chabbert et. al - http://www.dx.doi.org/10.15252/msb.20145776. A detailed description of the method is given in the software paper at https://doi.org/10.7717/peerj.1981' diff --git a/recipes/bioconductor-ddct/build.sh b/recipes/bioconductor-ddct/build.sh new file mode 100644 index 00000000000000..da43ce21683122 --- /dev/null +++ b/recipes/bioconductor-ddct/build.sh @@ -0,0 +1,4 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-ddct/meta.yaml b/recipes/bioconductor-ddct/meta.yaml new file mode 100644 index 00000000000000..f83789afcdeeba --- /dev/null +++ b/recipes/bioconductor-ddct/meta.yaml @@ -0,0 +1,41 @@ +{% set version = "1.34.0" %} +{% set name = "ddCt" %} +{% set bioc = "3.6" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + fn: '{{ name }}_{{ version }}.tar.gz' + url: + - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: aded934154e743047010037c1cdb6ef7603fa6c660df51ccddb616d55317da40 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ +requirements: + build: + - 'bioconductor-biobase >=1.10.0' + - bioconductor-biocgenerics + - r-base + - r-lattice + - 'r-rcolorbrewer >=0.1-3' + - r-xtable + run: + - 'bioconductor-biobase >=1.10.0' + - bioconductor-biocgenerics + - r-base + - r-lattice + - 'r-rcolorbrewer >=0.1-3' + - r-xtable +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: LGPL-3 + summary: 'The Delta-Delta-Ct (ddCt) Algorithm is an approximation method to determine relative gene expression with quantitative real-time PCR (qRT-PCR) experiments. Compared to other approaches, it requires no standard curve for each primer-target pair, therefore reducing the working load and yet returning accurate enough results as long as the assumptions of the amplification efficiency hold. The ddCt package implements a pipeline to collect, analyse and visualize qRT-PCR results, for example those from TaqMan SDM software, mainly using the ddCt method. The pipeline can be either invoked by a script in command-line or through the API consisting of S4-Classes, methods and functions.' diff --git a/recipes/bioconductor-deds/build.sh b/recipes/bioconductor-deds/build.sh new file mode 100644 index 00000000000000..da43ce21683122 --- /dev/null +++ b/recipes/bioconductor-deds/build.sh @@ -0,0 +1,4 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-deds/meta.yaml b/recipes/bioconductor-deds/meta.yaml new file mode 100644 index 00000000000000..8e29689eb63428 --- /dev/null +++ b/recipes/bioconductor-deds/meta.yaml @@ -0,0 +1,34 @@ +{% set version = "1.52.0" %} +{% set name = "DEDS" %} +{% set bioc = "3.6" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + fn: '{{ name }}_{{ version }}.tar.gz' + url: + - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: da08370a847214ab71c1317d341399c0158aee661b6844cac6d1af327b91f7a1 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ +requirements: + build: + - r-base + - gcc # [linux] + - llvm # [osx] + run: + - r-base + - libcxx # [osx] +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: LGPL + summary: 'This library contains functions that calculate various statistics of differential expression for microarray data, including t statistics, fold change, F statistics, SAM, moderated t and F statistics and B statistics. It also implements a new methodology called DEDS (Differential Expression via Distance Summary), which selects differentially expressed genes by integrating and summarizing a set of statistics using a weighted distance approach.' diff --git a/recipes/bioconductor-deepbluer/build.sh b/recipes/bioconductor-deepbluer/build.sh new file mode 100644 index 00000000000000..da43ce21683122 --- /dev/null +++ b/recipes/bioconductor-deepbluer/build.sh @@ -0,0 +1,4 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-deepbluer/meta.yaml b/recipes/bioconductor-deepbluer/meta.yaml new file mode 100644 index 00000000000000..f26f6d9c62291d --- /dev/null +++ b/recipes/bioconductor-deepbluer/meta.yaml @@ -0,0 +1,61 @@ +{% set version = "1.4.1" %} +{% set name = "DeepBlueR" %} +{% set bioc = "3.6" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + fn: '{{ name }}_{{ version }}.tar.gz' + url: + - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: 2cc33c6407d3fb784f8ba330c3b7c0bb1aa8ccf71a0d9f890d944558ab150f8f +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ +requirements: + build: + - bioconductor-genomeinfodb + - bioconductor-genomicranges + - bioconductor-rtracklayer + - r-base + - r-data.table + - r-diffr + - r-dplyr + - r-filehash + - r-foreach + - r-r.utils + - r-rcurl + - r-rjson + - r-settings + - r-stringr + - r-withr + - r-xml + run: + - bioconductor-genomeinfodb + - bioconductor-genomicranges + - bioconductor-rtracklayer + - r-base + - r-data.table + - r-diffr + - r-dplyr + - r-filehash + - r-foreach + - r-r.utils + - r-rcurl + - r-rjson + - r-settings + - r-stringr + - r-withr + - r-xml +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: 'GPL (>=2.0)' + summary: 'Accessing the DeepBlue Epigenetics Data Server through R.' diff --git a/recipes/bioconductor-deformats/build.sh b/recipes/bioconductor-deformats/build.sh new file mode 100644 index 00000000000000..da43ce21683122 --- /dev/null +++ b/recipes/bioconductor-deformats/build.sh @@ -0,0 +1,4 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-deformats/meta.yaml b/recipes/bioconductor-deformats/meta.yaml new file mode 100644 index 00000000000000..6f9349a7ecadba --- /dev/null +++ b/recipes/bioconductor-deformats/meta.yaml @@ -0,0 +1,43 @@ +{% set version = "1.6.1" %} +{% set name = "DEFormats" %} +{% set bioc = "3.6" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + fn: '{{ name }}_{{ version }}.tar.gz' + url: + - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: a9dcdcdeb8fa6ec107c17abf0eebe18c74297fd68f09f3b549080d628e2d3df2 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ +requirements: + build: + - bioconductor-deseq2 + - 'bioconductor-edger >=3.13.4' + - bioconductor-genomicranges + - bioconductor-summarizedexperiment + - r-base + - r-checkmate + - r-data.table + run: + - bioconductor-deseq2 + - 'bioconductor-edger >=3.13.4' + - bioconductor-genomicranges + - bioconductor-summarizedexperiment + - r-base + - r-checkmate + - r-data.table +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: GPL-3 + summary: 'Convert between different data formats used by differential gene expression analysis tools.' diff --git a/recipes/bioconductor-degraph/build.sh b/recipes/bioconductor-degraph/build.sh new file mode 100644 index 00000000000000..da43ce21683122 --- /dev/null +++ b/recipes/bioconductor-degraph/build.sh @@ -0,0 +1,4 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-degraph/meta.yaml b/recipes/bioconductor-degraph/meta.yaml new file mode 100644 index 00000000000000..fcab6ee6293a74 --- /dev/null +++ b/recipes/bioconductor-degraph/meta.yaml @@ -0,0 +1,51 @@ +{% set version = "1.30.0" %} +{% set name = "DEGraph" %} +{% set bioc = "3.6" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + fn: '{{ name }}_{{ version }}.tar.gz' + url: + - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: 118e3be5f578b0cc7153f81e7cf54ba6b610dd006d541c7e9c7d6870f30e7c20 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ +requirements: + build: + - bioconductor-graph + - bioconductor-kegggraph + - bioconductor-ncigraph + - bioconductor-rbgl + - bioconductor-rgraphviz + - r-base + - r-lattice + - r-mvtnorm + - r-r.methodss3 + - r-r.utils + - r-rrcov + run: + - bioconductor-graph + - bioconductor-kegggraph + - bioconductor-ncigraph + - bioconductor-rbgl + - bioconductor-rgraphviz + - r-base + - r-lattice + - r-mvtnorm + - r-r.methodss3 + - r-r.utils + - r-rrcov +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: GPL-3 + summary: 'DEGraph implements recent hypothesis testing methods which directly assess whether a particular gene network is differentially expressed between two conditions. This is to be contrasted with the more classical two-step approaches which first test individual genes, then test gene sets for enrichment in differentially expressed genes. These recent methods take into account the topology of the network to yield more powerful detection procedures. DEGraph provides methods to easily test all KEGG pathways for differential expression on any gene expression data set and tools to visualize the results.' diff --git a/recipes/bioconductor-demand/build.sh b/recipes/bioconductor-demand/build.sh new file mode 100644 index 00000000000000..da43ce21683122 --- /dev/null +++ b/recipes/bioconductor-demand/build.sh @@ -0,0 +1,4 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-demand/meta.yaml b/recipes/bioconductor-demand/meta.yaml new file mode 100644 index 00000000000000..f26c9ad2c77fe7 --- /dev/null +++ b/recipes/bioconductor-demand/meta.yaml @@ -0,0 +1,33 @@ +{% set version = "1.8.0" %} +{% set name = "DeMAND" %} +{% set bioc = "3.6" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + fn: '{{ name }}_{{ version }}.tar.gz' + url: + - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: 03c0a71c8c77e68753539225a16eb540ba19d0c17123cac3bff17109ea60c5bd +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ +requirements: + build: + - r-base + - r-kernsmooth + run: + - r-base + - r-kernsmooth +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: 'file LICENSE' + summary: 'DEMAND predicts Drug MoA by interrogating a cell context specific regulatory network with a small number (N >= 6) of compound-induced gene expression signatures, to elucidate specific proteins whose interactions in the network is dysregulated by the compound.' diff --git a/recipes/bioconductor-dexus/build.sh b/recipes/bioconductor-dexus/build.sh new file mode 100644 index 00000000000000..da43ce21683122 --- /dev/null +++ b/recipes/bioconductor-dexus/build.sh @@ -0,0 +1,4 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-dexus/meta.yaml b/recipes/bioconductor-dexus/meta.yaml new file mode 100644 index 00000000000000..673c08515867e4 --- /dev/null +++ b/recipes/bioconductor-dexus/meta.yaml @@ -0,0 +1,36 @@ +{% set version = "1.18.0" %} +{% set name = "dexus" %} +{% set bioc = "3.6" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + fn: '{{ name }}_{{ version }}.tar.gz' + url: + - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + sha256: 2f566e4a6c91dcecc2554c013462d4618bb532e295513d0adc1f151c78283dd1 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ +requirements: + build: + - bioconductor-biocgenerics + - r-base + - gcc # [linux] + - llvm # [osx] + run: + - bioconductor-biocgenerics + - r-base + - libcxx # [osx] +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: 'LGPL (>= 2.0)' + summary: 'DEXUS identifies differentially expressed genes in RNA-Seq data under all possible study designs such as studies without replicates, without sample groups, and with unknown conditions. DEXUS works also for known conditions, for example for RNA-Seq data with two or multiple conditions. RNA-Seq read count data can be provided both by the S4 class Count Data Set and by read count matrices. Differentially expressed transcripts can be visualized by heatmaps, in which unknown conditions, replicates, and samples groups are also indicated. This software is fast since the core algorithm is written in C. For very large data sets, a parallel version of DEXUS is provided in this package. DEXUS is a statistical model that is selected in a Bayesian framework by an EM algorithm. DEXUS does not need replicates to detect differentially expressed transcripts, since the replicates (or conditions) are estimated by the EM method for each transcript. The method provides an informative/non-informative value to extract differentially expressed transcripts at a desired significance level or power.' diff --git a/recipes/bioconductor-dfp/build.sh b/recipes/bioconductor-dfp/build.sh new file mode 100644 index 00000000000000..da43ce21683122 --- /dev/null +++ b/recipes/bioconductor-dfp/build.sh @@ -0,0 +1,4 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-dfp/meta.yaml b/recipes/bioconductor-dfp/meta.yaml new file mode 100644 index 00000000000000..1437330e2a2744 --- /dev/null +++ b/recipes/bioconductor-dfp/meta.yaml @@ -0,0 +1,33 @@ +{% set version = "1.36.0" %} +{% set name = "DFP" %} +{% set bioc = "3.6" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + fn: '{{ name }}_{{ version }}.tar.gz' + url: + - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: 337cda573c495f334387156617b437a74d95293f358377164f99a7fcd8afef84 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ +requirements: + build: + - 'bioconductor-biobase >=2.5.5' + - r-base + run: + - 'bioconductor-biobase >=2.5.5' + - r-base +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: GPL-2 + summary: 'This package provides a supervised technique able to identify differentially expressed genes, based on the construction of \emph{Fuzzy Patterns} (FPs). The Fuzzy Patterns are built by means of applying 3 Membership Functions to discretized gene expression values.' diff --git a/recipes/bioconductor-diffgeneanalysis/build.sh b/recipes/bioconductor-diffgeneanalysis/build.sh new file mode 100644 index 00000000000000..da43ce21683122 --- /dev/null +++ b/recipes/bioconductor-diffgeneanalysis/build.sh @@ -0,0 +1,4 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-diffgeneanalysis/meta.yaml b/recipes/bioconductor-diffgeneanalysis/meta.yaml new file mode 100644 index 00000000000000..1ad35093dbdbfd --- /dev/null +++ b/recipes/bioconductor-diffgeneanalysis/meta.yaml @@ -0,0 +1,33 @@ +{% set version = "1.60.0" %} +{% set name = "diffGeneAnalysis" %} +{% set bioc = "3.6" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + fn: '{{ name }}_{{ version }}.tar.gz' + url: + - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: e38295ee0f2bdf73ec4c9e5a5572236c17d709b5f3cec7003644b1cc921dda2d +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ +requirements: + build: + - r-base + - 'r-minpack.lm >=1.0-4' + run: + - r-base + - 'r-minpack.lm >=1.0-4' +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: GPL + summary: 'Analyze microarray data' diff --git a/recipes/bioconductor-diffloop/build.sh b/recipes/bioconductor-diffloop/build.sh new file mode 100644 index 00000000000000..da43ce21683122 --- /dev/null +++ b/recipes/bioconductor-diffloop/build.sh @@ -0,0 +1,4 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-diffloop/meta.yaml b/recipes/bioconductor-diffloop/meta.yaml new file mode 100644 index 00000000000000..8228284c34e717 --- /dev/null +++ b/recipes/bioconductor-diffloop/meta.yaml @@ -0,0 +1,73 @@ +{% set version = "1.6.0" %} +{% set name = "diffloop" %} +{% set bioc = "3.6" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + fn: '{{ name }}_{{ version }}.tar.gz' + url: + - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + sha256: cc9a352e8b6c5393adf8b36a75947a98e1a88d5348960622fecbbac66ae4663f +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ +requirements: + build: + - bioconductor-biobase + - bioconductor-biomart + - bioconductor-edger + - bioconductor-genomeinfodb + - bioconductor-genomicranges + - bioconductor-iranges + - bioconductor-limma + - bioconductor-rtracklayer + - bioconductor-s4vectors + - bioconductor-sushi + - r-base + - r-data.table + - r-dplyr + - r-foreach + - r-ggplot2 + - r-locfit + - r-matrixstats + - r-pbapply + - r-plyr + - r-readr + - r-reshape2 + - r-statmod + run: + - bioconductor-biobase + - bioconductor-biomart + - bioconductor-edger + - bioconductor-genomeinfodb + - bioconductor-genomicranges + - bioconductor-iranges + - bioconductor-limma + - bioconductor-rtracklayer + - bioconductor-s4vectors + - bioconductor-sushi + - r-base + - r-data.table + - r-dplyr + - r-foreach + - r-ggplot2 + - r-locfit + - r-matrixstats + - r-pbapply + - r-plyr + - r-readr + - r-reshape2 + - r-statmod +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: 'MIT + file LICENSE' + summary: 'A suite of tools for subsetting, visualizing, annotating, and statistically analyzing the results of one or more ChIA-PET experiments or other assays that infer chromatin loops.' diff --git a/recipes/bioconductor-director/build.sh b/recipes/bioconductor-director/build.sh new file mode 100644 index 00000000000000..da43ce21683122 --- /dev/null +++ b/recipes/bioconductor-director/build.sh @@ -0,0 +1,4 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-director/meta.yaml b/recipes/bioconductor-director/meta.yaml new file mode 100644 index 00000000000000..17630861bcbadd --- /dev/null +++ b/recipes/bioconductor-director/meta.yaml @@ -0,0 +1,33 @@ +{% set version = "1.4.0" %} +{% set name = "Director" %} +{% set bioc = "3.6" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + fn: '{{ name }}_{{ version }}.tar.gz' + url: + - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: 6876551f960cda6a2458e22edd9ce05f0d8f188134a4dc9e43263cea785504fb +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ +requirements: + build: + - r-base + - r-htmltools + run: + - r-base + - r-htmltools +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: 'GPL-3 + file LICENSE' + summary: 'Director is an R package designed to streamline the visualization of molecular effects in regulatory cascades. It utilizes the R package htmltools and a modified Sankey plugin of the JavaScript library D3 to provide a fast and easy, browser-enabled solution to discovering potentially interesting downstream effects of regulatory and/or co-expressed molecules. The diagrams are robust, interactive, and packaged as highly-portable HTML files that eliminate the need for third-party software to view. This enables a straightforward approach for scientists to interpret the data produced, and bioinformatics developers an alternative means to present relevant data.' diff --git a/recipes/bioconductor-dnabarcodes/build.sh b/recipes/bioconductor-dnabarcodes/build.sh new file mode 100644 index 00000000000000..da43ce21683122 --- /dev/null +++ b/recipes/bioconductor-dnabarcodes/build.sh @@ -0,0 +1,4 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-dnabarcodes/meta.yaml b/recipes/bioconductor-dnabarcodes/meta.yaml new file mode 100644 index 00000000000000..56aacc54682484 --- /dev/null +++ b/recipes/bioconductor-dnabarcodes/meta.yaml @@ -0,0 +1,40 @@ +{% set version = "1.8.0" %} +{% set name = "DNABarcodes" %} +{% set bioc = "3.6" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + fn: '{{ name }}_{{ version }}.tar.gz' + url: + - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: 57e8d2375709e7402437b560f78270c55f88cec1d0e43e0b01fc948d2ce57774 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ +requirements: + build: + - r-base + - r-bh + - r-matrix + - 'r-rcpp >=0.11.2' + - gcc # [linux] + - llvm # [osx] + run: + - r-base + - r-bh + - r-matrix + - 'r-rcpp >=0.11.2' + - libcxx # [osx] +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: GPL-2 + summary: 'The package offers a function to create DNA barcode sets capable of correcting insertion, deletion, and substitution errors. Existing barcodes can be analysed regarding their minimal, maximal and average distances between barcodes. Finally, reads that start with a (possibly mutated) barcode can be demultiplexed, i.e., assigned to their original reference barcode.' diff --git a/recipes/bioconductor-doqtl/build.sh b/recipes/bioconductor-doqtl/build.sh new file mode 100644 index 00000000000000..da43ce21683122 --- /dev/null +++ b/recipes/bioconductor-doqtl/build.sh @@ -0,0 +1,4 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-doqtl/meta.yaml b/recipes/bioconductor-doqtl/meta.yaml new file mode 100644 index 00000000000000..a1860d5a650f4a --- /dev/null +++ b/recipes/bioconductor-doqtl/meta.yaml @@ -0,0 +1,78 @@ +{% set version = "1.14.0" %} +{% set name = "DOQTL" %} +{% set bioc = "3.6" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + fn: '{{ name }}_{{ version }}.tar.gz' + url: + - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: e5fe9820a6a02d54a25206dbb37d0b033861728519069668a9291e450982fb42 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ +requirements: + build: + - bioconductor-annotate + - bioconductor-annotationtools + - bioconductor-biobase + - bioconductor-biocgenerics + - bioconductor-biomart + - bioconductor-bsgenome.mmusculus.ucsc.mm10 + - bioconductor-genomicranges + - bioconductor-iranges + - bioconductor-rhdf5 + - bioconductor-rsamtools + - bioconductor-variantannotation + - r-base + - r-corpcor + - r-doparallel + - r-foreach + - r-fpc + - r-hwriter + - r-iterators + - r-mclust + - r-qtlrel + - r-regress + - r-runit + - r-xml + - gcc # [linux] + - llvm # [osx] + run: + - bioconductor-annotate + - bioconductor-annotationtools + - bioconductor-biobase + - bioconductor-biocgenerics + - bioconductor-biomart + - bioconductor-bsgenome.mmusculus.ucsc.mm10 + - bioconductor-genomicranges + - bioconductor-iranges + - bioconductor-rhdf5 + - bioconductor-rsamtools + - bioconductor-variantannotation + - r-base + - r-corpcor + - r-doparallel + - r-foreach + - r-fpc + - r-hwriter + - r-iterators + - r-mclust + - r-qtlrel + - r-regress + - r-runit + - r-xml + - libcxx # [osx] +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: GPL-3 + summary: 'DOQTL is a quantitative trait locus (QTL) mapping pipeline designed for Diversity Outbred mice and other multi-parent outbred populations. The package reads in data from genotyping arrays and perform haplotype reconstruction using a hidden Markov model (HMM). The haplotype probabilities from the HMM are then used to perform linkage mapping. When founder sequences are available, DOQTL can use the haplotype reconstructions to impute the founder sequences onto DO genomes and perform association mapping.' diff --git a/recipes/bioconductor-drugvsdisease/build.sh b/recipes/bioconductor-drugvsdisease/build.sh new file mode 100644 index 00000000000000..da43ce21683122 --- /dev/null +++ b/recipes/bioconductor-drugvsdisease/build.sh @@ -0,0 +1,4 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-drugvsdisease/meta.yaml b/recipes/bioconductor-drugvsdisease/meta.yaml new file mode 100644 index 00000000000000..4a3492ddaa6ec5 --- /dev/null +++ b/recipes/bioconductor-drugvsdisease/meta.yaml @@ -0,0 +1,61 @@ +{% set version = "2.20.1" %} +{% set name = "DrugVsDisease" %} +{% set bioc = "3.6" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + fn: '{{ name }}_{{ version }}.tar.gz' + url: + - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: 53c2cb62af1cdd4e636aced0387f589e0cafed2f3918daa8fd355da6385f892f +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ +requirements: + build: + - bioconductor-affy + - bioconductor-annotate + - bioconductor-arrayexpress + - bioconductor-biocgenerics + - bioconductor-biomart + - bioconductor-cmap2data + - bioconductor-drugvsdiseasedata + - bioconductor-geoquery + - bioconductor-hgu133a.db + - bioconductor-hgu133a2.db + - bioconductor-hgu133plus2.db + - bioconductor-limma + - bioconductor-qvalue + - r-base + - r-runit + - r-xtable + run: + - bioconductor-affy + - bioconductor-annotate + - bioconductor-arrayexpress + - bioconductor-biocgenerics + - bioconductor-biomart + - bioconductor-cmap2data + - bioconductor-drugvsdiseasedata + - bioconductor-geoquery + - bioconductor-hgu133a.db + - bioconductor-hgu133a2.db + - bioconductor-hgu133plus2.db + - bioconductor-limma + - bioconductor-qvalue + - r-base + - r-runit + - r-xtable +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: GPL-3 + summary: 'This package generates ranked lists of differential gene expression for either disease or drug profiles. Input data can be downloaded from Array Express or GEO, or from local CEL files. Ranked lists of differential expression and associated p-values are calculated using Limma. Enrichment scores (Subramanian et al. PNAS 2005) are calculated to a reference set of default drug or disease profiles, or a set of custom data supplied by the user. Network visualisation of significant scores are output in Cytoscape format.' diff --git a/recipes/bioconductor-drugvsdiseasedata/meta.yaml b/recipes/bioconductor-drugvsdiseasedata/meta.yaml new file mode 100644 index 00000000000000..5f3734c911372f --- /dev/null +++ b/recipes/bioconductor-drugvsdiseasedata/meta.yaml @@ -0,0 +1,32 @@ +{% set version = "1.14.0" %} +{% set name = "DrugVsDiseasedata" %} +{% set bioc = "3.6" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + fn: '{{ name }}_{{ version }}.tar.gz' + url: + - 'http://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: 7a1e7f9d3dc3000b388cbab04ba6adc49104065a225359c428c96a87d89a250c +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ +requirements: + build: + - r-base + run: + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'http://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' + license: GPL-3 + summary: 'Data package which provides default disease expression profiles, clusters and annotation information for use with the DrugVsDisease package.' diff --git a/recipes/bioconductor-drugvsdiseasedata/post-link.sh b/recipes/bioconductor-drugvsdiseasedata/post-link.sh new file mode 100644 index 00000000000000..c992173b13b77f --- /dev/null +++ b/recipes/bioconductor-drugvsdiseasedata/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="DrugVsDiseasedata_1.14.0.tar.gz" +URLS=( + "http://bioconductor.org/packages/3.6/data/experiment/src/contrib/DrugVsDiseasedata_1.14.0.tar.gz" + "https://bioarchive.galaxyproject.org/DrugVsDiseasedata_1.14.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-drugvsdiseasedata/bioconductor-drugvsdiseasedata_1.14.0_src_all.tar.gz" +) +MD5="6623685264db20d9ab1ec5bd51989e50" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING \ No newline at end of file diff --git a/recipes/bioconductor-drugvsdiseasedata/pre-unlink.sh b/recipes/bioconductor-drugvsdiseasedata/pre-unlink.sh new file mode 100644 index 00000000000000..92d93f388e2e84 --- /dev/null +++ b/recipes/bioconductor-drugvsdiseasedata/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ DrugVsDiseasedata diff --git a/recipes/bioconductor-easyrnaseq/build.sh b/recipes/bioconductor-easyrnaseq/build.sh new file mode 100644 index 00000000000000..da43ce21683122 --- /dev/null +++ b/recipes/bioconductor-easyrnaseq/build.sh @@ -0,0 +1,4 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-easyrnaseq/meta.yaml b/recipes/bioconductor-easyrnaseq/meta.yaml new file mode 100644 index 00000000000000..850e9fe8eabb85 --- /dev/null +++ b/recipes/bioconductor-easyrnaseq/meta.yaml @@ -0,0 +1,67 @@ +{% set version = "2.14.0" %} +{% set name = "easyRNASeq" %} +{% set bioc = "3.6" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + fn: '{{ name }}_{{ version }}.tar.gz' + url: + - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: 7d9d71012c9dce33cd7938e3639ba394858438b14d016c8b02b35cc6935c8086 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ +requirements: + build: + - 'bioconductor-biobase >=2.31.3' + - 'bioconductor-biocgenerics >=0.17.2' + - 'bioconductor-biocparallel >=1.5.1' + - 'bioconductor-biomart >=2.27.2' + - 'bioconductor-biostrings >=2.39.3' + - 'bioconductor-deseq >=1.23.0' + - 'bioconductor-edger >=3.13.4' + - 'bioconductor-genomeinfodb >=1.7.3' + - 'bioconductor-genomeintervals >=1.27.0' + - 'bioconductor-genomicalignments >=1.7.3' + - 'bioconductor-genomicranges >=1.23.16' + - 'bioconductor-iranges >=2.5.27' + - 'bioconductor-rsamtools >=1.23.1' + - 'bioconductor-s4vectors >=0.9.38' + - 'bioconductor-shortread >=1.29.1' + - 'bioconductor-summarizedexperiment >=1.1.11' + - r-base + - r-locfit + - 'r-lsd >=3.0' + run: + - 'bioconductor-biobase >=2.31.3' + - 'bioconductor-biocgenerics >=0.17.2' + - 'bioconductor-biocparallel >=1.5.1' + - 'bioconductor-biomart >=2.27.2' + - 'bioconductor-biostrings >=2.39.3' + - 'bioconductor-deseq >=1.23.0' + - 'bioconductor-edger >=3.13.4' + - 'bioconductor-genomeinfodb >=1.7.3' + - 'bioconductor-genomeintervals >=1.27.0' + - 'bioconductor-genomicalignments >=1.7.3' + - 'bioconductor-genomicranges >=1.23.16' + - 'bioconductor-iranges >=2.5.27' + - 'bioconductor-rsamtools >=1.23.1' + - 'bioconductor-s4vectors >=0.9.38' + - 'bioconductor-shortread >=1.29.1' + - 'bioconductor-summarizedexperiment >=1.1.11' + - r-base + - r-locfit + - 'r-lsd >=3.0' +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Calculates the coverage of high-throughput short-reads against a genome of reference and summarizes it per feature of interest (e.g. exon, gene, transcript). The data can be normalized as ''RPKM'' or by the ''DESeq'' or ''edgeR'' package.' diff --git a/recipes/bioconductor-edda/build.sh b/recipes/bioconductor-edda/build.sh new file mode 100644 index 00000000000000..da43ce21683122 --- /dev/null +++ b/recipes/bioconductor-edda/build.sh @@ -0,0 +1,4 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-edda/meta.yaml b/recipes/bioconductor-edda/meta.yaml new file mode 100644 index 00000000000000..94663718b88a2c --- /dev/null +++ b/recipes/bioconductor-edda/meta.yaml @@ -0,0 +1,46 @@ +{% set version = "1.16.0" %} +{% set name = "EDDA" %} +{% set bioc = "3.6" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + fn: '{{ name }}_{{ version }}.tar.gz' + url: + - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: 602823ecbfd955f6437928048711c863672ee743143fd2d262b659380fb81300 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ +requirements: + build: + - bioconductor-bayseq + - bioconductor-deseq + - bioconductor-edger + - r-base + - 'r-rcpp >=0.10.4' + - r-rocr + - r-snow + - gcc # [linux] + - llvm # [osx] + run: + - bioconductor-bayseq + - bioconductor-deseq + - bioconductor-edger + - r-base + - 'r-rcpp >=0.10.4' + - r-rocr + - r-snow + - libcxx # [osx] +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: 'GPL (>= 2)' + summary: 'EDDA can aid in the design of a range of common experiments such as RNA-seq, Nanostring assays, RIP-seq and Metagenomic sequencing, and enables researchers to comprehensively investigate the impact of experimental decisions on the ability to detect differential abundance. This work was published on 3 December 2014 at Genome Biology under the title "The importance of study design for detecting differentially abundant features in high-throughput experiments" (http://genomebiology.com/2014/15/12/527).' diff --git a/recipes/bioconductor-empiricalbrownsmethod/build.sh b/recipes/bioconductor-empiricalbrownsmethod/build.sh new file mode 100644 index 00000000000000..da43ce21683122 --- /dev/null +++ b/recipes/bioconductor-empiricalbrownsmethod/build.sh @@ -0,0 +1,4 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-empiricalbrownsmethod/meta.yaml b/recipes/bioconductor-empiricalbrownsmethod/meta.yaml new file mode 100644 index 00000000000000..1273967a378466 --- /dev/null +++ b/recipes/bioconductor-empiricalbrownsmethod/meta.yaml @@ -0,0 +1,31 @@ +{% set version = "1.6.0" %} +{% set name = "EmpiricalBrownsMethod" %} +{% set bioc = "3.6" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + fn: '{{ name }}_{{ version }}.tar.gz' + url: + - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: 1ebd334bac4be2e562ae4aecc03637f8041ee832c0629a229ea2f245aa5561f3 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ +requirements: + build: + - r-base + run: + - r-base +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: 'MIT + file LICENSE' + summary: 'Combining P-values from multiple statistical tests is common in bioinformatics. However, this procedure is non-trivial for dependent P-values. This package implements an empirical adaptation of Brown’s Method (an extension of Fisher’s Method) for combining dependent P-values which is appropriate for highly correlated data sets found in high-throughput biological experiments.' diff --git a/recipes/bioconductor-encodexplorer/build.sh b/recipes/bioconductor-encodexplorer/build.sh new file mode 100644 index 00000000000000..da43ce21683122 --- /dev/null +++ b/recipes/bioconductor-encodexplorer/build.sh @@ -0,0 +1,4 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-encodexplorer/meta.yaml b/recipes/bioconductor-encodexplorer/meta.yaml new file mode 100644 index 00000000000000..2d34cf633ae3d8 --- /dev/null +++ b/recipes/bioconductor-encodexplorer/meta.yaml @@ -0,0 +1,51 @@ +{% set version = "2.4.0" %} +{% set name = "ENCODExplorer" %} +{% set bioc = "3.6" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + fn: '{{ name }}_{{ version }}.tar.gz' + url: + - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: de8ff9650f33ccf3befbdc2f527f802f26dede14f38ec5fe93008779d7bb8357 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ +requirements: + build: + - r-base + - r-data.table + - r-dplyr + - r-dt + - r-jsonlite + - r-rcurl + - r-shiny + - r-shinythemes + - r-stringi + - r-stringr + - r-tidyr + run: + - r-base + - r-data.table + - r-dplyr + - r-dt + - r-jsonlite + - r-rcurl + - r-shiny + - r-shinythemes + - r-stringi + - r-stringr + - r-tidyr +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'This package allows user to quickly access ENCODE project files metadata and give access to helper functions to query the ENCODE rest api, download ENCODE datasets and save the database in SQLite format.' diff --git a/recipes/bioconductor-enrichmentbrowser/build.sh b/recipes/bioconductor-enrichmentbrowser/build.sh new file mode 100644 index 00000000000000..da43ce21683122 --- /dev/null +++ b/recipes/bioconductor-enrichmentbrowser/build.sh @@ -0,0 +1,4 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-enrichmentbrowser/meta.yaml b/recipes/bioconductor-enrichmentbrowser/meta.yaml new file mode 100644 index 00000000000000..3839bbe3eaefc8 --- /dev/null +++ b/recipes/bioconductor-enrichmentbrowser/meta.yaml @@ -0,0 +1,77 @@ +{% set version = "2.8.5" %} +{% set name = "EnrichmentBrowser" %} +{% set bioc = "3.6" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + fn: '{{ name }}_{{ version }}.tar.gz' + url: + - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: f2b2e6ca297338e0a78e7627bd7d1f49d8686f10ea52e9a117db52de6b38b7ab +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ +requirements: + build: + - bioconductor-annotationdbi + - bioconductor-biocgraph + - bioconductor-complexheatmap + - bioconductor-deseq2 + - bioconductor-edaseq + - bioconductor-edger + - bioconductor-geneplotter + - bioconductor-go.db + - bioconductor-graph + - bioconductor-gseabase + - bioconductor-kegggraph + - bioconductor-keggrest + - bioconductor-limma + - bioconductor-pathview + - bioconductor-reportingtools + - bioconductor-rgraphviz + - bioconductor-s4vectors + - bioconductor-safe + - bioconductor-spia + - bioconductor-summarizedexperiment + - bioconductor-topgo + - r-base + - r-hwriter + - r-mass + run: + - bioconductor-annotationdbi + - bioconductor-biocgraph + - bioconductor-complexheatmap + - bioconductor-deseq2 + - bioconductor-edaseq + - bioconductor-edger + - bioconductor-geneplotter + - bioconductor-go.db + - bioconductor-graph + - bioconductor-gseabase + - bioconductor-kegggraph + - bioconductor-keggrest + - bioconductor-limma + - bioconductor-pathview + - bioconductor-reportingtools + - bioconductor-rgraphviz + - bioconductor-s4vectors + - bioconductor-safe + - bioconductor-spia + - bioconductor-summarizedexperiment + - bioconductor-topgo + - r-base + - r-hwriter + - r-mass +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'The EnrichmentBrowser package implements essential functionality for the enrichment analysis of gene expression data. The analysis combines the advantages of set-based and network-based enrichment analysis in order to derive high-confidence gene sets and biological pathways that are differentially regulated in the expression data under investigation. Besides, the package facilitates the visualization and exploration of such sets and pathways.' diff --git a/recipes/bioconductor-ensdb.hsapiens.v75/meta.yaml b/recipes/bioconductor-ensdb.hsapiens.v75/meta.yaml new file mode 100644 index 00000000000000..c5f43f9be7d9e5 --- /dev/null +++ b/recipes/bioconductor-ensdb.hsapiens.v75/meta.yaml @@ -0,0 +1,34 @@ +{% set version = "2.99.0" %} +{% set name = "EnsDb.Hsapiens.v75" %} +{% set bioc = "3.6" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + fn: '{{ name }}_{{ version }}.tar.gz' + url: + - 'http://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: 2c59f95959f344b2a3eaa65a00086b01a420823e30b0810fc81e49b08dcba64b +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ +requirements: + build: + - bioconductor-ensembldb + - r-base + run: + - bioconductor-ensembldb + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'http://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Exposes an annotation databases generated from Ensembl.' diff --git a/recipes/bioconductor-ensdb.hsapiens.v75/post-link.sh b/recipes/bioconductor-ensdb.hsapiens.v75/post-link.sh new file mode 100644 index 00000000000000..cf842670281820 --- /dev/null +++ b/recipes/bioconductor-ensdb.hsapiens.v75/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="EnsDb.Hsapiens.v75_2.99.0.tar.gz" +URLS=( + "http://bioconductor.org/packages/3.6/data/annotation/src/contrib/EnsDb.Hsapiens.v75_2.99.0.tar.gz" + "https://bioarchive.galaxyproject.org/EnsDb.Hsapiens.v75_2.99.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-ensdb.hsapiens.v75/bioconductor-ensdb.hsapiens.v75_2.99.0_src_all.tar.gz" +) +MD5="6c896475252903972bfc6c0eb0d8f334" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING \ No newline at end of file diff --git a/recipes/bioconductor-ensdb.hsapiens.v75/pre-unlink.sh b/recipes/bioconductor-ensdb.hsapiens.v75/pre-unlink.sh new file mode 100644 index 00000000000000..d4ad38fae03259 --- /dev/null +++ b/recipes/bioconductor-ensdb.hsapiens.v75/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ EnsDb.Hsapiens.v75 diff --git a/recipes/bioconductor-epigenomix/build.sh b/recipes/bioconductor-epigenomix/build.sh new file mode 100644 index 00000000000000..da43ce21683122 --- /dev/null +++ b/recipes/bioconductor-epigenomix/build.sh @@ -0,0 +1,4 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-epigenomix/meta.yaml b/recipes/bioconductor-epigenomix/meta.yaml new file mode 100644 index 00000000000000..3296ecf146a4d1 --- /dev/null +++ b/recipes/bioconductor-epigenomix/meta.yaml @@ -0,0 +1,51 @@ +{% set version = "1.18.0" %} +{% set name = "epigenomix" %} +{% set bioc = "3.6" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + fn: '{{ name }}_{{ version }}.tar.gz' + url: + - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + sha256: 973b9a3fe5c2ddba3be21c2d177a802faa80c631a50f0d8b7f168da9ba3ba674 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ +requirements: + build: + - bioconductor-beadarray + - bioconductor-biobase + - bioconductor-biocgenerics + - bioconductor-genomeinfodb + - bioconductor-genomicranges + - bioconductor-iranges + - bioconductor-rsamtools + - bioconductor-s4vectors + - bioconductor-summarizedexperiment + - r-base + - r-mcmcpack + run: + - bioconductor-beadarray + - bioconductor-biobase + - bioconductor-biocgenerics + - bioconductor-genomeinfodb + - bioconductor-genomicranges + - bioconductor-iranges + - bioconductor-rsamtools + - bioconductor-s4vectors + - bioconductor-summarizedexperiment + - r-base + - r-mcmcpack +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: LGPL-3 + summary: 'A package for the integrative analysis of RNA-seq or microarray based gene transcription and histone modification data obtained by ChIP-seq. The package provides methods for data preprocessing and matching as well as methods for fitting bayesian mixture models in order to detect genes with differences in both data types.' diff --git a/recipes/bioconductor-epivizr/build.sh b/recipes/bioconductor-epivizr/build.sh new file mode 100644 index 00000000000000..da43ce21683122 --- /dev/null +++ b/recipes/bioconductor-epivizr/build.sh @@ -0,0 +1,4 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-epivizr/meta.yaml b/recipes/bioconductor-epivizr/meta.yaml new file mode 100644 index 00000000000000..debc0128b59bac --- /dev/null +++ b/recipes/bioconductor-epivizr/meta.yaml @@ -0,0 +1,41 @@ +{% set version = "2.8.0" %} +{% set name = "epivizr" %} +{% set bioc = "3.6" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + fn: '{{ name }}_{{ version }}.tar.gz' + url: + - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + sha256: 7cb7bae00b0cea5a2db5b4e03581cb4cf3eb64c7e24269c02d5c70a625120e21 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ +requirements: + build: + - 'bioconductor-epivizrdata >=1.3.4' + - 'bioconductor-epivizrserver >=1.1.1' + - bioconductor-genomicranges + - bioconductor-iranges + - bioconductor-s4vectors + - r-base + run: + - 'bioconductor-epivizrdata >=1.3.4' + - 'bioconductor-epivizrserver >=1.1.1' + - bioconductor-genomicranges + - bioconductor-iranges + - bioconductor-s4vectors + - r-base +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'This package provides connections to the epiviz web app (http://epiviz.cbcb.umd.edu) for interactive visualization of genomic data. Objects in R/bioc interactive sessions can be displayed in genome browser tracks or plots to be explored by navigation through genomic regions. Fundamental Bioconductor data structures are supported (e.g., GenomicRanges and RangedSummarizedExperiment objects), while providing an easy mechanism to support other data structures (through package epivizrData). Visualizations (using d3.js) can be easily added to the web app as well.' diff --git a/recipes/bioconductor-epivizrdata/build.sh b/recipes/bioconductor-epivizrdata/build.sh new file mode 100644 index 00000000000000..da43ce21683122 --- /dev/null +++ b/recipes/bioconductor-epivizrdata/build.sh @@ -0,0 +1,4 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-epivizrdata/meta.yaml b/recipes/bioconductor-epivizrdata/meta.yaml new file mode 100644 index 00000000000000..75798dd2da0d58 --- /dev/null +++ b/recipes/bioconductor-epivizrdata/meta.yaml @@ -0,0 +1,51 @@ +{% set version = "1.6.0" %} +{% set name = "epivizrData" %} +{% set bioc = "3.6" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + fn: '{{ name }}_{{ version }}.tar.gz' + url: + - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: a4840fe556800430b75e34e7a0bfb7c453546f185e4e248bb5ed046c535f3180 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ +requirements: + build: + - bioconductor-biobase + - bioconductor-ensembldb + - 'bioconductor-epivizrserver >=1.1.1' + - bioconductor-genomeinfodb + - bioconductor-genomicfeatures + - bioconductor-genomicranges + - bioconductor-iranges + - bioconductor-organismdbi + - bioconductor-s4vectors + - 'bioconductor-summarizedexperiment >=0.2.0' + - r-base + run: + - bioconductor-biobase + - bioconductor-ensembldb + - 'bioconductor-epivizrserver >=1.1.1' + - bioconductor-genomeinfodb + - bioconductor-genomicfeatures + - bioconductor-genomicranges + - bioconductor-iranges + - bioconductor-organismdbi + - bioconductor-s4vectors + - 'bioconductor-summarizedexperiment >=0.2.0' + - r-base +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: 'MIT + file LICENSE' + summary: 'Serve data from Bioconductor Objects through a WebSocket connection.' diff --git a/recipes/bioconductor-epivizrserver/build.sh b/recipes/bioconductor-epivizrserver/build.sh new file mode 100644 index 00000000000000..da43ce21683122 --- /dev/null +++ b/recipes/bioconductor-epivizrserver/build.sh @@ -0,0 +1,4 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-epivizrserver/meta.yaml b/recipes/bioconductor-epivizrserver/meta.yaml new file mode 100644 index 00000000000000..1c92c0e26cc4d6 --- /dev/null +++ b/recipes/bioconductor-epivizrserver/meta.yaml @@ -0,0 +1,39 @@ +{% set version = "1.6.0" %} +{% set name = "epivizrServer" %} +{% set bioc = "3.6" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + fn: '{{ name }}_{{ version }}.tar.gz' + url: + - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: 2b84e5bbddf18ce04e0d79617b330aefb1830030b16e61431d8afb84b71f4161 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ +requirements: + build: + - r-base + - 'r-httpuv >=1.3.0' + - 'r-mime >=0.2' + - 'r-r6 >=2.0.0' + - r-rjson + run: + - r-base + - 'r-httpuv >=1.3.0' + - 'r-mime >=0.2' + - 'r-r6 >=2.0.0' + - r-rjson +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: 'MIT + file LICENSE' + summary: 'This package provides objects to manage WebSocket connections to epiviz apps. Other epivizr package use this infrastructure.' diff --git a/recipes/bioconductor-epivizrstandalone/build.sh b/recipes/bioconductor-epivizrstandalone/build.sh new file mode 100644 index 00000000000000..da43ce21683122 --- /dev/null +++ b/recipes/bioconductor-epivizrstandalone/build.sh @@ -0,0 +1,4 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-epivizrstandalone/meta.yaml b/recipes/bioconductor-epivizrstandalone/meta.yaml new file mode 100644 index 00000000000000..704c418b98ed54 --- /dev/null +++ b/recipes/bioconductor-epivizrstandalone/meta.yaml @@ -0,0 +1,45 @@ +{% set version = "1.6.0" %} +{% set name = "epivizrStandalone" %} +{% set bioc = "3.6" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + fn: '{{ name }}_{{ version }}.tar.gz' + url: + - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: 12fdcf19c658dba96ad9ecad30c38b8eea93f4486f3e717a3dc983d8ea146d65 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ +requirements: + build: + - bioconductor-biocgenerics + - 'bioconductor-epivizr >=2.3.6' + - bioconductor-epivizrserver + - bioconductor-genomeinfodb + - bioconductor-genomicfeatures + - bioconductor-s4vectors + - r-base + - r-git2r + run: + - bioconductor-biocgenerics + - 'bioconductor-epivizr >=2.3.6' + - bioconductor-epivizrserver + - bioconductor-genomeinfodb + - bioconductor-genomicfeatures + - bioconductor-s4vectors + - r-base + - r-git2r +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: 'MIT + file LICENSE' + summary: 'This package imports the epiviz visualization JavaScript app for genomic data interactive visualization. The ''epivizrServer'' package is used to provide a web server running completely within R. This standalone version allows to browse arbitrary genomes through genome annotations provided by Bioconductor packages.' diff --git a/recipes/bioconductor-esetvis/build.sh b/recipes/bioconductor-esetvis/build.sh new file mode 100644 index 00000000000000..da43ce21683122 --- /dev/null +++ b/recipes/bioconductor-esetvis/build.sh @@ -0,0 +1,4 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-esetvis/meta.yaml b/recipes/bioconductor-esetvis/meta.yaml new file mode 100644 index 00000000000000..287ca3489d88bc --- /dev/null +++ b/recipes/bioconductor-esetvis/meta.yaml @@ -0,0 +1,43 @@ +{% set version = "1.4.0" %} +{% set name = "esetVis" %} +{% set bioc = "3.6" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + fn: '{{ name }}_{{ version }}.tar.gz' + url: + - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: c1c28bf08e5c2819a974aeed222efa9709626e2ea2fd5163af5823df291a62f9 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ +requirements: + build: + - bioconductor-biobase + - bioconductor-mlp + - r-base + - r-hexbin + - r-mass + - r-mpm + - r-rtsne + run: + - bioconductor-biobase + - bioconductor-mlp + - r-base + - r-hexbin + - r-mass + - r-mpm + - r-rtsne +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: GPL-3 + summary: 'Utility functions for visualization of expressionSet (or SummarizedExperiment) Bioconductor object, including spectral map, tsne and linear discriminant analysis. Static plot via the ggplot2 package or interactive via the ggvis or rbokeh packages are available.' diff --git a/recipes/bioconductor-eudysbiome/build.sh b/recipes/bioconductor-eudysbiome/build.sh new file mode 100644 index 00000000000000..da43ce21683122 --- /dev/null +++ b/recipes/bioconductor-eudysbiome/build.sh @@ -0,0 +1,4 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-eudysbiome/meta.yaml b/recipes/bioconductor-eudysbiome/meta.yaml new file mode 100644 index 00000000000000..5e6814c7933680 --- /dev/null +++ b/recipes/bioconductor-eudysbiome/meta.yaml @@ -0,0 +1,39 @@ +{% set version = "1.8.0" %} +{% set name = "eudysbiome" %} +{% set bioc = "3.6" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + fn: '{{ name }}_{{ version }}.tar.gz' + url: + - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + sha256: 69480f65354e411a7b387edd7e99f39bfd6af2392e5535ac32b014ff5fcc5e8d +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ +requirements: + build: + - bioconductor-biostrings + - bioconductor-rsamtools + - r-base + - r-plyr + - r-r.utils + run: + - bioconductor-biostrings + - bioconductor-rsamtools + - r-base + - r-plyr + - r-r.utils +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: GPL-2 + summary: 'eudysbiome a package that permits to annotate the differential genera as harmful/harmless based on their ability to contribute to host diseases (as indicated in literature) or unknown based on their ambiguous genus classification. Further, the package statistically measures the eubiotic (harmless genera increase or harmful genera decrease) or dysbiotic(harmless genera decrease or harmful genera increase) impact of a given treatment or environmental change on the (gut-intestinal, GI) microbiome in comparison to the microbiome of the reference condition.' diff --git a/recipes/bioconductor-eximir/build.sh b/recipes/bioconductor-eximir/build.sh new file mode 100644 index 00000000000000..da43ce21683122 --- /dev/null +++ b/recipes/bioconductor-eximir/build.sh @@ -0,0 +1,4 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-eximir/meta.yaml b/recipes/bioconductor-eximir/meta.yaml new file mode 100644 index 00000000000000..ad631d06dbc720 --- /dev/null +++ b/recipes/bioconductor-eximir/meta.yaml @@ -0,0 +1,41 @@ +{% set version = "2.20.0" %} +{% set name = "ExiMiR" %} +{% set bioc = "3.6" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + fn: '{{ name }}_{{ version }}.tar.gz' + url: + - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: 7b93675e6e6567bff038092f4121029bb33eeb5a2f60636b13270164bce25d69 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ +requirements: + build: + - 'bioconductor-affy >=1.26.1' + - 'bioconductor-affyio >=1.13.3' + - 'bioconductor-biobase >=2.5.5' + - bioconductor-limma + - 'bioconductor-preprocesscore >=1.10.0' + - r-base + run: + - 'bioconductor-affy >=1.26.1' + - 'bioconductor-affyio >=1.13.3' + - 'bioconductor-biobase >=2.5.5' + - bioconductor-limma + - 'bioconductor-preprocesscore >=1.10.0' + - r-base +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: GPL-2 + summary: 'This package contains functions for reading raw data in ImaGene TXT format obtained from Exiqon miRCURY LNA arrays, annotating them with appropriate GAL files, and normalizing them using a spike-in probe-based method. Other platforms and data formats are also supported.' diff --git a/recipes/bioconductor-exomepeak/build.sh b/recipes/bioconductor-exomepeak/build.sh new file mode 100644 index 00000000000000..da43ce21683122 --- /dev/null +++ b/recipes/bioconductor-exomepeak/build.sh @@ -0,0 +1,4 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-exomepeak/meta.yaml b/recipes/bioconductor-exomepeak/meta.yaml new file mode 100644 index 00000000000000..ef85eec49a2399 --- /dev/null +++ b/recipes/bioconductor-exomepeak/meta.yaml @@ -0,0 +1,39 @@ +{% set version = "2.13.2" %} +{% set name = "exomePeak" %} +{% set bioc = "3.6" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + fn: '{{ name }}_{{ version }}.tar.gz' + url: + - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: 87562bfc22436c8d4cee85fa9dffeb16546732ac1b1c40375d1f605e591cdf05 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ +requirements: + build: + - bioconductor-genomicalignments + - 'bioconductor-genomicfeatures >=1.14.5' + - bioconductor-rsamtools + - bioconductor-rtracklayer + - r-base + run: + - bioconductor-genomicalignments + - 'bioconductor-genomicfeatures >=1.14.5' + - bioconductor-rsamtools + - bioconductor-rtracklayer + - r-base +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: GPL-2 + summary: 'The package is developed for the analysis of affinity-based epitranscriptome shortgun sequencing data from MeRIP-seq (maA-seq). It was built on the basis of the exomePeak MATLAB package (Meng, Jia, et al. "Exome-based analysis for RNA epigenome sequencing data." Bioinformatics 29.12 (2013): 1565-1567.) with new functions for differential analysis of two experimental conditions to unveil the dynamics in post-transcriptional regulation of the RNA methylome. The exomePeak R-package accepts and statistically supports multiple biological replicates, internally removes PCR artifacts and multi-mapping reads, outputs exome-based binding sites (RNA methylation sites) and detects differential post-transcriptional RNA modification sites between two experimental conditions in term of percentage rather the absolute amount. The package is still under active development, and we welcome all biology and computation scientist for all kinds of collaborations and communications. Please feel free to contact Dr. Jia Meng if you have any questions.' diff --git a/recipes/bioconductor-faahko/meta.yaml b/recipes/bioconductor-faahko/meta.yaml new file mode 100644 index 00000000000000..ed4ed0abc83497 --- /dev/null +++ b/recipes/bioconductor-faahko/meta.yaml @@ -0,0 +1,34 @@ +{% set version = "1.18.0" %} +{% set name = "faahKO" %} +{% set bioc = "3.6" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + fn: '{{ name }}_{{ version }}.tar.gz' + url: + - 'http://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: 3097c03851eb054c4beec9ca0b655ffaf328839d6d012e3d2e1f590df6e18328 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ +requirements: + build: + - bioconductor-xcms + - r-base + run: + - bioconductor-xcms + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'http://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' + license: LGPL + summary: 'Positive ionization mode data in NetCDF file format. Centroided subset from 200-600 m/z and 2500-4500 seconds. Data originally reported in "Assignment of Endogenous Substrates to Enzymes by Global Metabolite Profiling" Biochemistry; 2004; 43(45). Also includes detected peaks in an xcmsSet.' diff --git a/recipes/bioconductor-faahko/post-link.sh b/recipes/bioconductor-faahko/post-link.sh new file mode 100644 index 00000000000000..7e6fa81bfebade --- /dev/null +++ b/recipes/bioconductor-faahko/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="faahKO_1.18.0.tar.gz" +URLS=( + "http://bioconductor.org/packages/3.6/data/experiment/src/contrib/faahKO_1.18.0.tar.gz" + "https://bioarchive.galaxyproject.org/faahKO_1.18.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-faahko/bioconductor-faahko_1.18.0_src_all.tar.gz" +) +MD5="9fe453baeee61b8b070704e8738174b8" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING \ No newline at end of file diff --git a/recipes/bioconductor-faahko/pre-unlink.sh b/recipes/bioconductor-faahko/pre-unlink.sh new file mode 100644 index 00000000000000..13056100ec98a1 --- /dev/null +++ b/recipes/bioconductor-faahko/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ faahKO diff --git a/recipes/bioconductor-fabia/build.sh b/recipes/bioconductor-fabia/build.sh new file mode 100644 index 00000000000000..26dbe349a5be94 --- /dev/null +++ b/recipes/bioconductor-fabia/build.sh @@ -0,0 +1,13 @@ +#!/bin/bash + +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION + +if [[ "$(uname)" == "Darwin" ]]; then + export CC=clang + export LDFLAGS="${LDFLAGS} -headerpad_max_install_names" + export LDFLAGS="${LDFLAGS} -Wl,-rpath,$PREFIX/lib" +fi +autoconf + +$R CMD INSTALL --build . || (echo "error code: $?" ; cat config.log ; exit 1) diff --git a/recipes/bioconductor-fabia/meta.yaml b/recipes/bioconductor-fabia/meta.yaml new file mode 100644 index 00000000000000..e7cbdffcb2538f --- /dev/null +++ b/recipes/bioconductor-fabia/meta.yaml @@ -0,0 +1,44 @@ +{% set version = "2.24.0" %} +{% set name = "fabia" %} +{% set bioc = "3.6" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' + +source: + fn: '{{ name }}_{{ version }}.tar.gz' + url: + - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' + sha256: 073c3529e4812745fb69dfca6b32c498d02be65b586fe7af17e7f1f6847593b0 + patches: + - non-destructive-compile-link-flags.patch + +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + +requirements: + build: + - autoconf + - bioconductor-biobase + - r-base + - gcc # [not osx] + - llvm # [osx] + run: + - bioconductor-biobase + - r-base + - libgcc # [not osx] + - libgfortran # [osx] + +test: + commands: + - '$R -e "library(''{{ name }}'')"' + +about: + home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: 'LGPL (>= 2.1)' + summary: 'Biclustering by "Factor Analysis for Bicluster Acquisition" (FABIA). FABIA is a model-based technique for biclustering, that is clustering rows and columns simultaneously. Biclusters are found by factor analysis where both the factors and the loading matrix are sparse. FABIA is a multiplicative model that extracts linear dependencies between samples and feature patterns. It captures realistic non-Gaussian data distributions with heavy tails as observed in gene expression measurements. FABIA utilizes well understood model selection techniques like the EM algorithm and variational approaches and is embedded into a Bayesian framework. FABIA ranks biclusters according to their information content and separates spurious biclusters from true biclusters. The code is written in C.' diff --git a/recipes/bioconductor-fabia/non-destructive-compile-link-flags.patch b/recipes/bioconductor-fabia/non-destructive-compile-link-flags.patch new file mode 100644 index 00000000000000..5c7761a737545f --- /dev/null +++ b/recipes/bioconductor-fabia/non-destructive-compile-link-flags.patch @@ -0,0 +1,13 @@ +--- configure.ac ++++ configure.ac +@@ -11,5 +11,5 @@ +-CC=`"${R_HOME}/bin/R" CMD config CC` +-CPP=`"${R_HOME}/bin/R" CMD config CPP` +-CFLAGS=`"${R_HOME}/bin/R" CMD config CFLAGS` +-CPPFLAGS=`"${R_HOME}/bin/R" CMD config CPPFLAGS` +-LDFLAGS=`"${R_HOME}/bin/R" CMD config LDFLAGS` ++CC=${CC-`"${R_HOME}/bin/R" CMD config CC`} ++CPP=${CPP-`"${R_HOME}/bin/R" CMD config CPP`} ++CFLAGS="${CFLAGS} `"${R_HOME}/bin/R" CMD config CFLAGS`" ++CPPFLAGS="${CPPFLAGS} `"${R_HOME}/bin/R" CMD config CPPFLAGS`" ++LDFLAGS="${LDFLAGS} `"${R_HOME}/bin/R" CMD config LDFLAGS`" diff --git a/recipes/bioconductor-ffpe/build.sh b/recipes/bioconductor-ffpe/build.sh new file mode 100644 index 00000000000000..da43ce21683122 --- /dev/null +++ b/recipes/bioconductor-ffpe/build.sh @@ -0,0 +1,4 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-ffpe/meta.yaml b/recipes/bioconductor-ffpe/meta.yaml new file mode 100644 index 00000000000000..6a090a0f8e93c3 --- /dev/null +++ b/recipes/bioconductor-ffpe/meta.yaml @@ -0,0 +1,52 @@ +{% set version = "1.22.0" %} +{% set name = "ffpe" %} +{% set bioc = "3.6" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' + +source: + fn: '{{ name }}_{{ version }}.tar.gz' + url: + - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + sha256: 0400831fc0451f4847ad511452ab4868b77264da0bbcdd5a36bf374f160f1430 + +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + +requirements: + build: + - bioconductor-affy + - bioconductor-biobase + - bioconductor-biocgenerics + - bioconductor-lumi + - bioconductor-methylumi + - r-base + - r-sfsmisc + - r-ttr + - gcc + run: + - bioconductor-affy + - bioconductor-biobase + - bioconductor-biocgenerics + - bioconductor-lumi + - bioconductor-methylumi + - r-base + - r-sfsmisc + - r-ttr + - libgcc + +test: + commands: + - '$R -e "library(''{{ name }}'')"' + +about: + home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: 'GPL (>2)' + summary: 'Identify low-quality data using metrics developed for expression data derived from Formalin-Fixed, Paraffin-Embedded (FFPE) data. Also a function for making Concordance at the Top plots (CAT-plots).' diff --git a/recipes/bioconductor-findmyfriends/build.sh b/recipes/bioconductor-findmyfriends/build.sh new file mode 100644 index 00000000000000..da43ce21683122 --- /dev/null +++ b/recipes/bioconductor-findmyfriends/build.sh @@ -0,0 +1,4 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-findmyfriends/meta.yaml b/recipes/bioconductor-findmyfriends/meta.yaml new file mode 100644 index 00000000000000..2315f1b78f771b --- /dev/null +++ b/recipes/bioconductor-findmyfriends/meta.yaml @@ -0,0 +1,68 @@ +{% set version = "1.8.0" %} +{% set name = "FindMyFriends" %} +{% set bioc = "3.6" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + fn: '{{ name }}_{{ version }}.tar.gz' + url: + - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: 66a8f49d01f2770d8d7417bb70bc4695f5cffe5d4ae0a95b76bd50626583c68d +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ +requirements: + build: + - bioconductor-biobase + - bioconductor-biocgenerics + - bioconductor-biocparallel + - bioconductor-biostrings + - bioconductor-iranges + - bioconductor-kebabs + - bioconductor-s4vectors + - r-base + - r-digest + - r-dplyr + - r-filehash + - r-ggdendro + - r-ggplot2 + - r-gtable + - r-igraph + - r-matrix + - r-rcpp + - r-reshape2 + - gcc # [linux] + - llvm # [osx] + run: + - bioconductor-biobase + - bioconductor-biocgenerics + - bioconductor-biocparallel + - bioconductor-biostrings + - bioconductor-iranges + - bioconductor-kebabs + - bioconductor-s4vectors + - r-base + - r-digest + - r-dplyr + - r-filehash + - r-ggdendro + - r-ggplot2 + - r-gtable + - r-igraph + - r-matrix + - r-rcpp + - r-reshape2 + - libcxx # [osx] +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: 'GPL (>=2)' + summary: 'A framework for doing microbial comparative genomics in R. The main purpose of the package is assisting in the creation of pangenome matrices where genes from related organisms are grouped by similarity, as well as the analysis of these data. FindMyFriends provides many novel approaches to doing pangenome analysis and supports a gene grouping algorithm that scales linearly, thus making the creation of huge pangenomes feasible.' diff --git a/recipes/bioconductor-flowmatch/build.sh b/recipes/bioconductor-flowmatch/build.sh new file mode 100644 index 00000000000000..da43ce21683122 --- /dev/null +++ b/recipes/bioconductor-flowmatch/build.sh @@ -0,0 +1,4 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-flowmatch/meta.yaml b/recipes/bioconductor-flowmatch/meta.yaml new file mode 100644 index 00000000000000..e61db9caa1fe60 --- /dev/null +++ b/recipes/bioconductor-flowmatch/meta.yaml @@ -0,0 +1,40 @@ +{% set version = "1.14.0" %} +{% set name = "flowMatch" %} +{% set bioc = "3.6" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + fn: '{{ name }}_{{ version }}.tar.gz' + url: + - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: c33a4fec14fc5069a6da5756991b3531623edcf6f08413c74e5b9019780a0774 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ +requirements: + build: + - bioconductor-biobase + - bioconductor-flowcore + - r-base + - 'r-rcpp >=0.11.0' + - gcc # [linux] + - llvm # [osx] + run: + - bioconductor-biobase + - bioconductor-flowcore + - r-base + - 'r-rcpp >=0.11.0' + - libcxx # [osx] +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Matching cell populations and building meta-clusters and templates from a collection of FC samples.' diff --git a/recipes/r-ggsignif/build.sh b/recipes/bioconductor-flowq/build.sh similarity index 98% rename from recipes/r-ggsignif/build.sh rename to recipes/bioconductor-flowq/build.sh index 32bc29aa163621..b58dbca4d229fe 100644 --- a/recipes/r-ggsignif/build.sh +++ b/recipes/bioconductor-flowq/build.sh @@ -1,6 +1,4 @@ #!/bin/bash - mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION - $R CMD INSTALL --build . diff --git a/recipes/bioconductor-flowq/meta.yaml b/recipes/bioconductor-flowq/meta.yaml new file mode 100644 index 00000000000000..439305b68fea98 --- /dev/null +++ b/recipes/bioconductor-flowq/meta.yaml @@ -0,0 +1,62 @@ +{% set version = "1.38.0" %} +{% set name = "flowQ" %} +{% set bioc = "3.6" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' + +source: + fn: '{{ name }}_{{ version }}.tar.gz' + url: + - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: edafded694551f5bd706ca99e61b69a5859fba0d026d0bb688a71f72ac3bacef + +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + +requirements: + build: + - bioconductor-biocgenerics + - bioconductor-biodist + - bioconductor-flowcore + - bioconductor-flowviz + - bioconductor-geneplotter + - bioconductor-iranges + - bioconductor-parody + - r-base + - r-lattice + - r-latticeextra + - r-mvoutlier + - r-outliers + - r-rcolorbrewer + - imagemagick + run: + - bioconductor-biocgenerics + - bioconductor-biodist + - bioconductor-flowcore + - bioconductor-flowviz + - bioconductor-geneplotter + - bioconductor-iranges + - bioconductor-parody + - r-base + - r-lattice + - r-latticeextra + - r-mvoutlier + - r-outliers + - r-rcolorbrewer + - imagemagick + +test: + commands: + - '$R -e "library(''{{ name }}'')"' + +about: + home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Provides quality control and quality assessment tools for flow cytometry data.' diff --git a/recipes/bioconductor-gaprediction/build.sh b/recipes/bioconductor-gaprediction/build.sh new file mode 100644 index 00000000000000..da43ce21683122 --- /dev/null +++ b/recipes/bioconductor-gaprediction/build.sh @@ -0,0 +1,4 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-gaprediction/meta.yaml b/recipes/bioconductor-gaprediction/meta.yaml new file mode 100644 index 00000000000000..00ed91aaed1bc8 --- /dev/null +++ b/recipes/bioconductor-gaprediction/meta.yaml @@ -0,0 +1,35 @@ +{% set version = "1.4.0" %} +{% set name = "GAprediction" %} +{% set bioc = "3.6" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + fn: '{{ name }}_{{ version }}.tar.gz' + url: + - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: 21954a61055d6264f87fa17a94e04f3da68b0cbd060618d997ff6e37a7b61382 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ +requirements: + build: + - r-base + - r-glmnet + - r-matrix + run: + - r-base + - r-glmnet + - r-matrix +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: 'GPL (>=2)' + summary: '[GAprediction] predicts gestational age using Illumina HumanMethylation450 CpG data.' diff --git a/recipes/bioconductor-gcatest/build.sh b/recipes/bioconductor-gcatest/build.sh new file mode 100644 index 00000000000000..da43ce21683122 --- /dev/null +++ b/recipes/bioconductor-gcatest/build.sh @@ -0,0 +1,4 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-gcatest/meta.yaml b/recipes/bioconductor-gcatest/meta.yaml new file mode 100644 index 00000000000000..825fcb26638a2b --- /dev/null +++ b/recipes/bioconductor-gcatest/meta.yaml @@ -0,0 +1,36 @@ +{% set version = "1.8.0" %} +{% set name = "gcatest" %} +{% set bioc = "3.6" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + fn: '{{ name }}_{{ version }}.tar.gz' + url: + - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + sha256: d65e011a9e04b585c0a05d714e572242763b6e1f418a80b6afd14647a4eaec6a +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ +requirements: + build: + - bioconductor-lfa + - r-base + - gcc # [linux] + - llvm # [osx] + run: + - bioconductor-lfa + - r-base + - libcxx # [osx] +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: GPL-3 + summary: 'GCAT is an association test for genome wide association studies that controls for population structure under a general class of trait. models.' diff --git a/recipes/bioconductor-generxcluster/build.sh b/recipes/bioconductor-generxcluster/build.sh new file mode 100644 index 00000000000000..da43ce21683122 --- /dev/null +++ b/recipes/bioconductor-generxcluster/build.sh @@ -0,0 +1,4 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-generxcluster/meta.yaml b/recipes/bioconductor-generxcluster/meta.yaml new file mode 100644 index 00000000000000..05fc204afe1fe0 --- /dev/null +++ b/recipes/bioconductor-generxcluster/meta.yaml @@ -0,0 +1,38 @@ +{% set version = "1.14.0" %} +{% set name = "geneRxCluster" %} +{% set bioc = "3.6" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + fn: '{{ name }}_{{ version }}.tar.gz' + url: + - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: f7497e687420ac412036ed4ec5064e0df497c1a76298832e6981e3141cb41464 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ +requirements: + build: + - bioconductor-genomicranges + - bioconductor-iranges + - r-base + - gcc # [linux] + - llvm # [osx] + run: + - bioconductor-genomicranges + - bioconductor-iranges + - r-base + - libcxx # [osx] +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: 'GPL (>= 2)' + summary: 'Detect Differential Clustering of Genomic Sites such as gene therapy integrations. The package provides some functions for exploring genomic insertion sites originating from two different sources. Possibly, the two sources are two different gene therapy vectors. Vectors are preferred that target sensitive regions less frequently, motivating the search for localized clusters of insertions and comparison of the clusters formed by integration of different vectors. Scan statistics allow the discovery of spatial differences in clustering and calculation of False Discovery Rates (FDRs) providing statistical methods for comparing retroviral vectors. A scan statistic for comparing two vectors using multiple window widths to detect clustering differentials and compute FDRs is implemented here.' diff --git a/recipes/bioconductor-geneselector/build.sh b/recipes/bioconductor-geneselector/build.sh new file mode 100644 index 00000000000000..da43ce21683122 --- /dev/null +++ b/recipes/bioconductor-geneselector/build.sh @@ -0,0 +1,4 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-geneselector/meta.yaml b/recipes/bioconductor-geneselector/meta.yaml new file mode 100644 index 00000000000000..84e84a1569a5db --- /dev/null +++ b/recipes/bioconductor-geneselector/meta.yaml @@ -0,0 +1,44 @@ +{% set version = "2.28.0" %} +{% set name = "GeneSelector" %} +{% set bioc = "3.6" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + fn: '{{ name }}_{{ version }}.tar.gz' + url: + - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: 3a292ef0236ad9004a98636379ce85636d8a325a148158dfd3836bfeac168139 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ +requirements: + build: + - bioconductor-biobase + - bioconductor-limma + - bioconductor-multtest + - bioconductor-siggenes + - r-base + - r-samr + - gcc # [linux] + - llvm # [osx] + run: + - bioconductor-biobase + - bioconductor-limma + - bioconductor-multtest + - bioconductor-siggenes + - r-base + - r-samr + - libcxx # [osx] +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: 'GPL (>= 2)' + summary: 'The term ''GeneSelector'' refers to a filter selecting those genes which are consistently identified as differentially expressed using various statistical procedures. ''Selected'' genes are those present at the top of the list in various ranking methods (currently 14). In addition, the stability of the findings can be taken into account in the final ranking by examining perturbed versions of the original data set, e.g. by leaving samples, swapping class labels, generating bootstrap replicates or adding noise. Given multiple ranked lists, one can use aggregation methods in order to find a synthesis.' diff --git a/recipes/bioconductor-genetclassifier/build.sh b/recipes/bioconductor-genetclassifier/build.sh new file mode 100644 index 00000000000000..da43ce21683122 --- /dev/null +++ b/recipes/bioconductor-genetclassifier/build.sh @@ -0,0 +1,4 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-genetclassifier/meta.yaml b/recipes/bioconductor-genetclassifier/meta.yaml new file mode 100644 index 00000000000000..90e97b01d79acc --- /dev/null +++ b/recipes/bioconductor-genetclassifier/meta.yaml @@ -0,0 +1,39 @@ +{% set version = "1.18.0" %} +{% set name = "geNetClassifier" %} +{% set bioc = "3.6" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + fn: '{{ name }}_{{ version }}.tar.gz' + url: + - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: 88384956517f1c6e638eabb5a576709493c7eff16344ecbe1217cfcd96cc1b93 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ +requirements: + build: + - 'bioconductor-biobase >=2.5.5' + - bioconductor-ebarrays + - bioconductor-minet + - r-base + - r-e1071 + run: + - 'bioconductor-biobase >=2.5.5' + - bioconductor-ebarrays + - bioconductor-minet + - r-base + - r-e1071 +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: 'GPL (>= 2)' + summary: 'Comprehensive package to automatically train and validate a multi-class SVM classifier based on gene expression data. Provides transparent selection of gene markers, their coexpression networks, and an interface to query the classifier.' diff --git a/recipes/bioconductor-geneticsdesign/build.sh b/recipes/bioconductor-geneticsdesign/build.sh new file mode 100644 index 00000000000000..da43ce21683122 --- /dev/null +++ b/recipes/bioconductor-geneticsdesign/build.sh @@ -0,0 +1,4 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-geneticsdesign/meta.yaml b/recipes/bioconductor-geneticsdesign/meta.yaml new file mode 100644 index 00000000000000..2e67c6a39f39ba --- /dev/null +++ b/recipes/bioconductor-geneticsdesign/meta.yaml @@ -0,0 +1,37 @@ +{% set version = "1.46.0" %} +{% set name = "GeneticsDesign" %} +{% set bioc = "3.6" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + fn: '{{ name }}_{{ version }}.tar.gz' + url: + - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: 16d14fc331ee2c55b67e278c4c59a72c7a1adf4728040bb5e837c9d0b7e79a9c +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ +requirements: + build: + - r-base + - r-gmodels + - 'r-gtools >=2.4.0' + - r-mvtnorm + run: + - r-base + - r-gmodels + - 'r-gtools >=2.4.0' + - r-mvtnorm +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: GPL-2 + summary: 'This package contains functions useful for designing genetics studies, including power and sample-size calculations.' diff --git a/recipes/bioconductor-genogam/build.sh b/recipes/bioconductor-genogam/build.sh new file mode 100644 index 00000000000000..da43ce21683122 --- /dev/null +++ b/recipes/bioconductor-genogam/build.sh @@ -0,0 +1,4 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-genogam/meta.yaml b/recipes/bioconductor-genogam/meta.yaml new file mode 100644 index 00000000000000..8f81e46f2bcbe2 --- /dev/null +++ b/recipes/bioconductor-genogam/meta.yaml @@ -0,0 +1,59 @@ +{% set version = "1.6.0" %} +{% set name = "GenoGAM" %} +{% set bioc = "3.6" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + fn: '{{ name }}_{{ version }}.tar.gz' + url: + - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: 031ae9656882d0525ada94f7f6f48185d504e56a10c761e2b0ef6665e3556ab7 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ +requirements: + build: + - 'bioconductor-biocparallel >=1.5.17' + - 'bioconductor-biostrings >=2.39.14' + - 'bioconductor-deseq2 >=1.11.23' + - 'bioconductor-genomeinfodb >=1.7.6' + - 'bioconductor-genomicalignments >=1.7.17' + - 'bioconductor-genomicranges >=1.29.14' + - 'bioconductor-iranges >=2.11.16' + - 'bioconductor-rsamtools >=1.18.2' + - 'bioconductor-s4vectors >=0.9.34' + - 'bioconductor-summarizedexperiment >=1.1.19' + - r-base + - 'r-data.table >=1.9.4' + - 'r-futile.logger >=1.4.1' + - 'r-mgcv >=1.8' + - 'r-reshape2 >=1.4.1' + run: + - 'bioconductor-biocparallel >=1.5.17' + - 'bioconductor-biostrings >=2.39.14' + - 'bioconductor-deseq2 >=1.11.23' + - 'bioconductor-genomeinfodb >=1.7.6' + - 'bioconductor-genomicalignments >=1.7.17' + - 'bioconductor-genomicranges >=1.29.14' + - 'bioconductor-iranges >=2.11.16' + - 'bioconductor-rsamtools >=1.18.2' + - 'bioconductor-s4vectors >=0.9.34' + - 'bioconductor-summarizedexperiment >=1.1.19' + - r-base + - 'r-data.table >=1.9.4' + - 'r-futile.logger >=1.4.1' + - 'r-mgcv >=1.8' + - 'r-reshape2 >=1.4.1' +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: GPL-2 + summary: 'This package allows statistical analysis of genome-wide data with smooth functions using generalized additive models based on the implementation from the R-package ''mgcv''. It provides methods for the statistical analysis of ChIP-Seq data including inference of protein occupancy, and pointwise and region-wise differential analysis. Estimation of dispersion and smoothing parameters is performed by cross-validation. Scaling of generalized additive model fitting to whole chromosomes is achieved by parallelization over overlapping genomic intervals.' diff --git a/recipes/bioconductor-genrank/build.sh b/recipes/bioconductor-genrank/build.sh new file mode 100644 index 00000000000000..da43ce21683122 --- /dev/null +++ b/recipes/bioconductor-genrank/build.sh @@ -0,0 +1,4 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-genrank/meta.yaml b/recipes/bioconductor-genrank/meta.yaml new file mode 100644 index 00000000000000..bca29d01b1c6cb --- /dev/null +++ b/recipes/bioconductor-genrank/meta.yaml @@ -0,0 +1,37 @@ +{% set version = "1.6.0" %} +{% set name = "GenRank" %} +{% set bioc = "3.6" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + fn: '{{ name }}_{{ version }}.tar.gz' + url: + - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: 9faf025ae5802305165115f117a110b2d77ac0ad4cc8254437a45d3bf110331c +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ +requirements: + build: + - bioconductor-survcomp + - r-base + - r-matrixstats + - r-reshape2 + run: + - bioconductor-survcomp + - r-base + - r-matrixstats + - r-reshape2 +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Methods for ranking genes based on convergent evidence obtained from multiple independent evidence layers. This package adapts three methods that are popular for meta-analysis.' diff --git a/recipes/bioconductor-geosubmission/build.sh b/recipes/bioconductor-geosubmission/build.sh new file mode 100644 index 00000000000000..da43ce21683122 --- /dev/null +++ b/recipes/bioconductor-geosubmission/build.sh @@ -0,0 +1,4 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-geosubmission/meta.yaml b/recipes/bioconductor-geosubmission/meta.yaml new file mode 100644 index 00000000000000..2cea3752480f1d --- /dev/null +++ b/recipes/bioconductor-geosubmission/meta.yaml @@ -0,0 +1,35 @@ +{% set version = "1.30.0" %} +{% set name = "GEOsubmission" %} +{% set bioc = "3.6" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + fn: '{{ name }}_{{ version }}.tar.gz' + url: + - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: e8a640fe21bbf931bf652d4aae532b46872dc4b01e140b1dbb9fc933e9a9896a +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ +requirements: + build: + - bioconductor-affy + - bioconductor-biobase + - r-base + run: + - bioconductor-affy + - bioconductor-biobase + - r-base +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: 'GPL (>= 2)' + summary: 'Helps to easily submit a microarray dataset and the associated sample information to GEO by preparing a single file for upload (direct deposit).' diff --git a/recipes/bioconductor-golubesets/meta.yaml b/recipes/bioconductor-golubesets/meta.yaml new file mode 100644 index 00000000000000..c99867c9932a10 --- /dev/null +++ b/recipes/bioconductor-golubesets/meta.yaml @@ -0,0 +1,34 @@ +{% set version = "1.20.0" %} +{% set name = "golubEsets" %} +{% set bioc = "3.6" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + fn: '{{ name }}_{{ version }}.tar.gz' + url: + - 'http://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: e533ab15f3f28722dcc62a7105caa76fcc63617daa925c9a6d2dd11ad8a35e7f +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ +requirements: + build: + - 'bioconductor-biobase >=2.5.5' + - r-base + run: + - 'bioconductor-biobase >=2.5.5' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'http://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' + license: LGPL + summary: 'representation of public golub data with some covariate data of provenance unknown to the maintainer at present; now employs ExpressionSet format' diff --git a/recipes/bioconductor-golubesets/post-link.sh b/recipes/bioconductor-golubesets/post-link.sh new file mode 100644 index 00000000000000..6a112d488d76d3 --- /dev/null +++ b/recipes/bioconductor-golubesets/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="golubEsets_1.20.0.tar.gz" +URLS=( + "http://bioconductor.org/packages/3.6/data/experiment/src/contrib/golubEsets_1.20.0.tar.gz" + "https://bioarchive.galaxyproject.org/golubEsets_1.20.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-golubesets/bioconductor-golubesets_1.20.0_src_all.tar.gz" +) +MD5="318b22688927ad8baa67775e6b77b0c1" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING \ No newline at end of file diff --git a/recipes/bioconductor-golubesets/pre-unlink.sh b/recipes/bioconductor-golubesets/pre-unlink.sh new file mode 100644 index 00000000000000..b14e4802fd4039 --- /dev/null +++ b/recipes/bioconductor-golubesets/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ golubEsets diff --git a/recipes/bioconductor-gotools/build.sh b/recipes/bioconductor-gotools/build.sh new file mode 100644 index 00000000000000..da43ce21683122 --- /dev/null +++ b/recipes/bioconductor-gotools/build.sh @@ -0,0 +1,4 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-gotools/meta.yaml b/recipes/bioconductor-gotools/meta.yaml new file mode 100644 index 00000000000000..8279bc8fe8a934 --- /dev/null +++ b/recipes/bioconductor-gotools/meta.yaml @@ -0,0 +1,35 @@ +{% set version = "1.52.0" %} +{% set name = "goTools" %} +{% set bioc = "3.6" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + fn: '{{ name }}_{{ version }}.tar.gz' + url: + - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: 59cc09b98200c2c0185453a9df3737bda396254b009ca31f57989f790d108a1f +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ +requirements: + build: + - bioconductor-annotationdbi + - bioconductor-go.db + - r-base + run: + - bioconductor-annotationdbi + - bioconductor-go.db + - r-base +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: GPL-2 + summary: 'Wraper functions for description/comparison of oligo ID list using Gene Ontology database' diff --git a/recipes/bioconductor-gpls/build.sh b/recipes/bioconductor-gpls/build.sh new file mode 100644 index 00000000000000..da43ce21683122 --- /dev/null +++ b/recipes/bioconductor-gpls/build.sh @@ -0,0 +1,4 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-gpls/meta.yaml b/recipes/bioconductor-gpls/meta.yaml new file mode 100644 index 00000000000000..5e2c06f3130dbd --- /dev/null +++ b/recipes/bioconductor-gpls/meta.yaml @@ -0,0 +1,31 @@ +{% set version = "1.50.0" %} +{% set name = "gpls" %} +{% set bioc = "3.6" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + fn: '{{ name }}_{{ version }}.tar.gz' + url: + - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + sha256: 6f5442b8922a4b411f931e73b11429f4f996034804637fc61bef753ed061e36a +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ +requirements: + build: + - r-base + run: + - r-base +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Classification using generalized partial least squares for two-group and multi-group (more than 2 group) classification.' diff --git a/recipes/bioconductor-graphat/build.sh b/recipes/bioconductor-graphat/build.sh new file mode 100644 index 00000000000000..da43ce21683122 --- /dev/null +++ b/recipes/bioconductor-graphat/build.sh @@ -0,0 +1,4 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-graphat/meta.yaml b/recipes/bioconductor-graphat/meta.yaml new file mode 100644 index 00000000000000..c86a4317233508 --- /dev/null +++ b/recipes/bioconductor-graphat/meta.yaml @@ -0,0 +1,35 @@ +{% set version = "1.50.0" %} +{% set name = "GraphAT" %} +{% set bioc = "3.6" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + fn: '{{ name }}_{{ version }}.tar.gz' + url: + - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: d97e35562cd3e9f1c7c65cef91368dc68dfc3ab73fcdff239ae181495af82c43 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ +requirements: + build: + - bioconductor-graph + - r-base + - r-mcmcpack + run: + - bioconductor-graph + - r-base + - r-mcmcpack +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: LGPL + summary: 'Functions and data used in Balasubramanian, et al. (2004)' diff --git a/recipes/bioconductor-graphpac/build.sh b/recipes/bioconductor-graphpac/build.sh new file mode 100644 index 00000000000000..da43ce21683122 --- /dev/null +++ b/recipes/bioconductor-graphpac/build.sh @@ -0,0 +1,4 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-graphpac/meta.yaml b/recipes/bioconductor-graphpac/meta.yaml new file mode 100644 index 00000000000000..b0a2e923834747 --- /dev/null +++ b/recipes/bioconductor-graphpac/meta.yaml @@ -0,0 +1,39 @@ +{% set version = "1.20.0" %} +{% set name = "GraphPAC" %} +{% set bioc = "3.6" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + fn: '{{ name }}_{{ version }}.tar.gz' + url: + - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: eda3df7b7cf3917ff242655cda24e6433095e09af83dfe0aae6a8146c231193c +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ +requirements: + build: + - bioconductor-ipac + - r-base + - r-igraph + - r-rmallow + - r-tsp + run: + - bioconductor-ipac + - r-base + - r-igraph + - r-rmallow + - r-tsp +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: GPL-2 + summary: 'Identifies mutational clusters of amino acids in a protein while utilizing the proteins tertiary structure via a graph theoretical model.' diff --git a/recipes/bioconductor-grmetrics/build.sh b/recipes/bioconductor-grmetrics/build.sh new file mode 100644 index 00000000000000..da43ce21683122 --- /dev/null +++ b/recipes/bioconductor-grmetrics/build.sh @@ -0,0 +1,4 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-grmetrics/meta.yaml b/recipes/bioconductor-grmetrics/meta.yaml new file mode 100644 index 00000000000000..30445f512d5f1c --- /dev/null +++ b/recipes/bioconductor-grmetrics/meta.yaml @@ -0,0 +1,41 @@ +{% set version = "1.4.1" %} +{% set name = "GRmetrics" %} +{% set bioc = "3.6" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + fn: '{{ name }}_{{ version }}.tar.gz' + url: + - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: 6f80e19b7cbe10c698393e90e79bcf39647f22d04ee9b2c5bbf1c7adc2e22e86 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ +requirements: + build: + - bioconductor-s4vectors + - bioconductor-summarizedexperiment + - r-base + - r-drc + - r-ggplot2 + - r-plotly + run: + - bioconductor-s4vectors + - bioconductor-summarizedexperiment + - r-base + - r-drc + - r-ggplot2 + - r-plotly +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: GPL-3 + summary: 'Functions for calculating and visualizing growth-rate inhibition (GR) metrics.' diff --git a/recipes/bioconductor-gsalightning/build.sh b/recipes/bioconductor-gsalightning/build.sh new file mode 100644 index 00000000000000..da43ce21683122 --- /dev/null +++ b/recipes/bioconductor-gsalightning/build.sh @@ -0,0 +1,4 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-gsalightning/meta.yaml b/recipes/bioconductor-gsalightning/meta.yaml new file mode 100644 index 00000000000000..67b0e91b6d8b50 --- /dev/null +++ b/recipes/bioconductor-gsalightning/meta.yaml @@ -0,0 +1,35 @@ +{% set version = "1.6.0" %} +{% set name = "GSALightning" %} +{% set bioc = "3.6" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + fn: '{{ name }}_{{ version }}.tar.gz' + url: + - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: 5dd38e6dcef36728fc7fb7ea4c100b95d56ba97cf706f4b74f906a0755612dd9 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ +requirements: + build: + - r-base + - r-data.table + - r-matrix + run: + - r-base + - r-data.table + - r-matrix +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: 'GPL (>=2)' + summary: 'GSALightning provides a fast implementation of permutation-based gene set analysis for two-sample problem. This package is particularly useful when testing simultaneously a large number of gene sets, or when a large number of permutations is necessary for more accurate p-values estimation.' diff --git a/recipes/bioconductor-gsca/build.sh b/recipes/bioconductor-gsca/build.sh new file mode 100644 index 00000000000000..da43ce21683122 --- /dev/null +++ b/recipes/bioconductor-gsca/build.sh @@ -0,0 +1,4 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-gsca/meta.yaml b/recipes/bioconductor-gsca/meta.yaml new file mode 100644 index 00000000000000..f725f7d98d843a --- /dev/null +++ b/recipes/bioconductor-gsca/meta.yaml @@ -0,0 +1,45 @@ +{% set version = "2.8.0" %} +{% set name = "GSCA" %} +{% set bioc = "3.6" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + fn: '{{ name }}_{{ version }}.tar.gz' + url: + - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: d13fe52313daf563f250c0f7f02f06a19ed7a6be70f28f686321b920f36e33e5 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ +requirements: + build: + - bioconductor-rhdf5 + - r-base + - r-ggplot2 + - r-gplots + - r-rcolorbrewer + - r-reshape2 + - r-shiny + - r-sp + run: + - bioconductor-rhdf5 + - r-base + - r-ggplot2 + - r-gplots + - r-rcolorbrewer + - r-reshape2 + - r-shiny + - r-sp +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: GPL(>=2) + summary: 'GSCA takes as input several lists of activated and repressed genes. GSCA then searches through a compendium of publicly available gene expression profiles for biological contexts that are enriched with a specified pattern of gene expression. GSCA provides both traditional R functions and interactive, user-friendly user interface.' diff --git a/recipes/bioconductor-gsealm/build.sh b/recipes/bioconductor-gsealm/build.sh new file mode 100644 index 00000000000000..da43ce21683122 --- /dev/null +++ b/recipes/bioconductor-gsealm/build.sh @@ -0,0 +1,4 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-gsealm/meta.yaml b/recipes/bioconductor-gsealm/meta.yaml new file mode 100644 index 00000000000000..b72889dec8741f --- /dev/null +++ b/recipes/bioconductor-gsealm/meta.yaml @@ -0,0 +1,33 @@ +{% set version = "1.38.0" %} +{% set name = "GSEAlm" %} +{% set bioc = "3.6" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + fn: '{{ name }}_{{ version }}.tar.gz' + url: + - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: bf7f96d77e3f519823d03145e450ac622f3c239a9af210c327233ec6d63ae2cf +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ +requirements: + build: + - bioconductor-biobase + - r-base + run: + - bioconductor-biobase + - r-base +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Models and methods for fitting linear models to gene expression data, together with tools for computing and using various regression diagnostics.' diff --git a/recipes/bioconductor-gsreg/build.sh b/recipes/bioconductor-gsreg/build.sh new file mode 100644 index 00000000000000..da43ce21683122 --- /dev/null +++ b/recipes/bioconductor-gsreg/build.sh @@ -0,0 +1,4 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-gsreg/meta.yaml b/recipes/bioconductor-gsreg/meta.yaml new file mode 100644 index 00000000000000..a82b3205724803 --- /dev/null +++ b/recipes/bioconductor-gsreg/meta.yaml @@ -0,0 +1,42 @@ +{% set version = "1.12.0" %} +{% set name = "GSReg" %} +{% set bioc = "3.6" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + fn: '{{ name }}_{{ version }}.tar.gz' + url: + - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: c6034b862751f5fce5669f121dcddbd7e427b5bee3e7dd9a839a0437cd9ebfe5 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ +requirements: + build: + - bioconductor-annotationdbi + - bioconductor-genomicfeatures + - bioconductor-homo.sapiens + - bioconductor-org.hs.eg.db + - r-base + - gcc # [linux] + - llvm # [osx] + run: + - bioconductor-annotationdbi + - bioconductor-genomicfeatures + - bioconductor-homo.sapiens + - bioconductor-org.hs.eg.db + - r-base + - libcxx # [osx] +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: GPL-2 + summary: 'A package for gene set analysis based on the variability of expressions as well as a method to detect Alternative Splicing Events . It implements DIfferential RAnk Conservation (DIRAC) and gene set Expression Variation Analysis (EVA) methods. For detecting Differentially Spliced genes, it provides an implementation of the Spliced-EVA (SEVA).' diff --git a/recipes/bioconductor-gsri/build.sh b/recipes/bioconductor-gsri/build.sh new file mode 100644 index 00000000000000..da43ce21683122 --- /dev/null +++ b/recipes/bioconductor-gsri/build.sh @@ -0,0 +1,4 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-gsri/meta.yaml b/recipes/bioconductor-gsri/meta.yaml new file mode 100644 index 00000000000000..dd8e5c8b1e5bb3 --- /dev/null +++ b/recipes/bioconductor-gsri/meta.yaml @@ -0,0 +1,41 @@ +{% set version = "2.26.0" %} +{% set name = "GSRI" %} +{% set bioc = "3.6" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + fn: '{{ name }}_{{ version }}.tar.gz' + url: + - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: 5a12d448b6a939c9ba90772911f8f13fab12763c4ceff3008976e4631ca3518b +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ +requirements: + build: + - bioconductor-biobase + - bioconductor-genefilter + - bioconductor-gseabase + - 'bioconductor-les >=1.1.6' + - r-base + - r-fdrtool + run: + - bioconductor-biobase + - bioconductor-genefilter + - bioconductor-gseabase + - 'bioconductor-les >=1.1.6' + - r-base + - r-fdrtool +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: GPL-3 + summary: 'The GSRI package estimates the number of differentially expressed genes in gene sets, utilizing the concept of the Gene Set Regulation Index (GSRI).' diff --git a/recipes/bioconductor-guideseq/build.sh b/recipes/bioconductor-guideseq/build.sh new file mode 100644 index 00000000000000..da43ce21683122 --- /dev/null +++ b/recipes/bioconductor-guideseq/build.sh @@ -0,0 +1,4 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-guideseq/meta.yaml b/recipes/bioconductor-guideseq/meta.yaml new file mode 100644 index 00000000000000..4de54e5e2a45f8 --- /dev/null +++ b/recipes/bioconductor-guideseq/meta.yaml @@ -0,0 +1,63 @@ +{% set version = "1.8.0" %} +{% set name = "GUIDEseq" %} +{% set bioc = "3.6" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + fn: '{{ name }}_{{ version }}.tar.gz' + url: + - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: f8336a97486f5bcde8a743caeca617090a89961b2ee6f0dbd55c4583ebf852f7 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ +requirements: + build: + - bioconductor-biocgenerics + - bioconductor-biocparallel + - bioconductor-biostrings + - bioconductor-bsgenome + - bioconductor-chippeakanno + - bioconductor-crisprseek + - bioconductor-genomeinfodb + - 'bioconductor-genomicalignments >=1.7.3' + - bioconductor-genomicranges + - 'bioconductor-iranges >=2.5.5' + - bioconductor-limma + - bioconductor-rsamtools + - 'bioconductor-s4vectors >=0.9.6' + - r-base + - r-data.table + - r-hash + - r-matrixstats + run: + - bioconductor-biocgenerics + - bioconductor-biocparallel + - bioconductor-biostrings + - bioconductor-bsgenome + - bioconductor-chippeakanno + - bioconductor-crisprseek + - bioconductor-genomeinfodb + - 'bioconductor-genomicalignments >=1.7.3' + - bioconductor-genomicranges + - 'bioconductor-iranges >=2.5.5' + - bioconductor-limma + - bioconductor-rsamtools + - 'bioconductor-s4vectors >=0.9.6' + - r-base + - r-data.table + - r-hash + - r-matrixstats +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: 'GPL (>= 2)' + summary: 'The package implements GUIDE-seq analysis workflow including functions for obtaining unique insertion sites (proxy of cleavage sites), estimating the locations of the insertion sites, aka, peaks, merging estimated insertion sites from plus and minus strand, and performing off target search of the extended regions around insertion sites.' diff --git a/recipes/bioconductor-hapfabia/build.sh b/recipes/bioconductor-hapfabia/build.sh new file mode 100644 index 00000000000000..da43ce21683122 --- /dev/null +++ b/recipes/bioconductor-hapfabia/build.sh @@ -0,0 +1,4 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-hapfabia/meta.yaml b/recipes/bioconductor-hapfabia/meta.yaml new file mode 100644 index 00000000000000..4c5b5c65d94627 --- /dev/null +++ b/recipes/bioconductor-hapfabia/meta.yaml @@ -0,0 +1,42 @@ +{% set version = "1.20.0" %} +{% set name = "hapFabia" %} +{% set bioc = "3.6" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' + +source: + fn: '{{ name }}_{{ version }}.tar.gz' + url: + - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: b01e0ce9645f2cb5891106f362ecc9e1be53d6461907cde1df4f613d6015cc56 + +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + +requirements: + build: + - bioconductor-biobase + - 'bioconductor-fabia >=2.3.1' + - r-base + - gcc # [linux] + - llvm # [osx] + run: + - bioconductor-biobase + - 'bioconductor-fabia >=2.3.1' + - r-base + +test: + commands: + - '$R -e "library(''{{ name }}'')"' + +about: + home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: 'LGPL (>= 2.1)' + summary: 'A package to identify very short IBD segments in large sequencing data by FABIA biclustering. Two haplotypes are identical by descent (IBD) if they share a segment that both inherited from a common ancestor. Current IBD methods reliably detect long IBD segments because many minor alleles in the segment are concordant between the two haplotypes. However, many cohort studies contain unrelated individuals which share only short IBD segments. This package provides software to identify short IBD segments in sequencing data. Knowledge of short IBD segments are relevant for phasing of genotyping data, association studies, and for population genetics, where they shed light on the evolutionary history of humans. The package supports VCF formats, is based on sparse matrix operations, and provides visualization of haplotype clusters in different formats.' diff --git a/recipes/bioconductor-harman/build.sh b/recipes/bioconductor-harman/build.sh new file mode 100644 index 00000000000000..da43ce21683122 --- /dev/null +++ b/recipes/bioconductor-harman/build.sh @@ -0,0 +1,4 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-harman/meta.yaml b/recipes/bioconductor-harman/meta.yaml new file mode 100644 index 00000000000000..f77b6937c28e8e --- /dev/null +++ b/recipes/bioconductor-harman/meta.yaml @@ -0,0 +1,36 @@ +{% set version = "1.6.0" %} +{% set name = "Harman" %} +{% set bioc = "3.6" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + fn: '{{ name }}_{{ version }}.tar.gz' + url: + - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: d8bcc35b9aed9b05213f9e835ed6b544f563525f9a010b842cd3badd689f439f +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ +requirements: + build: + - r-base + - 'r-rcpp >=0.11.2' + - gcc # [linux] + - llvm # [osx] + run: + - r-base + - 'r-rcpp >=0.11.2' + - libcxx # [osx] +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: 'GPL-3 + file LICENCE' + summary: 'Harman is a PCA and constrained optimisation based technique that maximises the removal of batch effects from datasets, with the constraint that the probability of overcorrection (i.e. removing genuine biological signal along with batch noise) is kept to a fraction which is set by the end-user.' diff --git a/recipes/bioconductor-harshlight/build.sh b/recipes/bioconductor-harshlight/build.sh new file mode 100644 index 00000000000000..da43ce21683122 --- /dev/null +++ b/recipes/bioconductor-harshlight/build.sh @@ -0,0 +1,4 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-harshlight/meta.yaml b/recipes/bioconductor-harshlight/meta.yaml new file mode 100644 index 00000000000000..4bfa3ed6bf0c9a --- /dev/null +++ b/recipes/bioconductor-harshlight/meta.yaml @@ -0,0 +1,40 @@ +{% set version = "1.50.0" %} +{% set name = "Harshlight" %} +{% set bioc = "3.6" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + fn: '{{ name }}_{{ version }}.tar.gz' + url: + - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: c0a85d943b7ea1108db93fda3dfd708279a7abd3a77a003dd0039af55a229449 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ +requirements: + build: + - bioconductor-affy + - bioconductor-altcdfenvs + - bioconductor-biobase + - r-base + - gcc # [linux] + - llvm # [osx] + run: + - bioconductor-affy + - bioconductor-altcdfenvs + - bioconductor-biobase + - r-base + - libcxx # [osx] +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: 'GPL (>= 2)' + summary: 'The package is used to detect extended, diffuse and compact blemishes on microarray chips. Harshlight automatically marks the areas in a collection of chips (affybatch objects) and a corrected AffyBatch object is returned, in which the defected areas are substituted with NAs or the median of the values of the same probe in the other chips in the collection. The new version handle the substitute value as whole matrix to solve the memory problem.' diff --git a/recipes/bioconductor-help/build.sh b/recipes/bioconductor-help/build.sh new file mode 100644 index 00000000000000..da43ce21683122 --- /dev/null +++ b/recipes/bioconductor-help/build.sh @@ -0,0 +1,4 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-help/meta.yaml b/recipes/bioconductor-help/meta.yaml new file mode 100644 index 00000000000000..a94cb40b098683 --- /dev/null +++ b/recipes/bioconductor-help/meta.yaml @@ -0,0 +1,33 @@ +{% set version = "1.36.0" %} +{% set name = "HELP" %} +{% set bioc = "3.6" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + fn: '{{ name }}_{{ version }}.tar.gz' + url: + - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: 0c5a6ec4edc05ee0db003c435f7a6353f518ed130ffd0713794698e82ebf2608 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ +requirements: + build: + - bioconductor-biobase + - r-base + run: + - bioconductor-biobase + - r-base +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: 'GPL (>= 2)' + summary: 'The package contains a modular pipeline for analysis of HELP microarray data, and includes graphical and mathematical tools with more general applications.' diff --git a/recipes/bioconductor-hem/build.sh b/recipes/bioconductor-hem/build.sh new file mode 100644 index 00000000000000..da43ce21683122 --- /dev/null +++ b/recipes/bioconductor-hem/build.sh @@ -0,0 +1,4 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-hem/meta.yaml b/recipes/bioconductor-hem/meta.yaml new file mode 100644 index 00000000000000..b886be549c1b5d --- /dev/null +++ b/recipes/bioconductor-hem/meta.yaml @@ -0,0 +1,36 @@ +{% set version = "1.50.0" %} +{% set name = "HEM" %} +{% set bioc = "3.6" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + fn: '{{ name }}_{{ version }}.tar.gz' + url: + - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: 87c676b2fa9bd2d3fdc7debcb56ffef4aaea79c60df5468d6ca7e26f4835e682 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ +requirements: + build: + - bioconductor-biobase + - r-base + - gcc # [linux] + - llvm # [osx] + run: + - bioconductor-biobase + - r-base + - libcxx # [osx] +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: 'GPL (>= 2)' + summary: 'This package fits heterogeneous error models for analysis of microarray data' diff --git a/recipes/bioconductor-hgu133a2.db/meta.yaml b/recipes/bioconductor-hgu133a2.db/meta.yaml new file mode 100644 index 00000000000000..c3231a3831ae18 --- /dev/null +++ b/recipes/bioconductor-hgu133a2.db/meta.yaml @@ -0,0 +1,36 @@ +{% set version = "3.2.3" %} +{% set name = "hgu133a2.db" %} +{% set bioc = "3.6" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + fn: '{{ name }}_{{ version }}.tar.gz' + url: + - 'http://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + sha256: 687e3bcc499440778a7482599d1f0dad48ff8222737b0a22dcb32757921490eb +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ +requirements: + build: + - 'bioconductor-annotationdbi >=1.34.3' + - 'bioconductor-org.hs.eg.db >=3.3.0' + - r-base + run: + - 'bioconductor-annotationdbi >=1.34.3' + - 'bioconductor-org.hs.eg.db >=3.3.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'http://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Affymetrix Human Genome U133A 2.0 Array annotation data (chip hgu133a2) assembled using data from public repositories' diff --git a/recipes/bioconductor-hgu133a2.db/post-link.sh b/recipes/bioconductor-hgu133a2.db/post-link.sh new file mode 100644 index 00000000000000..eca43ab44d4a2e --- /dev/null +++ b/recipes/bioconductor-hgu133a2.db/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="hgu133a2.db_3.2.3.tar.gz" +URLS=( + "http://bioconductor.org/packages/3.6/data/annotation/src/contrib/hgu133a2.db_3.2.3.tar.gz" + "https://bioarchive.galaxyproject.org/hgu133a2.db_3.2.3.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-hgu133a2.db/bioconductor-hgu133a2.db_3.2.3_src_all.tar.gz" +) +MD5="15cad9bc3f5ef6fca5300638a9c8bb86" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING \ No newline at end of file diff --git a/recipes/bioconductor-hgu133a2.db/pre-unlink.sh b/recipes/bioconductor-hgu133a2.db/pre-unlink.sh new file mode 100644 index 00000000000000..2e987603412514 --- /dev/null +++ b/recipes/bioconductor-hgu133a2.db/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ hgu133a2.db diff --git a/recipes/bioconductor-hgu95av2.db/meta.yaml b/recipes/bioconductor-hgu95av2.db/meta.yaml new file mode 100644 index 00000000000000..57c2358954ffe1 --- /dev/null +++ b/recipes/bioconductor-hgu95av2.db/meta.yaml @@ -0,0 +1,36 @@ +{% set version = "3.2.3" %} +{% set name = "hgu95av2.db" %} +{% set bioc = "3.6" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + fn: '{{ name }}_{{ version }}.tar.gz' + url: + - 'http://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + sha256: c56a023573de68a82fba79952dd10774ea096a1eb3083b15ad3cb21bc2f35189 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ +requirements: + build: + - 'bioconductor-annotationdbi >=1.34.3' + - 'bioconductor-org.hs.eg.db >=3.3.0' + - r-base + run: + - 'bioconductor-annotationdbi >=1.34.3' + - 'bioconductor-org.hs.eg.db >=3.3.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'http://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Affymetrix Human Genome U95 Set annotation data (chip hgu95av2) assembled using data from public repositories' diff --git a/recipes/bioconductor-hgu95av2.db/post-link.sh b/recipes/bioconductor-hgu95av2.db/post-link.sh new file mode 100644 index 00000000000000..d10c50fa901267 --- /dev/null +++ b/recipes/bioconductor-hgu95av2.db/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="hgu95av2.db_3.2.3.tar.gz" +URLS=( + "http://bioconductor.org/packages/3.6/data/annotation/src/contrib/hgu95av2.db_3.2.3.tar.gz" + "https://bioarchive.galaxyproject.org/hgu95av2.db_3.2.3.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-hgu95av2.db/bioconductor-hgu95av2.db_3.2.3_src_all.tar.gz" +) +MD5="a0ee1ba7f115a1504ca89619a0bc56dd" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING \ No newline at end of file diff --git a/recipes/bioconductor-hgu95av2.db/pre-unlink.sh b/recipes/bioconductor-hgu95av2.db/pre-unlink.sh new file mode 100644 index 00000000000000..a702bf58ebf0f2 --- /dev/null +++ b/recipes/bioconductor-hgu95av2.db/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ hgu95av2.db diff --git a/recipes/bioconductor-hibag/build.sh b/recipes/bioconductor-hibag/build.sh new file mode 100644 index 00000000000000..da43ce21683122 --- /dev/null +++ b/recipes/bioconductor-hibag/build.sh @@ -0,0 +1,4 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-hibag/meta.yaml b/recipes/bioconductor-hibag/meta.yaml new file mode 100644 index 00000000000000..ed8411985928db --- /dev/null +++ b/recipes/bioconductor-hibag/meta.yaml @@ -0,0 +1,34 @@ +{% set version = "1.14.0" %} +{% set name = "HIBAG" %} +{% set bioc = "3.6" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + fn: '{{ name }}_{{ version }}.tar.gz' + url: + - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: b4f74bde8943961a88200c84b197e30a8d520eb8a6f88d42dd684e838d5b644e +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ +requirements: + build: + - r-base + - gcc # [linux] + - llvm # [osx] + run: + - r-base + - libcxx # [osx] +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: GPL-3 + summary: 'It is a software package for imputing HLA types using SNP data, and relies on a training set of HLA and SNP genotypes. HIBAG can be used by researchers with published parameter estimates instead of requiring access to large training sample datasets. It combines the concepts of attribute bagging, an ensemble classifier method, with haplotype inference for SNPs and HLA types. Attribute bagging is a technique which improves the accuracy and stability of classifier ensembles using bootstrap aggregating and random variable selection.' diff --git a/recipes/bioconductor-hitc/build.sh b/recipes/bioconductor-hitc/build.sh new file mode 100644 index 00000000000000..da43ce21683122 --- /dev/null +++ b/recipes/bioconductor-hitc/build.sh @@ -0,0 +1,4 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-hitc/meta.yaml b/recipes/bioconductor-hitc/meta.yaml new file mode 100644 index 00000000000000..647014fb983dcd --- /dev/null +++ b/recipes/bioconductor-hitc/meta.yaml @@ -0,0 +1,45 @@ +{% set version = "1.22.0" %} +{% set name = "HiTC" %} +{% set bioc = "3.6" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + fn: '{{ name }}_{{ version }}.tar.gz' + url: + - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: 77562f40fe7e692e70327ea77b72e132c7666ed5ec0005c5dfdf1a2f83ea0809 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ +requirements: + build: + - bioconductor-biostrings + - bioconductor-genomeinfodb + - bioconductor-genomicranges + - bioconductor-iranges + - bioconductor-rtracklayer + - r-base + - r-matrix + - r-rcolorbrewer + run: + - bioconductor-biostrings + - bioconductor-genomeinfodb + - bioconductor-genomicranges + - bioconductor-iranges + - bioconductor-rtracklayer + - r-base + - r-matrix + - r-rcolorbrewer +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'The HiTC package was developed to explore high-throughput ''C'' data such as 5C or Hi-C. Dedicated R classes as well as standard methods for quality controls, normalization, visualization, and further analysis are also provided.' diff --git a/recipes/bioconductor-hopach/build.sh b/recipes/bioconductor-hopach/build.sh new file mode 100644 index 00000000000000..da43ce21683122 --- /dev/null +++ b/recipes/bioconductor-hopach/build.sh @@ -0,0 +1,4 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-hopach/meta.yaml b/recipes/bioconductor-hopach/meta.yaml new file mode 100644 index 00000000000000..68bd6bcac615b9 --- /dev/null +++ b/recipes/bioconductor-hopach/meta.yaml @@ -0,0 +1,40 @@ +{% set version = "2.38.0" %} +{% set name = "hopach" %} +{% set bioc = "3.6" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + fn: '{{ name }}_{{ version }}.tar.gz' + url: + - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + sha256: dde929c9838c9857849b02ce25ace59150687f77bd0ad06e2eeadc35fe5a48ec +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ +requirements: + build: + - bioconductor-biobase + - bioconductor-biocgenerics + - r-base + - r-cluster + - gcc # [linux] + - llvm # [osx] + run: + - bioconductor-biobase + - bioconductor-biocgenerics + - r-base + - r-cluster + - libcxx # [osx] +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: 'GPL (>= 2)' + summary: 'The HOPACH clustering algorithm builds a hierarchical tree of clusters by recursively partitioning a data set, while ordering and possibly collapsing clusters at each level. The algorithm uses the Mean/Median Split Silhouette (MSS) criteria to identify the level of the tree with maximally homogeneous clusters. It also runs the tree down to produce a final ordered list of the elements. The non-parametric bootstrap allows one to estimate the probability that each element belongs to each cluster (fuzzy clustering).' diff --git a/recipes/bioconductor-htseqtools/build.sh b/recipes/bioconductor-htseqtools/build.sh new file mode 100644 index 00000000000000..da43ce21683122 --- /dev/null +++ b/recipes/bioconductor-htseqtools/build.sh @@ -0,0 +1,4 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-htseqtools/meta.yaml b/recipes/bioconductor-htseqtools/meta.yaml new file mode 100644 index 00000000000000..ef1998a3862efe --- /dev/null +++ b/recipes/bioconductor-htseqtools/meta.yaml @@ -0,0 +1,47 @@ +{% set version = "1.26.0" %} +{% set name = "htSeqTools" %} +{% set bioc = "3.6" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + fn: '{{ name }}_{{ version }}.tar.gz' + url: + - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: 9fe152ae580734ff31909e5f45fadc3ea76fb10434ec388cba4b4008065c2fd6 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ +requirements: + build: + - bioconductor-biobase + - 'bioconductor-biocgenerics >=0.1.0' + - bioconductor-bsgenome + - 'bioconductor-genomeinfodb >=1.1.3' + - 'bioconductor-genomicranges >=1.17.11' + - bioconductor-iranges + - bioconductor-s4vectors + - r-base + - r-mass + run: + - bioconductor-biobase + - 'bioconductor-biocgenerics >=0.1.0' + - bioconductor-bsgenome + - 'bioconductor-genomeinfodb >=1.1.3' + - 'bioconductor-genomicranges >=1.17.11' + - bioconductor-iranges + - bioconductor-s4vectors + - r-base + - r-mass +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: 'GPL (>=2)' + summary: 'We provide efficient, easy-to-use tools for High-Throughput Sequencing (ChIP-seq, RNAseq etc.). These include MDS plots (analogues to PCA), detecting inefficient immuno-precipitation or over-amplification artifacts, tools to identify and test for genomic regions with large accumulation of reads, and visualization of coverage profiles.' diff --git a/recipes/bioconductor-hybridmtest/build.sh b/recipes/bioconductor-hybridmtest/build.sh new file mode 100644 index 00000000000000..da43ce21683122 --- /dev/null +++ b/recipes/bioconductor-hybridmtest/build.sh @@ -0,0 +1,4 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-hybridmtest/meta.yaml b/recipes/bioconductor-hybridmtest/meta.yaml new file mode 100644 index 00000000000000..c5a373d9245286 --- /dev/null +++ b/recipes/bioconductor-hybridmtest/meta.yaml @@ -0,0 +1,39 @@ +{% set version = "1.22.0" %} +{% set name = "HybridMTest" %} +{% set bioc = "3.6" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + fn: '{{ name }}_{{ version }}.tar.gz' + url: + - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: 72e0867f646a15cc4689bcf6115ff7c6b6717bcd2f605436f7ecebafa8c22e53 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ +requirements: + build: + - bioconductor-biobase + - r-base + - r-fdrtool + - r-mass + - r-survival + run: + - bioconductor-biobase + - r-base + - r-fdrtool + - r-mass + - r-survival +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: 'GPL Version 2 or later' + summary: 'Performs hybrid multiple testing that incorporates method selection and assumption evaluations into the analysis using empirical Bayes probability (EBP) estimates obtained by Grenander density estimation. For instance, for 3-group comparison analysis, Hybrid Multiple testing considers EBPs as weighted EBPs between F-test and H-test with EBPs from Shapiro Wilk test of normality as weigth. Instead of just using EBPs from F-test only or using H-test only, this methodology combines both types of EBPs through EBPs from Shapiro Wilk test of normality. This methodology uses then the law of total EBPs.' diff --git a/recipes/bioconductor-hyperdraw/build.sh b/recipes/bioconductor-hyperdraw/build.sh new file mode 100644 index 00000000000000..da43ce21683122 --- /dev/null +++ b/recipes/bioconductor-hyperdraw/build.sh @@ -0,0 +1,4 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-hyperdraw/meta.yaml b/recipes/bioconductor-hyperdraw/meta.yaml new file mode 100644 index 00000000000000..cb40c93ca79d49 --- /dev/null +++ b/recipes/bioconductor-hyperdraw/meta.yaml @@ -0,0 +1,37 @@ +{% set version = "1.30.0" %} +{% set name = "hyperdraw" %} +{% set bioc = "3.6" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + fn: '{{ name }}_{{ version }}.tar.gz' + url: + - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + sha256: 199eb413797c62e8215c593f1689fdac9d8aaf88287943fa97add9759019d101 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ +requirements: + build: + - bioconductor-graph + - bioconductor-hypergraph + - bioconductor-rgraphviz + - r-base + run: + - bioconductor-graph + - bioconductor-hypergraph + - bioconductor-rgraphviz + - r-base +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: 'GPL (>= 2)' + summary: 'Functions for visualizing hypergraphs.' diff --git a/recipes/bioconductor-iaseq/build.sh b/recipes/bioconductor-iaseq/build.sh new file mode 100644 index 00000000000000..da43ce21683122 --- /dev/null +++ b/recipes/bioconductor-iaseq/build.sh @@ -0,0 +1,4 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-iaseq/meta.yaml b/recipes/bioconductor-iaseq/meta.yaml new file mode 100644 index 00000000000000..ecb6ad41f626c8 --- /dev/null +++ b/recipes/bioconductor-iaseq/meta.yaml @@ -0,0 +1,31 @@ +{% set version = "1.22.0" %} +{% set name = "iASeq" %} +{% set bioc = "3.6" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + fn: '{{ name }}_{{ version }}.tar.gz' + url: + - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: a2f524cf5e53c8a4c2582db11e5edba2861ff85d1f7c65c7659c40b3ff41e7ce +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ +requirements: + build: + - r-base + run: + - r-base +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: GPL-2 + summary: 'It fits correlation motif model to multiple RNAseq or ChIPseq studies to improve detection of allele-specific events and describe correlation patterns across studies.' diff --git a/recipes/bioconductor-ibh/build.sh b/recipes/bioconductor-ibh/build.sh new file mode 100644 index 00000000000000..da43ce21683122 --- /dev/null +++ b/recipes/bioconductor-ibh/build.sh @@ -0,0 +1,4 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-ibh/meta.yaml b/recipes/bioconductor-ibh/meta.yaml new file mode 100644 index 00000000000000..8c9fa737b543b9 --- /dev/null +++ b/recipes/bioconductor-ibh/meta.yaml @@ -0,0 +1,33 @@ +{% set version = "1.26.0" %} +{% set name = "ibh" %} +{% set bioc = "3.6" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + fn: '{{ name }}_{{ version }}.tar.gz' + url: + - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + sha256: d5f281ecf80e390feac5910e862f5fa500c379da07e797870720a10adc50c121 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ +requirements: + build: + - bioconductor-simpintlists + - r-base + run: + - bioconductor-simpintlists + - r-base +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: 'GPL (>= 2)' + summary: 'This package contains methods for calculating Interaction Based Homogeneity to evaluate fitness of gene lists to an interaction network which is useful for evaluation of clustering results and gene list analysis. BioGRID interactions are used in the calculation. The user can also provide their own interactions.' diff --git a/recipes/bioconductor-ichip/build.sh b/recipes/bioconductor-ichip/build.sh new file mode 100644 index 00000000000000..da43ce21683122 --- /dev/null +++ b/recipes/bioconductor-ichip/build.sh @@ -0,0 +1,4 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-ichip/meta.yaml b/recipes/bioconductor-ichip/meta.yaml new file mode 100644 index 00000000000000..776d5abcdb2a14 --- /dev/null +++ b/recipes/bioconductor-ichip/meta.yaml @@ -0,0 +1,36 @@ +{% set version = "1.32.0" %} +{% set name = "iChip" %} +{% set bioc = "3.6" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + fn: '{{ name }}_{{ version }}.tar.gz' + url: + - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: 801f1b2d172aec0ac67d89688ded007272672af2bd6db5589756fa356dd99709 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ +requirements: + build: + - bioconductor-limma + - r-base + - gcc # [linux] + - llvm # [osx] + run: + - bioconductor-limma + - r-base + - libcxx # [osx] +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: 'GPL (>= 2)' + summary: 'This package uses hidden Ising models to identify enriched genomic regions in ChIP-chip data. It can be used to analyze the data from multiple platforms (e.g., Affymetrix, Agilent, and NimbleGen), and the data with single to multiple replicates.' diff --git a/recipes/bioconductor-icobra/build.sh b/recipes/bioconductor-icobra/build.sh new file mode 100644 index 00000000000000..da43ce21683122 --- /dev/null +++ b/recipes/bioconductor-icobra/build.sh @@ -0,0 +1,4 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-icobra/meta.yaml b/recipes/bioconductor-icobra/meta.yaml new file mode 100644 index 00000000000000..00d7b8ab1b58c3 --- /dev/null +++ b/recipes/bioconductor-icobra/meta.yaml @@ -0,0 +1,53 @@ +{% set version = "1.6.0" %} +{% set name = "iCOBRA" %} +{% set bioc = "3.6" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + fn: '{{ name }}_{{ version }}.tar.gz' + url: + - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: 4dc3c2b7c90b7f16d21fd94b162338d19b1cc41730b279f7d5dbf2844c3b50f8 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ +requirements: + build: + - bioconductor-limma + - r-base + - r-dplyr + - r-dt + - 'r-ggplot2 >=2.0.0' + - r-reshape2 + - r-rocr + - r-scales + - 'r-shiny >=0.9.1.9008' + - r-shinybs + - r-shinydashboard + - r-upsetr + run: + - bioconductor-limma + - r-base + - r-dplyr + - r-dt + - 'r-ggplot2 >=2.0.0' + - r-reshape2 + - r-rocr + - r-scales + - 'r-shiny >=0.9.1.9008' + - r-shinybs + - r-shinydashboard + - r-upsetr +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: 'GPL (>=2)' + summary: 'This package provides functions for calculation and visualization of performance metrics for evaluation of ranking and binary classification (assignment) methods. It also contains a shiny application for interactive exploration of results.' diff --git a/recipes/bioconductor-illuminahumanmethylationepicanno.ilm10b2.hg19/meta.yaml b/recipes/bioconductor-illuminahumanmethylationepicanno.ilm10b2.hg19/meta.yaml new file mode 100644 index 00000000000000..701fbc77c77f2d --- /dev/null +++ b/recipes/bioconductor-illuminahumanmethylationepicanno.ilm10b2.hg19/meta.yaml @@ -0,0 +1,34 @@ +{% set version = "0.6.0" %} +{% set name = "IlluminaHumanMethylationEPICanno.ilm10b2.hg19" %} +{% set bioc = "3.6" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + fn: '{{ name }}_{{ version }}.tar.gz' + url: + - 'http://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: 4decdbc78a6a8d02bf8aecb0d6e1d81134ae9dbc2375add52574f07829e8cd69 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ +requirements: + build: + - 'bioconductor-minfi >=1.19.15' + - r-base + run: + - 'bioconductor-minfi >=1.19.15' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'http://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'An annotation package for Illumina''s EPIC methylation arrays.' diff --git a/recipes/bioconductor-illuminahumanmethylationepicanno.ilm10b2.hg19/post-link.sh b/recipes/bioconductor-illuminahumanmethylationepicanno.ilm10b2.hg19/post-link.sh new file mode 100644 index 00000000000000..a5c6748d47c0e7 --- /dev/null +++ b/recipes/bioconductor-illuminahumanmethylationepicanno.ilm10b2.hg19/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="IlluminaHumanMethylationEPICanno.ilm10b2.hg19_0.6.0.tar.gz" +URLS=( + "http://bioconductor.org/packages/3.6/data/annotation/src/contrib/IlluminaHumanMethylationEPICanno.ilm10b2.hg19_0.6.0.tar.gz" + "https://bioarchive.galaxyproject.org/IlluminaHumanMethylationEPICanno.ilm10b2.hg19_0.6.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-illuminahumanmethylationepicanno.ilm10b2.hg19/bioconductor-illuminahumanmethylationepicanno.ilm10b2.hg19_0.6.0_src_all.tar.gz" +) +MD5="6a8e2398a0f930aa7828a1412fb21e88" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING \ No newline at end of file diff --git a/recipes/bioconductor-illuminahumanmethylationepicanno.ilm10b2.hg19/pre-unlink.sh b/recipes/bioconductor-illuminahumanmethylationepicanno.ilm10b2.hg19/pre-unlink.sh new file mode 100644 index 00000000000000..a130cd9b886341 --- /dev/null +++ b/recipes/bioconductor-illuminahumanmethylationepicanno.ilm10b2.hg19/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ IlluminaHumanMethylationEPICanno.ilm10b2.hg19 diff --git a/recipes/bioconductor-illuminahumanmethylationepicanno.ilm10b3.hg19/meta.yaml b/recipes/bioconductor-illuminahumanmethylationepicanno.ilm10b3.hg19/meta.yaml new file mode 100644 index 00000000000000..93fff5aceb7204 --- /dev/null +++ b/recipes/bioconductor-illuminahumanmethylationepicanno.ilm10b3.hg19/meta.yaml @@ -0,0 +1,34 @@ +{% set version = "0.6.0" %} +{% set name = "IlluminaHumanMethylationEPICanno.ilm10b3.hg19" %} +{% set bioc = "3.6" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + fn: '{{ name }}_{{ version }}.tar.gz' + url: + - 'http://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: 062aa3c78e3fc518849adc73b8540aa50f85ecab8ef91b535b48a1bfeedab3e5 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ +requirements: + build: + - 'bioconductor-minfi >=1.19.15' + - r-base + run: + - 'bioconductor-minfi >=1.19.15' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'http://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'An annotation package for Illumina''s EPIC methylation arrays.' diff --git a/recipes/bioconductor-illuminahumanmethylationepicanno.ilm10b3.hg19/post-link.sh b/recipes/bioconductor-illuminahumanmethylationepicanno.ilm10b3.hg19/post-link.sh new file mode 100644 index 00000000000000..7af53e9ce94373 --- /dev/null +++ b/recipes/bioconductor-illuminahumanmethylationepicanno.ilm10b3.hg19/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="IlluminaHumanMethylationEPICanno.ilm10b3.hg19_0.6.0.tar.gz" +URLS=( + "http://bioconductor.org/packages/3.6/data/annotation/src/contrib/IlluminaHumanMethylationEPICanno.ilm10b3.hg19_0.6.0.tar.gz" + "https://bioarchive.galaxyproject.org/IlluminaHumanMethylationEPICanno.ilm10b3.hg19_0.6.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-illuminahumanmethylationepicanno.ilm10b3.hg19/bioconductor-illuminahumanmethylationepicanno.ilm10b3.hg19_0.6.0_src_all.tar.gz" +) +MD5="2dac8e889486386eaea1bb7ce1beea2e" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING \ No newline at end of file diff --git a/recipes/bioconductor-illuminahumanmethylationepicanno.ilm10b3.hg19/pre-unlink.sh b/recipes/bioconductor-illuminahumanmethylationepicanno.ilm10b3.hg19/pre-unlink.sh new file mode 100644 index 00000000000000..435ac98d0aca26 --- /dev/null +++ b/recipes/bioconductor-illuminahumanmethylationepicanno.ilm10b3.hg19/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ IlluminaHumanMethylationEPICanno.ilm10b3.hg19 diff --git a/recipes/bioconductor-illuminahumanmethylationepicanno.ilm10b4.hg19/meta.yaml b/recipes/bioconductor-illuminahumanmethylationepicanno.ilm10b4.hg19/meta.yaml new file mode 100644 index 00000000000000..5d39101adb9bd3 --- /dev/null +++ b/recipes/bioconductor-illuminahumanmethylationepicanno.ilm10b4.hg19/meta.yaml @@ -0,0 +1,34 @@ +{% set version = "0.6.0" %} +{% set name = "IlluminaHumanMethylationEPICanno.ilm10b4.hg19" %} +{% set bioc = "3.6" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + fn: '{{ name }}_{{ version }}.tar.gz' + url: + - 'http://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: 2c8128126b63e7fa805a5f3b02449367dca9c3be3eb5f6300acc718826590719 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ +requirements: + build: + - 'bioconductor-minfi >=1.19.15' + - r-base + run: + - 'bioconductor-minfi >=1.19.15' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'http://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'An annotation package for Illumina''s EPIC methylation arrays.' diff --git a/recipes/bioconductor-illuminahumanmethylationepicanno.ilm10b4.hg19/post-link.sh b/recipes/bioconductor-illuminahumanmethylationepicanno.ilm10b4.hg19/post-link.sh new file mode 100644 index 00000000000000..642158fa1154ca --- /dev/null +++ b/recipes/bioconductor-illuminahumanmethylationepicanno.ilm10b4.hg19/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="IlluminaHumanMethylationEPICanno.ilm10b4.hg19_0.6.0.tar.gz" +URLS=( + "http://bioconductor.org/packages/3.6/data/annotation/src/contrib/IlluminaHumanMethylationEPICanno.ilm10b4.hg19_0.6.0.tar.gz" + "https://bioarchive.galaxyproject.org/IlluminaHumanMethylationEPICanno.ilm10b4.hg19_0.6.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-illuminahumanmethylationepicanno.ilm10b4.hg19/bioconductor-illuminahumanmethylationepicanno.ilm10b4.hg19_0.6.0_src_all.tar.gz" +) +MD5="2d0c05917bcbf9ba1e354380d4e17a77" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING \ No newline at end of file diff --git a/recipes/bioconductor-illuminahumanmethylationepicanno.ilm10b4.hg19/pre-unlink.sh b/recipes/bioconductor-illuminahumanmethylationepicanno.ilm10b4.hg19/pre-unlink.sh new file mode 100644 index 00000000000000..bd49b2b380443a --- /dev/null +++ b/recipes/bioconductor-illuminahumanmethylationepicanno.ilm10b4.hg19/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ IlluminaHumanMethylationEPICanno.ilm10b4.hg19 diff --git a/recipes/bioconductor-illuminahumanmethylationepicmanifest/meta.yaml b/recipes/bioconductor-illuminahumanmethylationepicmanifest/meta.yaml new file mode 100644 index 00000000000000..d37007c49c9ecf --- /dev/null +++ b/recipes/bioconductor-illuminahumanmethylationepicmanifest/meta.yaml @@ -0,0 +1,34 @@ +{% set version = "0.3.0" %} +{% set name = "IlluminaHumanMethylationEPICmanifest" %} +{% set bioc = "3.6" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + fn: '{{ name }}_{{ version }}.tar.gz' + url: + - 'http://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: e39a69d98486cec981e97c56f45bbe47d2ccb5bbb66a1b16fa0685575493902a +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ +requirements: + build: + - bioconductor-minfi + - r-base + run: + - bioconductor-minfi + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'http://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'A manifest package for Illumina''s EPIC methylation arrays.' diff --git a/recipes/bioconductor-illuminahumanmethylationepicmanifest/post-link.sh b/recipes/bioconductor-illuminahumanmethylationepicmanifest/post-link.sh new file mode 100644 index 00000000000000..a950c7331a0951 --- /dev/null +++ b/recipes/bioconductor-illuminahumanmethylationepicmanifest/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="IlluminaHumanMethylationEPICmanifest_0.3.0.tar.gz" +URLS=( + "http://bioconductor.org/packages/3.6/data/annotation/src/contrib/IlluminaHumanMethylationEPICmanifest_0.3.0.tar.gz" + "https://bioarchive.galaxyproject.org/IlluminaHumanMethylationEPICmanifest_0.3.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-illuminahumanmethylationepicmanifest/bioconductor-illuminahumanmethylationepicmanifest_0.3.0_src_all.tar.gz" +) +MD5="c6b0268de177badfe0b8184002da7e16" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING \ No newline at end of file diff --git a/recipes/bioconductor-illuminahumanmethylationepicmanifest/pre-unlink.sh b/recipes/bioconductor-illuminahumanmethylationepicmanifest/pre-unlink.sh new file mode 100644 index 00000000000000..f6d9224e8dc12f --- /dev/null +++ b/recipes/bioconductor-illuminahumanmethylationepicmanifest/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ IlluminaHumanMethylationEPICmanifest diff --git a/recipes/bioconductor-impulsede/build.sh b/recipes/bioconductor-impulsede/build.sh new file mode 100644 index 00000000000000..da43ce21683122 --- /dev/null +++ b/recipes/bioconductor-impulsede/build.sh @@ -0,0 +1,4 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-impulsede/meta.yaml b/recipes/bioconductor-impulsede/meta.yaml new file mode 100644 index 00000000000000..d6d464db2f67c1 --- /dev/null +++ b/recipes/bioconductor-impulsede/meta.yaml @@ -0,0 +1,35 @@ +{% set version = "1.4.0" %} +{% set name = "ImpulseDE" %} +{% set bioc = "3.6" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + fn: '{{ name }}_{{ version }}.tar.gz' + url: + - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: 013b366155309ae595bae6dce37e9d081dfc2c929027ee8b53029959efcc8112 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ +requirements: + build: + - r-amap + - r-base + - r-boot + run: + - r-amap + - r-base + - r-boot +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: GPL-3 + summary: 'ImpulseDE is suited to capture single impulse-like patterns in high throughput time series datasets. By fitting a representative impulse model to each gene, it reports differentially expressed genes whether across time points in a single experiment or between two time courses from two experiments. To optimize the running time, the code makes use of clustering steps and multi-threading.' diff --git a/recipes/bioconductor-inpower/build.sh b/recipes/bioconductor-inpower/build.sh new file mode 100644 index 00000000000000..da43ce21683122 --- /dev/null +++ b/recipes/bioconductor-inpower/build.sh @@ -0,0 +1,4 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-inpower/meta.yaml b/recipes/bioconductor-inpower/meta.yaml new file mode 100644 index 00000000000000..1f9962f6c821f2 --- /dev/null +++ b/recipes/bioconductor-inpower/meta.yaml @@ -0,0 +1,33 @@ +{% set version = "1.14.0" %} +{% set name = "INPower" %} +{% set bioc = "3.6" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + fn: '{{ name }}_{{ version }}.tar.gz' + url: + - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: 7b1dc0eec9f4ff676161575d6bd4da6d7400fccecd57b8613f105f93941ba59d +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ +requirements: + build: + - r-base + - r-mvtnorm + run: + - r-base + - r-mvtnorm +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: 'GPL-2 + file LICENSE' + summary: 'An R package for computing the number of susceptibility SNPs and power of future studies' diff --git a/recipes/bioconductor-inspect/build.sh b/recipes/bioconductor-inspect/build.sh new file mode 100644 index 00000000000000..da43ce21683122 --- /dev/null +++ b/recipes/bioconductor-inspect/build.sh @@ -0,0 +1,4 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-inspect/meta.yaml b/recipes/bioconductor-inspect/meta.yaml new file mode 100644 index 00000000000000..529bdc8e12fd1d --- /dev/null +++ b/recipes/bioconductor-inspect/meta.yaml @@ -0,0 +1,57 @@ +{% set version = "1.8.0" %} +{% set name = "INSPEcT" %} +{% set bioc = "3.6" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + fn: '{{ name }}_{{ version }}.tar.gz' + url: + - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: a16dbf2bd2d0a1c893ce4f6f82ae534f22548f12f9f0d3e782b92cc070f47fec +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ +requirements: + build: + - bioconductor-biobase + - bioconductor-biocgenerics + - bioconductor-biocparallel + - bioconductor-genomicalignments + - bioconductor-genomicfeatures + - bioconductor-genomicranges + - bioconductor-iranges + - bioconductor-preprocesscore + - bioconductor-rsamtools + - bioconductor-s4vectors + - r-base + - r-desolve + - r-proc + - r-rootsolve + run: + - bioconductor-biobase + - bioconductor-biocgenerics + - bioconductor-biocparallel + - bioconductor-genomicalignments + - bioconductor-genomicfeatures + - bioconductor-genomicranges + - bioconductor-iranges + - bioconductor-preprocesscore + - bioconductor-rsamtools + - bioconductor-s4vectors + - r-base + - r-desolve + - r-proc + - r-rootsolve +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: GPL-2 + summary: 'INSPEcT (INference of Synthesis, Processing and dEgradation rates in Time-Course experiments) analyses 4sU-seq and RNA-seq time-course data in order to evaluate synthesis, processing and degradation rates and asses via modeling the rates that determines changes in mature mRNA levels.' diff --git a/recipes/bioconductor-interactivedisplay/build.sh b/recipes/bioconductor-interactivedisplay/build.sh new file mode 100644 index 00000000000000..da43ce21683122 --- /dev/null +++ b/recipes/bioconductor-interactivedisplay/build.sh @@ -0,0 +1,4 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-interactivedisplay/meta.yaml b/recipes/bioconductor-interactivedisplay/meta.yaml new file mode 100644 index 00000000000000..4e4af70264a4a7 --- /dev/null +++ b/recipes/bioconductor-interactivedisplay/meta.yaml @@ -0,0 +1,53 @@ +{% set version = "1.16.0" %} +{% set name = "interactiveDisplay" %} +{% set bioc = "3.6" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + fn: '{{ name }}_{{ version }}.tar.gz' + url: + - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: 2febc7f7e1be31ba594e08ba8f9712d0587285893c6c32f8db39dad1ddbafd07 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ +requirements: + build: + - bioconductor-annotationdbi + - bioconductor-biocgenerics + - bioconductor-category + - 'bioconductor-interactivedisplaybase >=1.7.3' + - r-base + - r-ggplot2 + - r-gridsvg + - r-plyr + - r-rcolorbrewer + - r-reshape2 + - r-shiny + - r-xml + run: + - bioconductor-annotationdbi + - bioconductor-biocgenerics + - bioconductor-category + - 'bioconductor-interactivedisplaybase >=1.7.3' + - r-base + - r-ggplot2 + - r-gridsvg + - r-plyr + - r-rcolorbrewer + - r-reshape2 + - r-shiny + - r-xml +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'The interactiveDisplay package contains the methods needed to generate interactive Shiny based display methods for Bioconductor objects.' diff --git a/recipes/bioconductor-inversion/build.sh b/recipes/bioconductor-inversion/build.sh new file mode 100644 index 00000000000000..da43ce21683122 --- /dev/null +++ b/recipes/bioconductor-inversion/build.sh @@ -0,0 +1,4 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-inversion/meta.yaml b/recipes/bioconductor-inversion/meta.yaml new file mode 100644 index 00000000000000..90bc35a6af0996 --- /dev/null +++ b/recipes/bioconductor-inversion/meta.yaml @@ -0,0 +1,36 @@ +{% set version = "1.26.0" %} +{% set name = "inveRsion" %} +{% set bioc = "3.6" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + fn: '{{ name }}_{{ version }}.tar.gz' + url: + - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: b151f3ff6207edf8da6aadf8d77497045272db06a3d3e03658f016de27b1ee89 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ +requirements: + build: + - r-base + - r-haplo.stats + - gcc # [linux] + - llvm # [osx] + run: + - r-base + - r-haplo.stats + - libcxx # [osx] +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: 'GPL (>= 2)' + summary: 'Package to find genetic inversions in genotype (SNP array) data.' diff --git a/recipes/bioconductor-ipac/build.sh b/recipes/bioconductor-ipac/build.sh new file mode 100644 index 00000000000000..da43ce21683122 --- /dev/null +++ b/recipes/bioconductor-ipac/build.sh @@ -0,0 +1,4 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-ipac/meta.yaml b/recipes/bioconductor-ipac/meta.yaml new file mode 100644 index 00000000000000..991b83f493a0e4 --- /dev/null +++ b/recipes/bioconductor-ipac/meta.yaml @@ -0,0 +1,39 @@ +{% set version = "1.22.0" %} +{% set name = "iPAC" %} +{% set bioc = "3.6" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + fn: '{{ name }}_{{ version }}.tar.gz' + url: + - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: f9053904d89b7a54da678a83c971e72f94186338e882beba9055a239debeb6f4 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ +requirements: + build: + - bioconductor-biostrings + - bioconductor-multtest + - r-base + - r-gdata + - r-scatterplot3d + run: + - bioconductor-biostrings + - bioconductor-multtest + - r-base + - r-gdata + - r-scatterplot3d +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: GPL-2 + summary: 'iPAC is a novel tool to identify somatic amino acid mutation clustering within proteins while taking into account protein structure.' diff --git a/recipes/bioconductor-ippd/build.sh b/recipes/bioconductor-ippd/build.sh new file mode 100644 index 00000000000000..da43ce21683122 --- /dev/null +++ b/recipes/bioconductor-ippd/build.sh @@ -0,0 +1,4 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-ippd/meta.yaml b/recipes/bioconductor-ippd/meta.yaml new file mode 100644 index 00000000000000..758905ab5fdfe7 --- /dev/null +++ b/recipes/bioconductor-ippd/meta.yaml @@ -0,0 +1,44 @@ +{% set version = "1.26.0" %} +{% set name = "IPPD" %} +{% set bioc = "3.6" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + fn: '{{ name }}_{{ version }}.tar.gz' + url: + - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: 2e505fcf1e5025c3057ae7616d1d3ab5135bf19a202e982cc613659d66a15d68 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ +requirements: + build: + - r-base + - r-bitops + - r-digest + - r-mass + - r-matrix + - r-xml + - gcc # [linux] + - llvm # [osx] + run: + - r-base + - r-bitops + - r-digest + - r-mass + - r-matrix + - r-xml + - libcxx # [osx] +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: 'GPL (version 2 or later)' + summary: 'The package provides functionality to extract isotopic peak patterns from raw mass spectra. This is done by fitting a large set of template basis functions to the raw spectrum using either nonnegative least squares or least absolute deviation fittting. The package offers a flexible function which tries to estimate model parameters in a way tailored to the peak shapes in the data. The package also provides functionality to process LCMS runs.' diff --git a/recipes/bioconductor-iseq/build.sh b/recipes/bioconductor-iseq/build.sh new file mode 100644 index 00000000000000..da43ce21683122 --- /dev/null +++ b/recipes/bioconductor-iseq/build.sh @@ -0,0 +1,4 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-iseq/meta.yaml b/recipes/bioconductor-iseq/meta.yaml new file mode 100644 index 00000000000000..313153d25a8225 --- /dev/null +++ b/recipes/bioconductor-iseq/meta.yaml @@ -0,0 +1,34 @@ +{% set version = "1.30.0" %} +{% set name = "iSeq" %} +{% set bioc = "3.6" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + fn: '{{ name }}_{{ version }}.tar.gz' + url: + - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: 3b84c53f24767267423624ea81c88b0c9b65aca8ecaebf8f0cedcd091ba9d767 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ +requirements: + build: + - r-base + - gcc # [linux] + - llvm # [osx] + run: + - r-base + - libcxx # [osx] +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: 'GPL (>= 2)' + summary: 'This package uses Bayesian hidden Ising models to identify IP-enriched genomic regions from ChIP-seq data. It can be used to analyze ChIP-seq data with and without controls and replicates.' diff --git a/recipes/bioconductor-isolde/build.sh b/recipes/bioconductor-isolde/build.sh new file mode 100644 index 00000000000000..da43ce21683122 --- /dev/null +++ b/recipes/bioconductor-isolde/build.sh @@ -0,0 +1,4 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-isolde/meta.yaml b/recipes/bioconductor-isolde/meta.yaml new file mode 100644 index 00000000000000..effa50ec895196 --- /dev/null +++ b/recipes/bioconductor-isolde/meta.yaml @@ -0,0 +1,34 @@ +{% set version = "1.6.0" %} +{% set name = "ISoLDE" %} +{% set bioc = "3.6" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + fn: '{{ name }}_{{ version }}.tar.gz' + url: + - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: 797f3d70e1078e47365f138c3fc2ef77ef65c41a447d1f4195bef176931ab40b +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ +requirements: + build: + - r-base + - gcc # [linux] + - llvm # [osx] + run: + - r-base + - libcxx # [osx] +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: 'GPL (>= 2.0)' + summary: 'This package provides ISoLDE a new method for identifying imprinted genes. This method is dedicated to data arising from RNA sequencing technologies. The ISoLDE package implements original statistical methodology described in the publication below.' diff --git a/recipes/bioconductor-iterativebma/build.sh b/recipes/bioconductor-iterativebma/build.sh new file mode 100644 index 00000000000000..da43ce21683122 --- /dev/null +++ b/recipes/bioconductor-iterativebma/build.sh @@ -0,0 +1,4 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-iterativebma/meta.yaml b/recipes/bioconductor-iterativebma/meta.yaml new file mode 100644 index 00000000000000..7d5a7186265fd1 --- /dev/null +++ b/recipes/bioconductor-iterativebma/meta.yaml @@ -0,0 +1,37 @@ +{% set version = "1.36.0" %} +{% set name = "iterativeBMA" %} +{% set bioc = "3.6" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + fn: '{{ name }}_{{ version }}.tar.gz' + url: + - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: 6c49d0fe3f33a8003b688bd5300e6dde3cca6c7e045cdeb2322185c822766832 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ +requirements: + build: + - 'bioconductor-biobase >=2.5.5' + - r-base + - r-bma + - r-leaps + run: + - 'bioconductor-biobase >=2.5.5' + - r-base + - r-bma + - r-leaps +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: 'GPL (>= 2)' + summary: 'The iterative Bayesian Model Averaging (BMA) algorithm is a variable selection and classification algorithm with an application of classifying 2-class microarray samples, as described in Yeung, Bumgarner and Raftery (Bioinformatics 2005, 21: 2394-2402).' diff --git a/recipes/bioconductor-iterativebmasurv/build.sh b/recipes/bioconductor-iterativebmasurv/build.sh new file mode 100644 index 00000000000000..da43ce21683122 --- /dev/null +++ b/recipes/bioconductor-iterativebmasurv/build.sh @@ -0,0 +1,4 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-iterativebmasurv/meta.yaml b/recipes/bioconductor-iterativebmasurv/meta.yaml new file mode 100644 index 00000000000000..f652eb0c0e86c9 --- /dev/null +++ b/recipes/bioconductor-iterativebmasurv/meta.yaml @@ -0,0 +1,37 @@ +{% set version = "1.36.0" %} +{% set name = "iterativeBMAsurv" %} +{% set bioc = "3.6" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + fn: '{{ name }}_{{ version }}.tar.gz' + url: + - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: b1f2d77d70931771a78319e6c4f00cc085d50324ea0cffae8584e9c8d3b5d824 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ +requirements: + build: + - r-base + - r-bma + - r-leaps + - r-survival + run: + - r-base + - r-bma + - r-leaps + - r-survival +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: 'GPL (>= 2)' + summary: 'The iterative Bayesian Model Averaging (BMA) algorithm for survival analysis is a variable selection method for applying survival analysis to microarray data.' diff --git a/recipes/bioconductor-kegglincs/build.sh b/recipes/bioconductor-kegglincs/build.sh new file mode 100644 index 00000000000000..da43ce21683122 --- /dev/null +++ b/recipes/bioconductor-kegglincs/build.sh @@ -0,0 +1,4 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-kegglincs/meta.yaml b/recipes/bioconductor-kegglincs/meta.yaml new file mode 100644 index 00000000000000..edfe02de9afd92 --- /dev/null +++ b/recipes/bioconductor-kegglincs/meta.yaml @@ -0,0 +1,55 @@ +{% set version = "1.4.0" %} +{% set name = "KEGGlincs" %} +{% set bioc = "3.6" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + fn: '{{ name }}_{{ version }}.tar.gz' + url: + - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: d8920cecc27219f510cda690b9446fafe1528801b25bc75183a200714083889e +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ +requirements: + build: + - bioconductor-annotationdbi + - bioconductor-hgu133a.db + - bioconductor-kegggraph + - bioconductor-keggrest + - bioconductor-kodata + - 'bioconductor-org.hs.eg.db >=3.3.0' + - r-base + - r-gtools + - r-httr + - r-igraph + - r-plyr + - r-rjsonio + - r-xml + run: + - bioconductor-annotationdbi + - bioconductor-hgu133a.db + - bioconductor-kegggraph + - bioconductor-keggrest + - bioconductor-kodata + - 'bioconductor-org.hs.eg.db >=3.3.0' + - r-base + - r-gtools + - r-httr + - r-igraph + - r-plyr + - r-rjsonio + - r-xml +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: GPL-3 + summary: 'See what is going on ''under the hood'' of KEGG pathways by explicitly re-creating the pathway maps from information obtained from KGML files.' diff --git a/recipes/bioconductor-keggorthology/build.sh b/recipes/bioconductor-keggorthology/build.sh new file mode 100644 index 00000000000000..da43ce21683122 --- /dev/null +++ b/recipes/bioconductor-keggorthology/build.sh @@ -0,0 +1,4 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-keggorthology/meta.yaml b/recipes/bioconductor-keggorthology/meta.yaml new file mode 100644 index 00000000000000..e7b31e4f329608 --- /dev/null +++ b/recipes/bioconductor-keggorthology/meta.yaml @@ -0,0 +1,39 @@ +{% set version = "2.30.0" %} +{% set name = "keggorthology" %} +{% set bioc = "3.6" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + fn: '{{ name }}_{{ version }}.tar.gz' + url: + - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + sha256: 96212cea18230facf342e2a99096835b83940f5a2149019b2a694f2bc63afa84 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ +requirements: + build: + - bioconductor-annotationdbi + - bioconductor-graph + - bioconductor-hgu95av2.db + - r-base + - r-dbi + run: + - bioconductor-annotationdbi + - bioconductor-graph + - bioconductor-hgu95av2.db + - r-base + - r-dbi +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'graphical representation of the Feb 2010 KEGG Orthology. The KEGG orthology is a set of pathway IDs that are not to be confused with the KEGG ortholog IDs.' diff --git a/recipes/bioconductor-kimod/build.sh b/recipes/bioconductor-kimod/build.sh new file mode 100644 index 00000000000000..da43ce21683122 --- /dev/null +++ b/recipes/bioconductor-kimod/build.sh @@ -0,0 +1,4 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-kimod/meta.yaml b/recipes/bioconductor-kimod/meta.yaml new file mode 100644 index 00000000000000..1d42595dd27466 --- /dev/null +++ b/recipes/bioconductor-kimod/meta.yaml @@ -0,0 +1,35 @@ +{% set version = "1.6.0" %} +{% set name = "kimod" %} +{% set bioc = "3.6" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + fn: '{{ name }}_{{ version }}.tar.gz' + url: + - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + sha256: ac2fed88431f934bc321ec41fcdfbcbba2fa059c46d08cf43e629ebfcc5e6955 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ +requirements: + build: + - bioconductor-biobase + - r-base + - r-cluster + run: + - bioconductor-biobase + - r-base + - r-cluster +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: 'GPL (>=2)' + summary: 'This package allows to work with mixed omics data (transcriptomics, proteomics, microarray-chips, rna-seq data), introducing the following improvements: distance options (for numeric and/or categorical variables) for each of the tables, bootstrap resampling techniques on the residuals matrices for all methods, that enable perform confidence ellipses for the projection of individuals, variables and biplot methodology to project variables (gene expression) on the compromise. Since the main purpose of the package is to use these techniques to omic data analysis, it includes an example data from four different microarray platforms (i.e.,Agilent, Affymetrix HGU 95, Affymetrix HGU 133 and Affymetrix HGU 133plus 2.0) on the NCI-60 cell lines.NCI60_4arrays is a list containing the NCI-60 microarray data with only few hundreds of genes randomly selected in each platform to keep the size of the package small. The data are the same that the package omicade4 used to implement the co-inertia analysis. The references in packages follow the style of the APA-6th norm.' diff --git a/recipes/bioconductor-kodata/meta.yaml b/recipes/bioconductor-kodata/meta.yaml new file mode 100644 index 00000000000000..519eff34a54c75 --- /dev/null +++ b/recipes/bioconductor-kodata/meta.yaml @@ -0,0 +1,32 @@ +{% set version = "1.4.0" %} +{% set name = "KOdata" %} +{% set bioc = "3.6" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + fn: '{{ name }}_{{ version }}.tar.gz' + url: + - 'http://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: 397b5a16e14fa9d62ac0987856a9d483ead2527a40aab512cd8551a5ed582eb6 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ +requirements: + build: + - r-base + run: + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'http://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' + license: 'MIT + file LICENSE' + summary: 'Contains consensus genomic signatures (CGS) for experimental cell-line specific gene knock-outs as well as baseline gene expression data for a subset of experimental cell-lines. Intended for use with package KEGGlincs.' diff --git a/recipes/bioconductor-kodata/post-link.sh b/recipes/bioconductor-kodata/post-link.sh new file mode 100644 index 00000000000000..24172062c8693f --- /dev/null +++ b/recipes/bioconductor-kodata/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="KOdata_1.4.0.tar.gz" +URLS=( + "http://bioconductor.org/packages/3.6/data/experiment/src/contrib/KOdata_1.4.0.tar.gz" + "https://bioarchive.galaxyproject.org/KOdata_1.4.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-kodata/bioconductor-kodata_1.4.0_src_all.tar.gz" +) +MD5="205ff9b0327541c7fae4a83f6092b892" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING \ No newline at end of file diff --git a/recipes/bioconductor-kodata/pre-unlink.sh b/recipes/bioconductor-kodata/pre-unlink.sh new file mode 100644 index 00000000000000..e9ae1523a67560 --- /dev/null +++ b/recipes/bioconductor-kodata/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ KOdata diff --git a/recipes/bioconductor-lbe/build.sh b/recipes/bioconductor-lbe/build.sh new file mode 100644 index 00000000000000..da43ce21683122 --- /dev/null +++ b/recipes/bioconductor-lbe/build.sh @@ -0,0 +1,4 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-lbe/meta.yaml b/recipes/bioconductor-lbe/meta.yaml new file mode 100644 index 00000000000000..e3efa81f639046 --- /dev/null +++ b/recipes/bioconductor-lbe/meta.yaml @@ -0,0 +1,31 @@ +{% set version = "1.46.0" %} +{% set name = "LBE" %} +{% set bioc = "3.6" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + fn: '{{ name }}_{{ version }}.tar.gz' + url: + - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: 209bfcc9a21c4a2559f73b3a4aa75077f432ddad9d4cb62df3c150f99bb7061c +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ +requirements: + build: + - r-base + run: + - r-base +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: GPL-2 + summary: 'LBE is an efficient procedure for estimating the proportion of true null hypotheses, the false discovery rate (and so the q-values) in the framework of estimating procedures based on the marginal distribution of the p-values without assumption for the alternative hypothesis.' diff --git a/recipes/bioconductor-les/build.sh b/recipes/bioconductor-les/build.sh new file mode 100644 index 00000000000000..da43ce21683122 --- /dev/null +++ b/recipes/bioconductor-les/build.sh @@ -0,0 +1,4 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-les/meta.yaml b/recipes/bioconductor-les/meta.yaml new file mode 100644 index 00000000000000..43c91ac345a55d --- /dev/null +++ b/recipes/bioconductor-les/meta.yaml @@ -0,0 +1,39 @@ +{% set version = "1.28.0" %} +{% set name = "les" %} +{% set bioc = "3.6" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + fn: '{{ name }}_{{ version }}.tar.gz' + url: + - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + sha256: e9e493b1dc2725beec76cb0260bb8d0b4ac0762788f38a0e0b118825d87bc777 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ +requirements: + build: + - r-base + - r-boot + - r-fdrtool + - r-gplots + - r-rcolorbrewer + run: + - r-base + - r-boot + - r-fdrtool + - r-gplots + - r-rcolorbrewer +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: GPL-3 + summary: 'The ''les'' package estimates Loci of Enhanced Significance (LES) in tiling microarray data. These are regions of regulation such as found in differential transcription, CHiP-chip, or DNA modification analysis. The package provides a universal framework suitable for identifying differential effects in tiling microarray data sets, and is independent of the underlying statistics at the level of single probes.' diff --git a/recipes/bioconductor-lfa/build.sh b/recipes/bioconductor-lfa/build.sh new file mode 100644 index 00000000000000..da43ce21683122 --- /dev/null +++ b/recipes/bioconductor-lfa/build.sh @@ -0,0 +1,4 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-lfa/meta.yaml b/recipes/bioconductor-lfa/meta.yaml new file mode 100644 index 00000000000000..800e75fc1bf1b4 --- /dev/null +++ b/recipes/bioconductor-lfa/meta.yaml @@ -0,0 +1,36 @@ +{% set version = "1.8.0" %} +{% set name = "lfa" %} +{% set bioc = "3.6" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + fn: '{{ name }}_{{ version }}.tar.gz' + url: + - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + sha256: 70e7638bb4d4acb8a4e71c01357a6118ce6570342bafd36267a262cec500801b +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ +requirements: + build: + - r-base + - r-corpcor + - gcc # [linux] + - llvm # [osx] + run: + - r-base + - r-corpcor + - libcxx # [osx] +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: GPL-3 + summary: 'LFA is a method for a PCA analogue on Binomial data via estimation of latent structure in the natural parameter.' diff --git a/recipes/bioconductor-linc/build.sh b/recipes/bioconductor-linc/build.sh new file mode 100644 index 00000000000000..da43ce21683122 --- /dev/null +++ b/recipes/bioconductor-linc/build.sh @@ -0,0 +1,4 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-linc/meta.yaml b/recipes/bioconductor-linc/meta.yaml new file mode 100644 index 00000000000000..edebe333fdb384 --- /dev/null +++ b/recipes/bioconductor-linc/meta.yaml @@ -0,0 +1,60 @@ +{% set version = "1.6.0" %} +{% set name = "LINC" %} +{% set bioc = "3.6" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + fn: '{{ name }}_{{ version }}.tar.gz' + url: + - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: cde9f0069dd8a1db8483a969dddd7107d16fd89a76ba867305664c5d2fcb8b4a +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ +requirements: + build: + - bioconductor-biobase + - bioconductor-clusterprofiler + - bioconductor-dose + - bioconductor-ggtree + - bioconductor-org.hs.eg.db + - bioconductor-reactomepa + - bioconductor-sva + - r-ape + - r-base + - r-ggplot2 + - r-gridextra + - r-png + - 'r-rcpp >=0.11.0' + - r-reshape2 + - gcc # [linux] + - llvm # [osx] + run: + - bioconductor-biobase + - bioconductor-clusterprofiler + - bioconductor-dose + - bioconductor-ggtree + - bioconductor-org.hs.eg.db + - bioconductor-reactomepa + - bioconductor-sva + - r-ape + - r-base + - r-ggplot2 + - r-gridextra + - r-png + - 'r-rcpp >=0.11.0' + - r-reshape2 + - libcxx # [osx] +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'This package provides methods to compute co-expression networks of lincRNAs and protein-coding genes. Biological terms associated with the sets of protein-coding genes predict the biological contexts of lincRNAs according to the ''Guilty by Association'' approach.' diff --git a/recipes/bioconductor-liquidassociation/build.sh b/recipes/bioconductor-liquidassociation/build.sh new file mode 100644 index 00000000000000..da43ce21683122 --- /dev/null +++ b/recipes/bioconductor-liquidassociation/build.sh @@ -0,0 +1,4 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-liquidassociation/meta.yaml b/recipes/bioconductor-liquidassociation/meta.yaml new file mode 100644 index 00000000000000..0feb76b290bc35 --- /dev/null +++ b/recipes/bioconductor-liquidassociation/meta.yaml @@ -0,0 +1,39 @@ +{% set version = "1.32.0" %} +{% set name = "LiquidAssociation" %} +{% set bioc = "3.6" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + fn: '{{ name }}_{{ version }}.tar.gz' + url: + - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: 8ed8895daf684d68196ea3e2464300c3968bb0535da84dc19a949b33822e2750 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ +requirements: + build: + - bioconductor-biobase + - bioconductor-org.sc.sgd.db + - bioconductor-yeastcc + - r-base + - r-geepack + run: + - bioconductor-biobase + - bioconductor-org.sc.sgd.db + - bioconductor-yeastcc + - r-base + - r-geepack +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: 'GPL (>=3)' + summary: 'The package contains functions for calculate direct and model-based estimators for liquid association. It also provides functions for testing the existence of liquid association given a gene triplet data.' diff --git a/recipes/bioconductor-lmdme/build.sh b/recipes/bioconductor-lmdme/build.sh new file mode 100644 index 00000000000000..da43ce21683122 --- /dev/null +++ b/recipes/bioconductor-lmdme/build.sh @@ -0,0 +1,4 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-lmdme/meta.yaml b/recipes/bioconductor-lmdme/meta.yaml new file mode 100644 index 00000000000000..046e50524008c1 --- /dev/null +++ b/recipes/bioconductor-lmdme/meta.yaml @@ -0,0 +1,37 @@ +{% set version = "1.20.0" %} +{% set name = "lmdme" %} +{% set bioc = "3.6" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + fn: '{{ name }}_{{ version }}.tar.gz' + url: + - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + sha256: c32a048d9c26b6b1faab9f9694ba52110918ca240f8dd617b8978954b873829c +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ +requirements: + build: + - bioconductor-limma + - bioconductor-stemhypoxia + - r-base + - r-pls + run: + - bioconductor-limma + - bioconductor-stemhypoxia + - r-base + - r-pls +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: 'GPL (>=2)' + summary: 'linear ANOVA decomposition of Multivariate Designed Experiments implementation based on limma lmFit. Features: i)Flexible formula type interface, ii) Fast limma based implementation, iii) p-values for each estimated coefficient levels in each factor, iv) F values for factor effects and v) plotting functions for PCA and PLS.' diff --git a/recipes/bioconductor-lobstahs/build.sh b/recipes/bioconductor-lobstahs/build.sh new file mode 100644 index 00000000000000..da43ce21683122 --- /dev/null +++ b/recipes/bioconductor-lobstahs/build.sh @@ -0,0 +1,4 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-lobstahs/meta.yaml b/recipes/bioconductor-lobstahs/meta.yaml new file mode 100644 index 00000000000000..b11236c128ea8c --- /dev/null +++ b/recipes/bioconductor-lobstahs/meta.yaml @@ -0,0 +1,35 @@ +{% set version = "1.4.0" %} +{% set name = "LOBSTAHS" %} +{% set bioc = "3.6" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + fn: '{{ name }}_{{ version }}.tar.gz' + url: + - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: a4175dc76a2ce2b6a1653350ed0590cbcdb46c8c79aac11730380bb4553d7eeb +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ +requirements: + build: + - bioconductor-camera + - bioconductor-xcms + - r-base + run: + - bioconductor-camera + - bioconductor-xcms + - r-base +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: 'GPL (>= 3) + file LICENSE' + summary: 'LOBSTAHS is a multifunction package for screening, annotation, and putative identification of mass spectral features in large, HPLC-MS lipid datasets. In silico data for a wide range of lipids, oxidized lipids, and oxylipins can be generated from user-supplied structural criteria with a database generation function. LOBSTAHS then applies these databases to assign putative compound identities to features in any high-mass accuracy dataset that has been processed using xcms and CAMERA. Users can then apply a series of orthogonal screening criteria based on adduct ion formation patterns, chromatographic retention time, and other properties, to evaluate and assign confidence scores to this list of preliminary assignments. During the screening routine, LOBSTAHS rejects assignments that do not meet the specified criteria, identifies potential isomers and isobars, and assigns a variety of annotation codes to assist the user in evaluating the accuracy of each assignment.' diff --git a/recipes/bioconductor-lol/build.sh b/recipes/bioconductor-lol/build.sh new file mode 100644 index 00000000000000..da43ce21683122 --- /dev/null +++ b/recipes/bioconductor-lol/build.sh @@ -0,0 +1,4 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-lol/meta.yaml b/recipes/bioconductor-lol/meta.yaml new file mode 100644 index 00000000000000..e90bd236c7eb8c --- /dev/null +++ b/recipes/bioconductor-lol/meta.yaml @@ -0,0 +1,35 @@ +{% set version = "1.26.0" %} +{% set name = "lol" %} +{% set bioc = "3.6" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + fn: '{{ name }}_{{ version }}.tar.gz' + url: + - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + sha256: e3356066abce1843daf46078b28e36b927055e7e6c31e09958366e0cf8279403 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ +requirements: + build: + - r-base + - r-matrix + - r-penalized + run: + - r-base + - r-matrix + - r-penalized +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: GPL-2 + summary: 'Various optimization methods for Lasso inference with matrix warpper' diff --git a/recipes/bioconductor-lpeadj/build.sh b/recipes/bioconductor-lpeadj/build.sh new file mode 100644 index 00000000000000..da43ce21683122 --- /dev/null +++ b/recipes/bioconductor-lpeadj/build.sh @@ -0,0 +1,4 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-lpeadj/meta.yaml b/recipes/bioconductor-lpeadj/meta.yaml new file mode 100644 index 00000000000000..95d9c5c7681f3a --- /dev/null +++ b/recipes/bioconductor-lpeadj/meta.yaml @@ -0,0 +1,33 @@ +{% set version = "1.38.0" %} +{% set name = "LPEadj" %} +{% set bioc = "3.6" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + fn: '{{ name }}_{{ version }}.tar.gz' + url: + - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: a2e5de18246415264d0490ff688c5ee80488cad5fb00a590f6acfc8f94ac0082 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ +requirements: + build: + - bioconductor-lpe + - r-base + run: + - bioconductor-lpe + - r-base +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: LGPL + summary: 'Two options are added to the LPE algorithm. The original LPE method sets all variances below the max variance in the ordered distribution of variances to the maximum variance. in LPEadj this option is turned off by default. The second option is to use a variance adjustment based on sample size rather than pi/2. By default the LPEadj uses the sample size based variance adjustment.' diff --git a/recipes/bioconductor-lpnet/build.sh b/recipes/bioconductor-lpnet/build.sh new file mode 100644 index 00000000000000..da43ce21683122 --- /dev/null +++ b/recipes/bioconductor-lpnet/build.sh @@ -0,0 +1,4 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-lpnet/meta.yaml b/recipes/bioconductor-lpnet/meta.yaml new file mode 100644 index 00000000000000..6513a90ca19546 --- /dev/null +++ b/recipes/bioconductor-lpnet/meta.yaml @@ -0,0 +1,35 @@ +{% set version = "2.10.0" %} +{% set name = "lpNet" %} +{% set bioc = "3.6" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + fn: '{{ name }}_{{ version }}.tar.gz' + url: + - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: 41ef36c643c3b5380c0d9bb139496c05bc8579d969f72c3c41d881a039f47d64 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ +requirements: + build: + - bioconductor-nem + - r-base + - r-lpsolve + run: + - bioconductor-nem + - r-base + - r-lpsolve +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: 'Artistic License 2.0' + summary: 'lpNet aims at infering biological networks, in particular signaling and gene networks. For that it takes perturbation data, either steady-state or time-series, as input and generates an LP model which allows the inference of signaling networks. For parameter identification either leave-one-out cross-validation or stratified n-fold cross-validation can be used.' diff --git a/recipes/bioconductor-lumihumanall.db/meta.yaml b/recipes/bioconductor-lumihumanall.db/meta.yaml new file mode 100644 index 00000000000000..e747c8d0d4e417 --- /dev/null +++ b/recipes/bioconductor-lumihumanall.db/meta.yaml @@ -0,0 +1,36 @@ +{% set version = "1.22.0" %} +{% set name = "lumiHumanAll.db" %} +{% set bioc = "3.6" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + fn: '{{ name }}_{{ version }}.tar.gz' + url: + - 'http://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: a2c1bd766e756eb7e01cf196c1809c8a282a4c4caaf1482a0d1961b2c2a8c24e +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ +requirements: + build: + - 'bioconductor-annotationdbi >=1.23.25' + - 'bioconductor-org.hs.eg.db >=2.10.1' + - r-base + run: + - 'bioconductor-annotationdbi >=1.23.25' + - 'bioconductor-org.hs.eg.db >=2.10.1' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'http://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Illumina Human Illumina expression annotation data (chip lumiHumanAll) assembled using data from public repositories' diff --git a/recipes/bioconductor-lumihumanall.db/post-link.sh b/recipes/bioconductor-lumihumanall.db/post-link.sh new file mode 100644 index 00000000000000..52e08acd78dcae --- /dev/null +++ b/recipes/bioconductor-lumihumanall.db/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="lumiHumanAll.db_1.22.0.tar.gz" +URLS=( + "http://bioconductor.org/packages/3.6/data/annotation/src/contrib/lumiHumanAll.db_1.22.0.tar.gz" + "https://bioarchive.galaxyproject.org/lumiHumanAll.db_1.22.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-lumihumanall.db/bioconductor-lumihumanall.db_1.22.0_src_all.tar.gz" +) +MD5="ce7e219b50833ceab203f0bbfb11d917" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING \ No newline at end of file diff --git a/recipes/bioconductor-lumihumanall.db/pre-unlink.sh b/recipes/bioconductor-lumihumanall.db/pre-unlink.sh new file mode 100644 index 00000000000000..7b699654765077 --- /dev/null +++ b/recipes/bioconductor-lumihumanall.db/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ lumiHumanAll.db diff --git a/recipes/bioconductor-lungcanceracvssccgeo/meta.yaml b/recipes/bioconductor-lungcanceracvssccgeo/meta.yaml new file mode 100644 index 00000000000000..a9267919a70802 --- /dev/null +++ b/recipes/bioconductor-lungcanceracvssccgeo/meta.yaml @@ -0,0 +1,32 @@ +{% set version = "1.14.0" %} +{% set name = "LungCancerACvsSCCGEO" %} +{% set bioc = "3.6" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + fn: '{{ name }}_{{ version }}.tar.gz' + url: + - 'http://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: 05e85af977bd740452edec788a24301aba9adc3a7bad29104ff4ea15a3a11974 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ +requirements: + build: + - r-base + run: + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'http://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' + license: GPL-2 + summary: 'This package contains 30 Affymetrix CEL files for 7 Adenocarcinoma (AC) and 8 Squamous cell carcinoma (SCC) lung cancer samples taken at random from 3 GEO datasets (GSE10245, GSE18842 and GSE2109) and other 15 samples from a dataset produced by the organizers of the IMPROVER Diagnostic Signature Challenge available from GEO (GSE43580).' diff --git a/recipes/bioconductor-lungcanceracvssccgeo/post-link.sh b/recipes/bioconductor-lungcanceracvssccgeo/post-link.sh new file mode 100644 index 00000000000000..f5e4e1389cdf98 --- /dev/null +++ b/recipes/bioconductor-lungcanceracvssccgeo/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="LungCancerACvsSCCGEO_1.14.0.tar.gz" +URLS=( + "http://bioconductor.org/packages/3.6/data/experiment/src/contrib/LungCancerACvsSCCGEO_1.14.0.tar.gz" + "https://bioarchive.galaxyproject.org/LungCancerACvsSCCGEO_1.14.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-lungcanceracvssccgeo/bioconductor-lungcanceracvssccgeo_1.14.0_src_all.tar.gz" +) +MD5="275e2efe74fcf1823f8547902537e175" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING \ No newline at end of file diff --git a/recipes/bioconductor-lungcanceracvssccgeo/pre-unlink.sh b/recipes/bioconductor-lungcanceracvssccgeo/pre-unlink.sh new file mode 100644 index 00000000000000..b47eeb6c9313fe --- /dev/null +++ b/recipes/bioconductor-lungcanceracvssccgeo/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ LungCancerACvsSCCGEO diff --git a/recipes/bioconductor-lvsmirna/build.sh b/recipes/bioconductor-lvsmirna/build.sh new file mode 100644 index 00000000000000..da43ce21683122 --- /dev/null +++ b/recipes/bioconductor-lvsmirna/build.sh @@ -0,0 +1,4 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-lvsmirna/meta.yaml b/recipes/bioconductor-lvsmirna/meta.yaml new file mode 100644 index 00000000000000..59b64c767deb99 --- /dev/null +++ b/recipes/bioconductor-lvsmirna/meta.yaml @@ -0,0 +1,52 @@ +{% set version = "1.28.0" %} +{% set name = "LVSmiRNA" %} +{% set bioc = "3.6" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + fn: '{{ name }}_{{ version }}.tar.gz' + url: + - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: bcd16c6920f0d0552696068e07625381a7e5daf8b678c321c001759df46c7624 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ +requirements: + build: + - bioconductor-affy + - bioconductor-biobase + - bioconductor-biocgenerics + - bioconductor-limma + - bioconductor-vsn + - bioconductor-zlibbioc + - r-base + - r-mass + - r-quantreg + - r-sparsem + - gcc # [linux] + - llvm # [osx] + run: + - bioconductor-affy + - bioconductor-biobase + - bioconductor-biocgenerics + - bioconductor-limma + - bioconductor-vsn + - bioconductor-zlibbioc + - r-base + - r-mass + - r-quantreg + - r-sparsem + - libcxx # [osx] +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: GPL-2 + summary: 'Normalization of Agilent miRNA arrays.' diff --git a/recipes/bioconductor-m3d/build.sh b/recipes/bioconductor-m3d/build.sh new file mode 100644 index 00000000000000..da43ce21683122 --- /dev/null +++ b/recipes/bioconductor-m3d/build.sh @@ -0,0 +1,4 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-m3d/meta.yaml b/recipes/bioconductor-m3d/meta.yaml new file mode 100644 index 00000000000000..68d38fedf3786f --- /dev/null +++ b/recipes/bioconductor-m3d/meta.yaml @@ -0,0 +1,48 @@ +{% set version = "1.12.0" %} +{% set name = "M3D" %} +{% set bioc = "3.6" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + fn: '{{ name }}_{{ version }}.tar.gz' + url: + - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: f49f19f08e965ec869f4fe5913c471e6fbb2874d0afff5a21a3af71428ef6bf0 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ +requirements: + build: + - bioconductor-biocgenerics + - bioconductor-biseq + - bioconductor-genomicranges + - bioconductor-iranges + - bioconductor-s4vectors + - bioconductor-summarizedexperiment + - r-base + - r-rcpp + - gcc # [linux] + - llvm # [osx] + run: + - bioconductor-biocgenerics + - bioconductor-biseq + - bioconductor-genomicranges + - bioconductor-iranges + - bioconductor-s4vectors + - bioconductor-summarizedexperiment + - r-base + - r-rcpp + - libcxx # [osx] +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: 'Artistic License 2.0' + summary: 'This package identifies statistically significantly differentially methylated regions of CpGs. It uses kernel methods (the Maximum Mean Discrepancy) to measure differences in methylation profiles, and relates these to inter-replicate changes, whilst accounting for variation in coverage profiles.' diff --git a/recipes/bioconductor-madseq/build.sh b/recipes/bioconductor-madseq/build.sh new file mode 100644 index 00000000000000..da43ce21683122 --- /dev/null +++ b/recipes/bioconductor-madseq/build.sh @@ -0,0 +1,4 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-madseq/meta.yaml b/recipes/bioconductor-madseq/meta.yaml new file mode 100644 index 00000000000000..852073110e001d --- /dev/null +++ b/recipes/bioconductor-madseq/meta.yaml @@ -0,0 +1,65 @@ +{% set version = "1.4.1" %} +{% set name = "MADSEQ" %} +{% set bioc = "3.6" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + fn: '{{ name }}_{{ version }}.tar.gz' + url: + - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: 0d52a0eec1af9bac3447d41cf4a86c2e65c770a68227c4192380ac164f538079 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ +requirements: + build: + - bioconductor-biostrings + - bioconductor-bsgenome + - bioconductor-bsgenome.hsapiens.ucsc.hg19 + - bioconductor-genomeinfodb + - bioconductor-genomicalignments + - bioconductor-genomicranges + - bioconductor-iranges + - bioconductor-preprocesscore + - bioconductor-rsamtools + - bioconductor-rtracklayer + - bioconductor-s4vectors + - bioconductor-summarizedexperiment + - bioconductor-variantannotation + - bioconductor-zlibbioc + - r-base + - r-coda + - 'r-rjags >=4-6' + - r-vgam + run: + - bioconductor-biostrings + - bioconductor-bsgenome + - bioconductor-bsgenome.hsapiens.ucsc.hg19 + - bioconductor-genomeinfodb + - bioconductor-genomicalignments + - bioconductor-genomicranges + - bioconductor-iranges + - bioconductor-preprocesscore + - bioconductor-rsamtools + - bioconductor-rtracklayer + - bioconductor-s4vectors + - bioconductor-summarizedexperiment + - bioconductor-variantannotation + - bioconductor-zlibbioc + - r-base + - r-coda + - 'r-rjags >=4-6' + - r-vgam +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: GPL(>=2) + summary: 'The MADSEQ package provides a group of hierarchical Bayeisan models for the detection of mosaic aneuploidy, the inference of the type of aneuploidy and also for the quantification of the fraction of aneuploid cells in the sample.' diff --git a/recipes/bioconductor-maigespack/build.sh b/recipes/bioconductor-maigespack/build.sh new file mode 100644 index 00000000000000..da43ce21683122 --- /dev/null +++ b/recipes/bioconductor-maigespack/build.sh @@ -0,0 +1,4 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-maigespack/meta.yaml b/recipes/bioconductor-maigespack/meta.yaml new file mode 100644 index 00000000000000..0c35a07fe7c4a6 --- /dev/null +++ b/recipes/bioconductor-maigespack/meta.yaml @@ -0,0 +1,42 @@ +{% set version = "1.42.0" %} +{% set name = "maigesPack" %} +{% set bioc = "3.6" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + fn: '{{ name }}_{{ version }}.tar.gz' + url: + - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: b2241940bd8edacc6f58f5fe913a1c3bfc4fc14331ef55276bded52cf29c22b1 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ +requirements: + build: + - bioconductor-convert + - bioconductor-graph + - bioconductor-limma + - bioconductor-marray + - r-base + - gcc # [linux] + - llvm # [osx] + run: + - bioconductor-convert + - bioconductor-graph + - bioconductor-limma + - bioconductor-marray + - r-base + - libcxx # [osx] +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: 'GPL (>= 2)' + summary: 'This package uses functions of various other packages together with other functions in a coordinated way to handle and analyse cDNA microarray data' diff --git a/recipes/bioconductor-mapredictdsc/build.sh b/recipes/bioconductor-mapredictdsc/build.sh new file mode 100644 index 00000000000000..da43ce21683122 --- /dev/null +++ b/recipes/bioconductor-mapredictdsc/build.sh @@ -0,0 +1,4 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-mapredictdsc/meta.yaml b/recipes/bioconductor-mapredictdsc/meta.yaml new file mode 100644 index 00000000000000..e845835c9bc1dc --- /dev/null +++ b/recipes/bioconductor-mapredictdsc/meta.yaml @@ -0,0 +1,55 @@ +{% set version = "1.16.0" %} +{% set name = "maPredictDSC" %} +{% set bioc = "3.6" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + fn: '{{ name }}_{{ version }}.tar.gz' + url: + - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: 782eb25ac55afba8545bb91d11a7aa8e7fb8267f67d4be5fa40b6466f4f99f0b +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ +requirements: + build: + - bioconductor-affy + - bioconductor-annotationdbi + - bioconductor-gcrma + - bioconductor-hgu133plus2.db + - bioconductor-limma + - bioconductor-lungcanceracvssccgeo + - bioconductor-roc + - r-base + - r-caret + - r-class + - r-e1071 + - r-mass + - r-rocr + run: + - bioconductor-affy + - bioconductor-annotationdbi + - bioconductor-gcrma + - bioconductor-hgu133plus2.db + - bioconductor-limma + - bioconductor-lungcanceracvssccgeo + - bioconductor-roc + - r-base + - r-caret + - r-class + - r-e1071 + - r-mass + - r-rocr +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: GPL-2 + summary: 'This package implements the classification pipeline of the best overall team (Team221) in the IMPROVER Diagnostic Signature Challenge. Additional functionality is added to compare 27 combinations of data preprocessing, feature selection and classifier types.' diff --git a/recipes/bioconductor-maskbad/build.sh b/recipes/bioconductor-maskbad/build.sh new file mode 100644 index 00000000000000..da43ce21683122 --- /dev/null +++ b/recipes/bioconductor-maskbad/build.sh @@ -0,0 +1,4 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-maskbad/meta.yaml b/recipes/bioconductor-maskbad/meta.yaml new file mode 100644 index 00000000000000..27c647802febf6 --- /dev/null +++ b/recipes/bioconductor-maskbad/meta.yaml @@ -0,0 +1,35 @@ +{% set version = "1.22.0" %} +{% set name = "maskBAD" %} +{% set bioc = "3.6" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + fn: '{{ name }}_{{ version }}.tar.gz' + url: + - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: e8520c0db92e73eb06e1a641b088f28c2cbc7ea5ea965f34f871f3f17ccae265 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ +requirements: + build: + - bioconductor-affy + - 'bioconductor-gcrma >=2.27.1' + - r-base + run: + - bioconductor-affy + - 'bioconductor-gcrma >=2.27.1' + - r-base +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: 'GPL version 2 or newer' + summary: 'Package includes functions to analyze and mask microarray expression data.' diff --git a/recipes/bioconductor-mcrestimate/build.sh b/recipes/bioconductor-mcrestimate/build.sh new file mode 100644 index 00000000000000..da43ce21683122 --- /dev/null +++ b/recipes/bioconductor-mcrestimate/build.sh @@ -0,0 +1,4 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-mcrestimate/meta.yaml b/recipes/bioconductor-mcrestimate/meta.yaml new file mode 100644 index 00000000000000..5fba6beeccd2ca --- /dev/null +++ b/recipes/bioconductor-mcrestimate/meta.yaml @@ -0,0 +1,43 @@ +{% set version = "2.34.0" %} +{% set name = "MCRestimate" %} +{% set bioc = "3.6" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + fn: '{{ name }}_{{ version }}.tar.gz' + url: + - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: 234beb71a27eb29c92a96e3c09c9928d7915b2ab63e7770fba8a346aea5d8ad8 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ +requirements: + build: + - 'bioconductor-biobase >=2.5.5' + - 'bioconductor-golubesets >=1.4.6' + - r-base + - 'r-e1071 >=1.5-12' + - 'r-pamr >=1.22' + - 'r-randomforest >=3.9-6' + - 'r-rcolorbrewer >=0.1-3' + run: + - 'bioconductor-biobase >=2.5.5' + - 'bioconductor-golubesets >=1.4.6' + - r-base + - 'r-e1071 >=1.5-12' + - 'r-pamr >=1.22' + - 'r-randomforest >=3.9-6' + - 'r-rcolorbrewer >=0.1-3' +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: 'GPL (>= 2)' + summary: 'This package includes a function for combining preprocessing and classification methods to calculate misclassification errors' diff --git a/recipes/bioconductor-measurementerror.cor/build.sh b/recipes/bioconductor-measurementerror.cor/build.sh new file mode 100644 index 00000000000000..da43ce21683122 --- /dev/null +++ b/recipes/bioconductor-measurementerror.cor/build.sh @@ -0,0 +1,4 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-measurementerror.cor/meta.yaml b/recipes/bioconductor-measurementerror.cor/meta.yaml new file mode 100644 index 00000000000000..df3b5487c541c0 --- /dev/null +++ b/recipes/bioconductor-measurementerror.cor/meta.yaml @@ -0,0 +1,31 @@ +{% set version = "1.50.0" %} +{% set name = "MeasurementError.cor" %} +{% set bioc = "3.6" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + fn: '{{ name }}_{{ version }}.tar.gz' + url: + - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: 485255ba0804cdc0560a6a15e4cb2c4f728e6a105e4aabfd401cccd3a04f7e3e +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ +requirements: + build: + - r-base + run: + - r-base +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: LGPL + summary: 'Two-stage measurement error model for correlation estimation with smaller bias than the usual sample correlation' diff --git a/recipes/bioconductor-medme/build.sh b/recipes/bioconductor-medme/build.sh new file mode 100644 index 00000000000000..da43ce21683122 --- /dev/null +++ b/recipes/bioconductor-medme/build.sh @@ -0,0 +1,4 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-medme/meta.yaml b/recipes/bioconductor-medme/meta.yaml new file mode 100644 index 00000000000000..b938b07dc0d6f5 --- /dev/null +++ b/recipes/bioconductor-medme/meta.yaml @@ -0,0 +1,40 @@ +{% set version = "1.38.0" %} +{% set name = "MEDME" %} +{% set bioc = "3.6" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + fn: '{{ name }}_{{ version }}.tar.gz' + url: + - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: 37154c7d207b4f5f03bc26e19c57b6a798ba9eb8fa666d073e99fcf1c24ff78c +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ +requirements: + build: + - bioconductor-biostrings + - r-base + - r-drc + - r-mass + - gcc # [linux] + - llvm # [osx] + run: + - bioconductor-biostrings + - r-base + - r-drc + - r-mass + - libcxx # [osx] +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: 'GPL (>= 2)' + summary: 'Description: MEDME allows the prediction of absolute and relative methylation levels based on measures obtained by MeDIP-microarray experiments' diff --git a/recipes/bioconductor-meigor/build.sh b/recipes/bioconductor-meigor/build.sh new file mode 100644 index 00000000000000..da43ce21683122 --- /dev/null +++ b/recipes/bioconductor-meigor/build.sh @@ -0,0 +1,4 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-meigor/meta.yaml b/recipes/bioconductor-meigor/meta.yaml new file mode 100644 index 00000000000000..bceaa4da695625 --- /dev/null +++ b/recipes/bioconductor-meigor/meta.yaml @@ -0,0 +1,39 @@ +{% set version = "1.12.0" %} +{% set name = "MEIGOR" %} +{% set bioc = "3.6" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + fn: '{{ name }}_{{ version }}.tar.gz' + url: + - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: db8717398347cf12e790303fd55287def0310056e985e198ccc7cc7dac3a9c17 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ +requirements: + build: + - bioconductor-cnorode + - r-base + - r-desolve + - r-rsolnp + - r-snowfall + run: + - bioconductor-cnorode + - r-base + - r-desolve + - r-rsolnp + - r-snowfall +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: GPL-3 + summary: 'Global Optimization' diff --git a/recipes/bioconductor-mesh.db/meta.yaml b/recipes/bioconductor-mesh.db/meta.yaml new file mode 100644 index 00000000000000..77d08e263dca26 --- /dev/null +++ b/recipes/bioconductor-mesh.db/meta.yaml @@ -0,0 +1,34 @@ +{% set version = "1.9.0" %} +{% set name = "MeSH.db" %} +{% set bioc = "3.6" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + fn: '{{ name }}_{{ version }}.tar.gz' + url: + - 'http://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: 7b4a3007127c0d6b912d4eb7ce21aedd68dc78951504a8953e819c6ef6eb92ee +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ +requirements: + build: + - bioconductor-meshdbi + - r-base + run: + - bioconductor-meshdbi + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'http://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'A set of annotation maps describing the entire MeSH assembled using data from MeSH.' diff --git a/recipes/bioconductor-mesh.db/post-link.sh b/recipes/bioconductor-mesh.db/post-link.sh new file mode 100644 index 00000000000000..603377e4b8c97e --- /dev/null +++ b/recipes/bioconductor-mesh.db/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="MeSH.db_1.9.0.tar.gz" +URLS=( + "http://bioconductor.org/packages/3.6/data/annotation/src/contrib/MeSH.db_1.9.0.tar.gz" + "https://bioarchive.galaxyproject.org/MeSH.db_1.9.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-mesh.db/bioconductor-mesh.db_1.9.0_src_all.tar.gz" +) +MD5="8e29b2c99bc3aa3ee25bc8c581d3dac8" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING \ No newline at end of file diff --git a/recipes/bioconductor-mesh.db/pre-unlink.sh b/recipes/bioconductor-mesh.db/pre-unlink.sh new file mode 100644 index 00000000000000..777f767821f8e6 --- /dev/null +++ b/recipes/bioconductor-mesh.db/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ MeSH.db diff --git a/recipes/bioconductor-meshes/build.sh b/recipes/bioconductor-meshes/build.sh new file mode 100644 index 00000000000000..da43ce21683122 --- /dev/null +++ b/recipes/bioconductor-meshes/build.sh @@ -0,0 +1,4 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-meshes/meta.yaml b/recipes/bioconductor-meshes/meta.yaml new file mode 100644 index 00000000000000..8b310803050d47 --- /dev/null +++ b/recipes/bioconductor-meshes/meta.yaml @@ -0,0 +1,41 @@ +{% set version = "1.4.0" %} +{% set name = "meshes" %} +{% set bioc = "3.6" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + fn: '{{ name }}_{{ version }}.tar.gz' + url: + - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + sha256: 020206f48961464fb1e38b35ed53b71d88f4a41dc629b747f85c036c8284e2eb +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ +requirements: + build: + - bioconductor-annotationdbi + - 'bioconductor-dose >=2.11.7' + - 'bioconductor-gosemsim >=1.99.3' + - bioconductor-mesh.db + - r-base + - r-rvcheck + run: + - bioconductor-annotationdbi + - 'bioconductor-dose >=2.11.7' + - 'bioconductor-gosemsim >=1.99.3' + - bioconductor-mesh.db + - r-base + - r-rvcheck +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'MeSH (Medical Subject Headings) is the NLM controlled vocabulary used to manually index articles for MEDLINE/PubMed. MeSH terms were associated by Entrez Gene ID by three methods, gendoo, gene2pubmed and RBBH. This association is fundamental for enrichment and semantic analyses. meshes supports enrichment analysis (over-representation and gene set enrichment analysis) of gene list or whole expression profile. The semantic comparisons of MeSH terms provide quantitative ways to compute similarities between genes and gene groups. meshes implemented five methods proposed by Resnik, Schlicker, Jiang, Lin and Wang respectively and supports more than 70 species.' diff --git a/recipes/bioconductor-metab/build.sh b/recipes/bioconductor-metab/build.sh new file mode 100644 index 00000000000000..da43ce21683122 --- /dev/null +++ b/recipes/bioconductor-metab/build.sh @@ -0,0 +1,4 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-metab/meta.yaml b/recipes/bioconductor-metab/meta.yaml new file mode 100644 index 00000000000000..aa8ef436f0de59 --- /dev/null +++ b/recipes/bioconductor-metab/meta.yaml @@ -0,0 +1,37 @@ +{% set version = "1.12.0" %} +{% set name = "Metab" %} +{% set bioc = "3.6" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + fn: '{{ name }}_{{ version }}.tar.gz' + url: + - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: c7de781da1c3fc0e13a77999f570e9df8f3532173d0d229b544363f8376cd73e +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ +requirements: + build: + - bioconductor-xcms + - r-base + - r-pander + - r-svdialogs + run: + - bioconductor-xcms + - r-base + - r-pander + - r-svdialogs +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: 'GPL (>=2)' + summary: 'Metab is an R package for high-throughput processing of metabolomics data analysed by the Automated Mass Spectral Deconvolution and Identification System (AMDIS) (http://chemdata.nist.gov/mass-spc/amdis/downloads/). In addition, it performs statistical hypothesis test (t-test) and analysis of variance (ANOVA). Doing so, Metab considerably speed up the data mining process in metabolomics and produces better quality results. Metab was developed using interactive features, allowing users with lack of R knowledge to appreciate its functionalities.' diff --git a/recipes/bioconductor-metabosignal/build.sh b/recipes/bioconductor-metabosignal/build.sh new file mode 100644 index 00000000000000..da43ce21683122 --- /dev/null +++ b/recipes/bioconductor-metabosignal/build.sh @@ -0,0 +1,4 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-metabosignal/meta.yaml b/recipes/bioconductor-metabosignal/meta.yaml new file mode 100644 index 00000000000000..3d3f555cf1c1af --- /dev/null +++ b/recipes/bioconductor-metabosignal/meta.yaml @@ -0,0 +1,53 @@ +{% set version = "1.8.0" %} +{% set name = "MetaboSignal" %} +{% set bioc = "3.6" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + fn: '{{ name }}_{{ version }}.tar.gz' + url: + - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: 29240127a63d40fa7ad31c5e5cb48a024b1a21e84db14f957b487bbf1c63cd63 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ +requirements: + build: + - bioconductor-annotationdbi + - bioconductor-biomart + - bioconductor-ensdb.hsapiens.v75 + - bioconductor-hpar + - bioconductor-kegggraph + - bioconductor-keggrest + - bioconductor-mwastools + - bioconductor-mygene + - bioconductor-org.hs.eg.db + - r-base + - r-igraph + - r-rcurl + run: + - bioconductor-annotationdbi + - bioconductor-biomart + - bioconductor-ensdb.hsapiens.v75 + - bioconductor-hpar + - bioconductor-kegggraph + - bioconductor-keggrest + - bioconductor-mwastools + - bioconductor-mygene + - bioconductor-org.hs.eg.db + - r-base + - r-igraph + - r-rcurl +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: GPL-3 + summary: 'MetaboSignal is an R package that allows merging, analyzing and customizing metabolic and signaling KEGG pathways. It is a network-based approach designed to explore the topological relationship between genes (signaling- or enzymatic-genes) and metabolites, representing a powerful tool to investigate the genetic landscape and regulatory networks of metabolic phenotypes.' diff --git a/recipes/bioconductor-methyanalysis/build.sh b/recipes/bioconductor-methyanalysis/build.sh new file mode 100644 index 00000000000000..da43ce21683122 --- /dev/null +++ b/recipes/bioconductor-methyanalysis/build.sh @@ -0,0 +1,4 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-methyanalysis/meta.yaml b/recipes/bioconductor-methyanalysis/meta.yaml new file mode 100644 index 00000000000000..4914dfe8c47fdc --- /dev/null +++ b/recipes/bioconductor-methyanalysis/meta.yaml @@ -0,0 +1,67 @@ +{% set version = "1.20.0" %} +{% set name = "methyAnalysis" %} +{% set bioc = "3.6" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + fn: '{{ name }}_{{ version }}.tar.gz' + url: + - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: 83e201c2f3c37f0e29be1f20c6e0384eeb5d48874789a9330ef21176c9d9af32 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ +requirements: + build: + - bioconductor-annotate + - bioconductor-annotationdbi + - 'bioconductor-biobase >=2.34.0' + - bioconductor-biocgenerics + - bioconductor-biomart + - bioconductor-genefilter + - bioconductor-genomeinfodb + - bioconductor-genomicfeatures + - bioconductor-genomicranges + - bioconductor-genoset + - bioconductor-gviz + - bioconductor-iranges + - bioconductor-lumi + - bioconductor-methylumi + - bioconductor-org.hs.eg.db + - bioconductor-rtracklayer + - bioconductor-summarizedexperiment + - bioconductor-variantannotation + - r-base + run: + - bioconductor-annotate + - bioconductor-annotationdbi + - 'bioconductor-biobase >=2.34.0' + - bioconductor-biocgenerics + - bioconductor-biomart + - bioconductor-genefilter + - bioconductor-genomeinfodb + - bioconductor-genomicfeatures + - bioconductor-genomicranges + - bioconductor-genoset + - bioconductor-gviz + - bioconductor-iranges + - bioconductor-lumi + - bioconductor-methylumi + - bioconductor-org.hs.eg.db + - bioconductor-rtracklayer + - bioconductor-summarizedexperiment + - bioconductor-variantannotation + - r-base +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'The methyAnalysis package aims for the DNA methylation data analysis and visualization. A MethyGenoSet class is defined to keep the chromosome location information together with the data. The package also includes functions of estimating the methylation levels from Methy-Seq data.' diff --git a/recipes/bioconductor-methylseekr/meta.yaml b/recipes/bioconductor-methylseekr/meta.yaml index 3e9c3bea488b15..96a32d55635fb0 100644 --- a/recipes/bioconductor-methylseekr/meta.yaml +++ b/recipes/bioconductor-methylseekr/meta.yaml @@ -12,7 +12,7 @@ source: - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' sha256: 546ad60c07f0b25a1b79b0aef23af305954449bd51e94b19d169e2b7a4503e34 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ @@ -33,6 +33,7 @@ requirements: - 'bioconductor-rtracklayer >=1.16.3' - r-base - 'r-mhsmm >=0.4.4' + - r-kernsmooth test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-mineica/build.sh b/recipes/bioconductor-mineica/build.sh new file mode 100644 index 00000000000000..da43ce21683122 --- /dev/null +++ b/recipes/bioconductor-mineica/build.sh @@ -0,0 +1,4 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-mineica/meta.yaml b/recipes/bioconductor-mineica/meta.yaml new file mode 100644 index 00000000000000..461fa55bcc0692 --- /dev/null +++ b/recipes/bioconductor-mineica/meta.yaml @@ -0,0 +1,83 @@ +{% set version = "1.18.0" %} +{% set name = "MineICA" %} +{% set bioc = "3.6" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + fn: '{{ name }}_{{ version }}.tar.gz' + url: + - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: beddc6b0f594a43aa5ebf9bbed8b872b6453600bd2f8bc72cca8ea49422cb8fd +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ +requirements: + build: + - bioconductor-annotate + - bioconductor-annotationdbi + - bioconductor-biobase + - 'bioconductor-biocgenerics >=0.13.8' + - bioconductor-biomart + - bioconductor-gostats + - bioconductor-graph + - bioconductor-lumi + - bioconductor-lumihumanall.db + - bioconductor-marray + - bioconductor-rgraphviz + - r-base + - r-cluster + - r-colorspace + - r-fastica + - r-foreach + - r-fpc + - r-ggplot2 + - r-gtools + - r-hmisc + - r-igraph + - r-jade + - r-mclust + - r-plyr + - r-rcolorbrewer + - r-scales + - r-xtable + run: + - bioconductor-annotate + - bioconductor-annotationdbi + - bioconductor-biobase + - 'bioconductor-biocgenerics >=0.13.8' + - bioconductor-biomart + - bioconductor-gostats + - bioconductor-graph + - bioconductor-lumi + - bioconductor-lumihumanall.db + - bioconductor-marray + - bioconductor-rgraphviz + - r-base + - r-cluster + - r-colorspace + - r-fastica + - r-foreach + - r-fpc + - r-ggplot2 + - r-gtools + - r-hmisc + - r-igraph + - r-jade + - r-mclust + - r-plyr + - r-rcolorbrewer + - r-scales + - r-xtable +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: GPL-2 + summary: 'The goal of MineICA is to perform Independent Component Analysis (ICA) on multiple transcriptome datasets, integrating additional data (e.g molecular, clinical and pathological). This Integrative ICA helps the biological interpretation of the components by studying their association with variables (e.g sample annotations) and gene sets, and enables the comparison of components from different datasets using correlation-based graph.' diff --git a/recipes/bioconductor-minet/build.sh b/recipes/bioconductor-minet/build.sh new file mode 100644 index 00000000000000..da43ce21683122 --- /dev/null +++ b/recipes/bioconductor-minet/build.sh @@ -0,0 +1,4 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-minet/meta.yaml b/recipes/bioconductor-minet/meta.yaml new file mode 100644 index 00000000000000..a475a723c6b403 --- /dev/null +++ b/recipes/bioconductor-minet/meta.yaml @@ -0,0 +1,36 @@ +{% set version = "3.36.0" %} +{% set name = "minet" %} +{% set bioc = "3.6" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + fn: '{{ name }}_{{ version }}.tar.gz' + url: + - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + sha256: c8dabac10814a69fab810600b60c85358fafa62d34a9363b7d176e77209fe9c5 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ +requirements: + build: + - r-base + - r-infotheo + - gcc # [linux] + - llvm # [osx] + run: + - r-base + - r-infotheo + - libcxx # [osx] +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: 'file LICENSE' + summary: 'This package implements various algorithms for inferring mutual information networks from data.' diff --git a/recipes/bioconductor-minimumdistance/build.sh b/recipes/bioconductor-minimumdistance/build.sh new file mode 100644 index 00000000000000..da43ce21683122 --- /dev/null +++ b/recipes/bioconductor-minimumdistance/build.sh @@ -0,0 +1,4 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-minimumdistance/meta.yaml b/recipes/bioconductor-minimumdistance/meta.yaml new file mode 100644 index 00000000000000..45ff737191c272 --- /dev/null +++ b/recipes/bioconductor-minimumdistance/meta.yaml @@ -0,0 +1,61 @@ +{% set version = "1.22.0" %} +{% set name = "MinimumDistance" %} +{% set bioc = "3.6" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + fn: '{{ name }}_{{ version }}.tar.gz' + url: + - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: 2ea74a8add036e054380cf5e8f73dc8b51b8f64e3917931602263115a2044fc8 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ +requirements: + build: + - bioconductor-biobase + - bioconductor-biocgenerics + - bioconductor-dnacopy + - bioconductor-genomeinfodb + - 'bioconductor-genomicranges >=1.17.16' + - bioconductor-iranges + - bioconductor-oligoclasses + - 'bioconductor-s4vectors >=0.9.25' + - 'bioconductor-summarizedexperiment >=0.2.0' + - 'bioconductor-vanillaice >=1.31.3' + - r-base + - r-data.table + - r-ff + - r-foreach + - r-lattice + - r-matrixstats + run: + - bioconductor-biobase + - bioconductor-biocgenerics + - bioconductor-dnacopy + - bioconductor-genomeinfodb + - 'bioconductor-genomicranges >=1.17.16' + - bioconductor-iranges + - bioconductor-oligoclasses + - 'bioconductor-s4vectors >=0.9.25' + - 'bioconductor-summarizedexperiment >=0.2.0' + - 'bioconductor-vanillaice >=1.31.3' + - r-base + - r-data.table + - r-ff + - r-foreach + - r-lattice + - r-matrixstats +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Analysis of de novo copy number variants in trios from high-dimensional genotyping platforms.' diff --git a/recipes/bioconductor-mirbaseversions.db/meta.yaml b/recipes/bioconductor-mirbaseversions.db/meta.yaml new file mode 100644 index 00000000000000..c320368ee0f0eb --- /dev/null +++ b/recipes/bioconductor-mirbaseversions.db/meta.yaml @@ -0,0 +1,40 @@ +{% set version = "0.99.5" %} +{% set name = "miRBaseVersions.db" %} +{% set bioc = "3.6" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + fn: '{{ name }}_{{ version }}.tar.gz' + url: + - 'http://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: 70835ad0b5653bfe2e770da5f75c121df01849dd9a549386d1d42e2f88efb333 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ +requirements: + build: + - bioconductor-annotationdbi + - r-base + - r-dbi + - r-gtools + - r-rsqlite + run: + - bioconductor-annotationdbi + - r-base + - r-dbi + - r-gtools + - r-rsqlite + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'http://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Annotation package containing all available miRNA names from all versions (data from http://www.mirbase.org/).' diff --git a/recipes/bioconductor-mirbaseversions.db/post-link.sh b/recipes/bioconductor-mirbaseversions.db/post-link.sh new file mode 100644 index 00000000000000..2b23170567b226 --- /dev/null +++ b/recipes/bioconductor-mirbaseversions.db/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="miRBaseVersions.db_0.99.5.tar.gz" +URLS=( + "http://bioconductor.org/packages/3.6/data/annotation/src/contrib/miRBaseVersions.db_0.99.5.tar.gz" + "https://bioarchive.galaxyproject.org/miRBaseVersions.db_0.99.5.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-mirbaseversions.db/bioconductor-mirbaseversions.db_0.99.5_src_all.tar.gz" +) +MD5="b67d191fa4c71f49ab5d24f3d785c82a" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING \ No newline at end of file diff --git a/recipes/bioconductor-mirbaseversions.db/pre-unlink.sh b/recipes/bioconductor-mirbaseversions.db/pre-unlink.sh new file mode 100644 index 00000000000000..34acff6c1215f6 --- /dev/null +++ b/recipes/bioconductor-mirbaseversions.db/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ miRBaseVersions.db diff --git a/recipes/bioconductor-mirintegrator/build.sh b/recipes/bioconductor-mirintegrator/build.sh new file mode 100644 index 00000000000000..da43ce21683122 --- /dev/null +++ b/recipes/bioconductor-mirintegrator/build.sh @@ -0,0 +1,4 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-mirintegrator/meta.yaml b/recipes/bioconductor-mirintegrator/meta.yaml new file mode 100644 index 00000000000000..4a9996249d9e03 --- /dev/null +++ b/recipes/bioconductor-mirintegrator/meta.yaml @@ -0,0 +1,43 @@ +{% set version = "1.8.0" %} +{% set name = "mirIntegrator" %} +{% set bioc = "3.6" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + fn: '{{ name }}_{{ version }}.tar.gz' + url: + - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: 05d58bdd586e6b80fb310e68575f320fea0c4d58e79a95ee88430f2a0ff6e817 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ +requirements: + build: + - bioconductor-annotationdbi + - bioconductor-graph + - bioconductor-org.hs.eg.db + - bioconductor-rgraphviz + - bioconductor-rontotools + - r-base + - r-ggplot2 + run: + - bioconductor-annotationdbi + - bioconductor-graph + - bioconductor-org.hs.eg.db + - bioconductor-rgraphviz + - bioconductor-rontotools + - r-base + - r-ggplot2 +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: 'GPL (>=3)' + summary: 'Tools for augmenting signaling pathways to perform pathway analysis of microRNA and mRNA expression levels.' diff --git a/recipes/bioconductor-mirnameconverter/build.sh b/recipes/bioconductor-mirnameconverter/build.sh new file mode 100644 index 00000000000000..da43ce21683122 --- /dev/null +++ b/recipes/bioconductor-mirnameconverter/build.sh @@ -0,0 +1,4 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-mirnameconverter/meta.yaml b/recipes/bioconductor-mirnameconverter/meta.yaml new file mode 100644 index 00000000000000..7ef5697d17c5ed --- /dev/null +++ b/recipes/bioconductor-mirnameconverter/meta.yaml @@ -0,0 +1,37 @@ +{% set version = "1.6.0" %} +{% set name = "miRNAmeConverter" %} +{% set bioc = "3.6" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + fn: '{{ name }}_{{ version }}.tar.gz' + url: + - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: 9cc7988e323fc6f9896ec4b6c6c04cf7e9bc183b380b4a1f6a527557f18b1ab2 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ +requirements: + build: + - bioconductor-annotationdbi + - bioconductor-mirbaseversions.db + - r-base + - r-dbi + run: + - bioconductor-annotationdbi + - bioconductor-mirbaseversions.db + - r-base + - r-dbi +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Package containing an S4 class for translating mature miRNA names to different miRBase versions, sequence retrieval, checking names for validity and detecting miRBase version of a given set of names (data from http://www.mirbase.org/).' diff --git a/recipes/bioconductor-missmethyl/build.sh b/recipes/bioconductor-missmethyl/build.sh new file mode 100644 index 00000000000000..da43ce21683122 --- /dev/null +++ b/recipes/bioconductor-missmethyl/build.sh @@ -0,0 +1,4 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-missmethyl/meta.yaml b/recipes/bioconductor-missmethyl/meta.yaml new file mode 100644 index 00000000000000..ab4dcb57dd8099 --- /dev/null +++ b/recipes/bioconductor-missmethyl/meta.yaml @@ -0,0 +1,59 @@ +{% set version = "1.12.0" %} +{% set name = "missMethyl" %} +{% set bioc = "3.6" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + fn: '{{ name }}_{{ version }}.tar.gz' + url: + - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: c35b7e3b64c7ea1cff0aa09deb4e8f1058110555a62ef5e02f859ad28fb777bb +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ +requirements: + build: + - bioconductor-annotationdbi + - bioconductor-go.db + - bioconductor-illuminahumanmethylation450kanno.ilmn12.hg19 + - bioconductor-illuminahumanmethylation450kmanifest + - bioconductor-illuminahumanmethylationepicanno.ilm10b2.hg19 + - bioconductor-illuminahumanmethylationepicmanifest + - bioconductor-limma + - bioconductor-methylumi + - bioconductor-minfi + - bioconductor-org.hs.eg.db + - r-base + - r-biasedurn + - r-ruv + - r-statmod + - r-stringr + run: + - bioconductor-annotationdbi + - bioconductor-go.db + - bioconductor-illuminahumanmethylation450kanno.ilmn12.hg19 + - bioconductor-illuminahumanmethylation450kmanifest + - bioconductor-illuminahumanmethylationepicanno.ilm10b2.hg19 + - bioconductor-illuminahumanmethylationepicmanifest + - bioconductor-limma + - bioconductor-methylumi + - bioconductor-minfi + - bioconductor-org.hs.eg.db + - r-base + - r-biasedurn + - r-ruv + - r-statmod + - r-stringr +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: GPL-2 + summary: 'Normalisation and testing for differential variability and differential methylation for data from Illumina''s Infinium HumanMethylation450 array. The normalisation procedure is subset-quantile within-array normalisation (SWAN), which allows Infinium I and II type probes on a single array to be normalised together. The test for differential variability is based on an empirical Bayes version of Levene''s test. Differential methylation testing is performed using RUV, which can adjust for systematic errors of unknown origin in high-dimensional data by using negative control probes. Gene ontology analysis is performed by taking into account the number of probes per gene on the array.' diff --git a/recipes/bioconductor-mlinterfaces/build.sh b/recipes/bioconductor-mlinterfaces/build.sh new file mode 100644 index 00000000000000..da43ce21683122 --- /dev/null +++ b/recipes/bioconductor-mlinterfaces/build.sh @@ -0,0 +1,4 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-mlinterfaces/meta.yaml b/recipes/bioconductor-mlinterfaces/meta.yaml new file mode 100644 index 00000000000000..b9a553cb2a1c38 --- /dev/null +++ b/recipes/bioconductor-mlinterfaces/meta.yaml @@ -0,0 +1,69 @@ +{% set version = "1.58.0" %} +{% set name = "MLInterfaces" %} +{% set bioc = "3.6" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + fn: '{{ name }}_{{ version }}.tar.gz' + url: + - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: da4e4ba5af1ad8c6e322ddc05f2064860e4f6dc01bb35c02f6dfeee9d700c6df +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ +requirements: + build: + - bioconductor-annotate + - bioconductor-biobase + - 'bioconductor-biocgenerics >=0.13.11' + - bioconductor-genefilter + - r-base + - r-cluster + - r-fpc + - r-gbm + - r-gdata + - r-ggvis + - r-hwriter + - r-mass + - r-mlbench + - r-pls + - r-rcolorbrewer + - r-rda + - r-rpart + - r-sfsmisc + - r-shiny + - 'r-threejs >=0.2.2' + run: + - bioconductor-annotate + - bioconductor-biobase + - 'bioconductor-biocgenerics >=0.13.11' + - bioconductor-genefilter + - r-base + - r-cluster + - r-fpc + - r-gbm + - r-gdata + - r-ggvis + - r-hwriter + - r-mass + - r-mlbench + - r-pls + - r-rcolorbrewer + - r-rda + - r-rpart + - r-sfsmisc + - r-shiny + - 'r-threejs >=0.2.2' +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: LGPL + summary: 'This package provides uniform interfaces to machine learning code for data in R and Bioconductor containers.' diff --git a/recipes/bioconductor-mqtl.nmr/build.sh b/recipes/bioconductor-mqtl.nmr/build.sh new file mode 100644 index 00000000000000..da43ce21683122 --- /dev/null +++ b/recipes/bioconductor-mqtl.nmr/build.sh @@ -0,0 +1,4 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-mqtl.nmr/meta.yaml b/recipes/bioconductor-mqtl.nmr/meta.yaml new file mode 100644 index 00000000000000..eea6651de668c7 --- /dev/null +++ b/recipes/bioconductor-mqtl.nmr/meta.yaml @@ -0,0 +1,42 @@ +{% set version = "1.12.0" %} +{% set name = "mQTL.NMR" %} +{% set bioc = "3.6" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + fn: '{{ name }}_{{ version }}.tar.gz' + url: + - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: 27ee15251211ec2c1155e3ed49bfdc1a381656913deca4ae80d07aeb54a23246 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ +requirements: + build: + - r-base + - r-genabel + - r-mass + - r-outliers + - r-qtl + - gcc # [linux] + - llvm # [osx] + run: + - r-base + - r-genabel + - r-mass + - r-outliers + - r-qtl + - libcxx # [osx] +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'mQTL.NMR provides a complete mQTL analysis pipeline for 1H NMR data. Distinctive features include normalisation using most-used approaches, peak alignment using RSPA approach, dimensionality reduction using SRV and binning approaches, and mQTL analysis for animal and human cohorts.' diff --git a/recipes/bioconductor-msnid/build.sh b/recipes/bioconductor-msnid/build.sh new file mode 100644 index 00000000000000..da43ce21683122 --- /dev/null +++ b/recipes/bioconductor-msnid/build.sh @@ -0,0 +1,4 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-msnid/meta.yaml b/recipes/bioconductor-msnid/meta.yaml new file mode 100644 index 00000000000000..9194b646aa1eaa --- /dev/null +++ b/recipes/bioconductor-msnid/meta.yaml @@ -0,0 +1,60 @@ +{% set version = "1.12.1" %} +{% set name = "MSnID" %} +{% set bioc = "3.6" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + fn: '{{ name }}_{{ version }}.tar.gz' + url: + - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: bddf02c93ecfe24159eac615e5ef14fd4efc50b89c1c93cccb0b3932270285ff +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ +requirements: + build: + - bioconductor-biobase + - 'bioconductor-msnbase >=1.12.1' + - 'bioconductor-mzid >=1.3.5' + - bioconductor-mzr + - bioconductor-protgenerics + - r-base + - r-data.table + - r-doparallel + - r-dplyr + - r-foreach + - r-iterators + - r-r.cache + - r-rcpp + - r-reshape2 + - gcc # [linux] + - llvm # [osx] + run: + - bioconductor-biobase + - 'bioconductor-msnbase >=1.12.1' + - 'bioconductor-mzid >=1.3.5' + - bioconductor-mzr + - bioconductor-protgenerics + - r-base + - r-data.table + - r-doparallel + - r-dplyr + - r-foreach + - r-iterators + - r-r.cache + - r-rcpp + - r-reshape2 + - libcxx # [osx] +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Extracts MS/MS ID data from mzIdentML (leveraging mzID package) or text files. After collating the search results from multiple datasets it assesses their identification quality and optimize filtering criteria to achieve the maximum number of identifications while not exceeding a specified false discovery rate. Also contains a number of utilities to explore the MS/MS results and assess missed and irregular enzymatic cleavages, mass measurement accuracy, etc.' diff --git a/recipes/bioconductor-multiassayexperiment/build.sh b/recipes/bioconductor-multiassayexperiment/build.sh new file mode 100644 index 00000000000000..da43ce21683122 --- /dev/null +++ b/recipes/bioconductor-multiassayexperiment/build.sh @@ -0,0 +1,4 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-multiassayexperiment/meta.yaml b/recipes/bioconductor-multiassayexperiment/meta.yaml new file mode 100644 index 00000000000000..7f963367696ef1 --- /dev/null +++ b/recipes/bioconductor-multiassayexperiment/meta.yaml @@ -0,0 +1,51 @@ +{% set version = "1.4.9" %} +{% set name = "MultiAssayExperiment" %} +{% set bioc = "3.6" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + fn: '{{ name }}_{{ version }}.tar.gz' + url: + - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: 983a2d790601cef7b33f03daf3c09611e8cffeed22cbf8a0f1c9dbd99d15794d +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ +requirements: + build: + - bioconductor-biobase + - bioconductor-biocgenerics + - 'bioconductor-genomicranges >=1.25.93' + - bioconductor-iranges + - bioconductor-s4vectors + - 'bioconductor-summarizedexperiment >=1.3.81' + - r-base + - r-reshape2 + - r-shiny + - r-shinydashboard + - r-tidyr + run: + - bioconductor-biobase + - bioconductor-biocgenerics + - 'bioconductor-genomicranges >=1.25.93' + - bioconductor-iranges + - bioconductor-s4vectors + - 'bioconductor-summarizedexperiment >=1.3.81' + - r-base + - r-reshape2 + - r-shiny + - r-shinydashboard + - r-tidyr +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Multi-assay ''omics experiments on a set of samples are increasingly commonplace in biomedical research. MultiAssayExperiment implements data structures and methods for representing, manipulating, and integrating multi-assay experiments via efficient construction, subsetting, and extraction operations. These methods are implemented matching Bioconductor user experience by straightforward extending concept and design of single-assay classes such as SummarizedExperiment or ExpressionSet.' diff --git a/recipes/bioconductor-multiclust/build.sh b/recipes/bioconductor-multiclust/build.sh new file mode 100644 index 00000000000000..da43ce21683122 --- /dev/null +++ b/recipes/bioconductor-multiclust/build.sh @@ -0,0 +1,4 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-multiclust/meta.yaml b/recipes/bioconductor-multiclust/meta.yaml new file mode 100644 index 00000000000000..9df57da170d6d4 --- /dev/null +++ b/recipes/bioconductor-multiclust/meta.yaml @@ -0,0 +1,43 @@ +{% set version = "1.8.2" %} +{% set name = "multiClust" %} +{% set bioc = "3.6" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + fn: '{{ name }}_{{ version }}.tar.gz' + url: + - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: 54d89a94cc076584b235d29446167c3718a529713b04b2024a46ecf7886c7106 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ +requirements: + build: + - bioconductor-ctc + - r-amap + - r-base + - r-cluster + - r-dendextend + - r-mclust + - r-survival + run: + - bioconductor-ctc + - r-amap + - r-base + - r-cluster + - r-dendextend + - r-mclust + - r-survival +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: 'GPL (>= 2)' + summary: 'Clustering is carried out to identify patterns in transcriptomics profiles to determine clinically relevant subgroups of patients. Feature (gene) selection is a critical and an integral part of the process. Currently, there are many feature selection and clustering methods to identify the relevant genes and perform clustering of samples. However, choosing an appropriate methodology is difficult. In addition, extensive feature selection methods have not been supported by the available packages. Hence, we developed an integrative R-package called multiClust that allows researchers to experiment with the choice of combination of methods for gene selection and clustering with ease. Using multiClust, we identified the best performing clustering methodology in the context of clinical outcome. Our observations demonstrate that simple methods such as variance-based ranking perform well on the majority of data sets, provided that the appropriate number of genes is selected. However, different gene ranking and selection methods remain relevant as no methodology works for all studies.' diff --git a/recipes/bioconductor-mwastools/build.sh b/recipes/bioconductor-mwastools/build.sh new file mode 100644 index 00000000000000..da43ce21683122 --- /dev/null +++ b/recipes/bioconductor-mwastools/build.sh @@ -0,0 +1,4 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-mwastools/meta.yaml b/recipes/bioconductor-mwastools/meta.yaml new file mode 100644 index 00000000000000..f1d37b0e7d680a --- /dev/null +++ b/recipes/bioconductor-mwastools/meta.yaml @@ -0,0 +1,57 @@ +{% set version = "1.2.0" %} +{% set name = "MWASTools" %} +{% set bioc = "3.6" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + fn: '{{ name }}_{{ version }}.tar.gz' + url: + - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: 096058b6ec448c9f9b566ab029a2395365b009e83bf6c584f0e67f8c2d36eb5d +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ +requirements: + build: + - bioconductor-complexheatmap + - bioconductor-kegggraph + - bioconductor-keggrest + - bioconductor-qvalue + - bioconductor-summarizedexperiment + - r-base + - r-boot + - r-car + - r-ggplot2 + - r-glm2 + - r-gridextra + - r-igraph + - r-ppcor + - r-rcurl + run: + - bioconductor-complexheatmap + - bioconductor-kegggraph + - bioconductor-keggrest + - bioconductor-qvalue + - bioconductor-summarizedexperiment + - r-base + - r-boot + - r-car + - r-ggplot2 + - r-glm2 + - r-gridextra + - r-igraph + - r-ppcor + - r-rcurl +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: 'CC BY-NC-ND 4.0' + summary: 'MWASTools provides a complete pipeline to perform metabolome-wide association studies. Key functionalities of the package include: quality control analysis of metabonomic data; MWAS using different association models (partial correlations; generalized linear models); model validation using non-parametric bootstrapping; visualization of MWAS results; NMR metabolite identification using STOCSY; and biological interpretation of MWAS results.' diff --git a/recipes/bioconductor-mygene/build.sh b/recipes/bioconductor-mygene/build.sh new file mode 100644 index 00000000000000..da43ce21683122 --- /dev/null +++ b/recipes/bioconductor-mygene/build.sh @@ -0,0 +1,4 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-mygene/meta.yaml b/recipes/bioconductor-mygene/meta.yaml new file mode 100644 index 00000000000000..d85c6525ad978b --- /dev/null +++ b/recipes/bioconductor-mygene/meta.yaml @@ -0,0 +1,45 @@ +{% set version = "1.14.0" %} +{% set name = "mygene" %} +{% set bioc = "3.6" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + fn: '{{ name }}_{{ version }}.tar.gz' + url: + - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + sha256: a446efd2261103702a2df190599f494b0a417dd147ce44582ea7a434b1be1363 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ +requirements: + build: + - bioconductor-genomicfeatures + - bioconductor-s4vectors + - r-base + - r-hmisc + - 'r-httr >=0.3' + - 'r-jsonlite >=0.9.7' + - r-plyr + - r-sqldf + run: + - bioconductor-genomicfeatures + - bioconductor-s4vectors + - r-base + - r-hmisc + - 'r-httr >=0.3' + - 'r-jsonlite >=0.9.7' + - r-plyr + - r-sqldf +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'MyGene.Info_ provides simple-to-use REST web services to query/retrieve gene annotation data. It''s designed with simplicity and performance emphasized. *mygene*, is an easy-to-use R wrapper to access MyGene.Info_ services.' diff --git a/recipes/bioconductor-ncdfflow/meta.yaml b/recipes/bioconductor-ncdfflow/meta.yaml index 6020dc0627a175..490dcb470473d1 100644 --- a/recipes/bioconductor-ncdfflow/meta.yaml +++ b/recipes/bioconductor-ncdfflow/meta.yaml @@ -12,12 +12,13 @@ source: - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' sha256: 68017eb7a8f9f7b0eb88ce28eaf70d874615bfcba009560650e7e3d5bea378e7 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ requirements: build: + - gcc - bioconductor-biobase - bioconductor-biocgenerics - 'bioconductor-flowcore >=1.37.15' @@ -27,8 +28,9 @@ requirements: - r-base - r-bh - r-rcpparmadillo - - hdf5 + - hdf5 {{CONDA_HDF5}}* run: + - libgcc - bioconductor-biobase - bioconductor-biocgenerics - 'bioconductor-flowcore >=1.37.15' @@ -38,7 +40,7 @@ requirements: - r-base - r-bh - r-rcpparmadillo - - hdf5 + - hdf5 {{CONDA_HDF5}}* test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-org.ce.eg.db/3.2.3/meta.yaml b/recipes/bioconductor-org.ce.eg.db/3.2.3/meta.yaml new file mode 100644 index 00000000000000..71f2f180e1c5d6 --- /dev/null +++ b/recipes/bioconductor-org.ce.eg.db/3.2.3/meta.yaml @@ -0,0 +1,34 @@ +{% set version = "3.2.3" %} +{% set name = "org.Ce.eg.db" %} +{% set bioc = "3.2" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + fn: '{{ name }}_{{ version }}.tar.gz' + url: + - 'http://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: 5c877ae23bc79534cd332756fd1ea8fd1c9829502afe6a34f664e0e501e814b4 +build: + number: 1 + rpaths: + - lib/R/lib/ + - lib/ +requirements: + build: + - 'bioconductor-annotationdbi >=1.31.19' + - r-base + run: + - 'bioconductor-annotationdbi >=1.31.19' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'http://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Genome wide annotation for Worm, primarily based on mapping using Entrez Gene identifiers.' diff --git a/recipes/bioconductor-org.ce.eg.db/3.2.3/post-link.sh b/recipes/bioconductor-org.ce.eg.db/3.2.3/post-link.sh new file mode 100644 index 00000000000000..ebb58c1b71a3a7 --- /dev/null +++ b/recipes/bioconductor-org.ce.eg.db/3.2.3/post-link.sh @@ -0,0 +1,47 @@ +#!/bin/bash +FN="org.Ce.eg.db_3.2.3.tar.gz" +URLS=( + "http://bioconductor.org/packages/3.2/data/annotation/src/contrib/org.Ce.eg.db_3.2.3.tar.gz" + "https://bioarchive.galaxyproject.org/org.Ce.eg.db_3.2.3.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-org.ce.eg.db/bioconductor-org.ce.eg.db_3.2.3_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-org.ce.eg.db/bioconductor-org.ce.eg.db_3.2.3_src_all.tar.gz" +) +MD5="7c85c6469114956030ec18f8952238d8" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING \ No newline at end of file diff --git a/recipes/bioconductor-org.ce.eg.db/3.2.3/pre-unlink.sh b/recipes/bioconductor-org.ce.eg.db/3.2.3/pre-unlink.sh new file mode 100644 index 00000000000000..10f38db2bb0b8d --- /dev/null +++ b/recipes/bioconductor-org.ce.eg.db/3.2.3/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ org.Ce.eg.db diff --git a/recipes/bioconductor-org.ce.eg.db/3.4.1/meta.yaml b/recipes/bioconductor-org.ce.eg.db/3.4.1/meta.yaml new file mode 100644 index 00000000000000..92ab8d3c007821 --- /dev/null +++ b/recipes/bioconductor-org.ce.eg.db/3.4.1/meta.yaml @@ -0,0 +1,34 @@ +{% set version = "3.4.1" %} +{% set name = "org.Ce.eg.db" %} +{% set bioc = "3.5" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + fn: '{{ name }}_{{ version }}.tar.gz' + url: + - 'http://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: d5a49481dd45e1fd969f6f811e375f821f5a466036c29142b94115486b661db4 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ +requirements: + build: + - 'bioconductor-annotationdbi >=1.37.4' + - r-base + run: + - 'bioconductor-annotationdbi >=1.37.4' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'http://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Genome wide annotation for Worm, primarily based on mapping using Entrez Gene identifiers.' diff --git a/recipes/bioconductor-org.ce.eg.db/3.4.1/post-link.sh b/recipes/bioconductor-org.ce.eg.db/3.4.1/post-link.sh new file mode 100644 index 00000000000000..118746043931fb --- /dev/null +++ b/recipes/bioconductor-org.ce.eg.db/3.4.1/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="org.Ce.eg.db_3.4.1.tar.gz" +URLS=( + "http://bioconductor.org/packages/3.5/data/annotation/src/contrib/org.Ce.eg.db_3.4.1.tar.gz" + "https://bioarchive.galaxyproject.org/org.Ce.eg.db_3.4.1.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-org.ce.eg.db/bioconductor-org.ce.eg.db_3.4.1_src_all.tar.gz" +) +MD5="2f073d0ee9590a04341e67fceea71965" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING \ No newline at end of file diff --git a/recipes/bioconductor-org.ce.eg.db/3.4.1/pre-unlink.sh b/recipes/bioconductor-org.ce.eg.db/3.4.1/pre-unlink.sh new file mode 100644 index 00000000000000..10f38db2bb0b8d --- /dev/null +++ b/recipes/bioconductor-org.ce.eg.db/3.4.1/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ org.Ce.eg.db diff --git a/recipes/bioconductor-org.ce.eg.db/meta.yaml b/recipes/bioconductor-org.ce.eg.db/meta.yaml index 7a55dc1a77705f..e424358ddc9eab 100644 --- a/recipes/bioconductor-org.ce.eg.db/meta.yaml +++ b/recipes/bioconductor-org.ce.eg.db/meta.yaml @@ -1,32 +1,34 @@ -package: - name: bioconductor-org.ce.eg.db - version: 3.2.3 +{% set version = "3.5.0" %} +{% set name = "org.Ce.eg.db" %} +{% set bioc = "3.6" %} +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' source: - fn: org.Ce.eg.db_3.2.3.tar.gz - url: https://bioc.ism.ac.jp/packages/3.2/data/annotation/src/contrib/org.Ce.eg.db_3.2.3.tar.gz - md5: 7c85c6469114956030ec18f8952238d8 - + fn: '{{ name }}_{{ version }}.tar.gz' + url: + - 'http://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: 692ecae53641e32e19ee9211934a3d7babdc88ae0282bc34e4fe57da2364ef09 build: number: 0 rpaths: - lib/R/lib/ - lib/ - requirements: build: - - bioconductor-annotationdbi >=1.31.19 + - 'bioconductor-annotationdbi >=1.39.3' - r-base run: - - bioconductor-annotationdbi >=1.31.19 + - 'bioconductor-annotationdbi >=1.39.3' - r-base - + - wget test: commands: - - $R -e "library('org.Ce.eg.db')" - + - '$R -e "library(''{{ name }}'')"' about: - home: http://bioconductor.org/packages/release/data/annotation/html/org.Ce.eg.db.html + home: 'http://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' license: Artistic-2.0 - summary: 'Genome wide annotation for Worm, - primarily based on mapping using Entrez Gene identifiers.' + summary: 'Genome wide annotation for Worm, primarily based on mapping using Entrez Gene identifiers.' diff --git a/recipes/bioconductor-org.ce.eg.db/post-link.sh b/recipes/bioconductor-org.ce.eg.db/post-link.sh index 6db3896a1e6730..28858e26213868 100644 --- a/recipes/bioconductor-org.ce.eg.db/post-link.sh +++ b/recipes/bioconductor-org.ce.eg.db/post-link.sh @@ -1,10 +1,11 @@ #!/bin/bash -FN="org.Ce.eg.db_3.4.1.tar.gz" +FN="org.Ce.eg.db_3.5.0.tar.gz" URLS=( - "http://bioconductor.org/packages/3.5/data/annotation/src/contrib/org.Ce.eg.db_3.4.1.tar.gz" - "https://depot.galaxyproject.org/software/org.Ce.eg.db/org.Ce.eg.db_3.4.1_src_all.tar.gz" + "http://bioconductor.org/packages/3.6/data/annotation/src/contrib/org.Ce.eg.db_3.5.0.tar.gz" + "https://bioarchive.galaxyproject.org/org.Ce.eg.db_3.5.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-org.ce.eg.db/bioconductor-org.ce.eg.db_3.5.0_src_all.tar.gz" ) - MD5="2f073d0ee9590a04341e67fceea71965" +MD5="c33ea27e95df69fd1dd64d3ba1672d20" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -20,7 +21,7 @@ for URL in ${URLS[@]}; do # Platform-specific md5sum checks. if [[ $(uname -s) == "Linux" ]]; then - if [[ $(md5sum -c <<<"$MD5 $TARBALL") ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then SUCCESS=1 break fi @@ -40,5 +41,6 @@ if [[ $SUCCESS != 1 ]]; then fi # Install and clean up -R CMD INSTALL --build $TARBALL -rm $TARBALL \ No newline at end of file +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING \ No newline at end of file diff --git a/recipes/bioconductor-org.ce.eg.db/pre-unlink.sh b/recipes/bioconductor-org.ce.eg.db/pre-unlink.sh new file mode 100644 index 00000000000000..10f38db2bb0b8d --- /dev/null +++ b/recipes/bioconductor-org.ce.eg.db/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ org.Ce.eg.db diff --git a/recipes/bioconductor-pathostat/build.sh b/recipes/bioconductor-pathostat/build.sh new file mode 100644 index 00000000000000..da43ce21683122 --- /dev/null +++ b/recipes/bioconductor-pathostat/build.sh @@ -0,0 +1,4 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-pathostat/meta.yaml b/recipes/bioconductor-pathostat/meta.yaml new file mode 100644 index 00000000000000..f8dc4307198581 --- /dev/null +++ b/recipes/bioconductor-pathostat/meta.yaml @@ -0,0 +1,83 @@ +{% set version = "1.4.1" %} +{% set name = "PathoStat" %} +{% set bioc = "3.6" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + fn: '{{ name }}_{{ version }}.tar.gz' + url: + - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: e8c498faa8ca42f645abe8fcc28a2754987ed345cd9c362cb155d3c22b8180aa +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ +requirements: + build: + - bioconductor-batchqc + - bioconductor-biocstyle + - bioconductor-deseq2 + - bioconductor-edger + - bioconductor-limma + - bioconductor-phyloseq + - bioconductor-preprocesscore + - r-alluvial + - r-ape + - r-base + - r-corpcor + - r-dplyr + - r-dt + - r-ggplot2 + - r-gtools + - r-knitr + - r-matrixstats + - r-mcmcpack + - r-pander + - r-plyr + - r-rentrez + - r-reshape2 + - r-rmarkdown + - r-scales + - r-shiny + - r-tidyr + - r-xml + run: + - bioconductor-batchqc + - bioconductor-biocstyle + - bioconductor-deseq2 + - bioconductor-edger + - bioconductor-limma + - bioconductor-phyloseq + - bioconductor-preprocesscore + - r-alluvial + - r-ape + - r-base + - r-corpcor + - r-dplyr + - r-dt + - r-ggplot2 + - r-gtools + - r-knitr + - r-matrixstats + - r-mcmcpack + - r-pander + - r-plyr + - r-rentrez + - r-reshape2 + - r-rmarkdown + - r-scales + - r-shiny + - r-tidyr + - r-xml +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: 'GPL (>= 2)' + summary: 'The purpose of this package is to perform Statistical Microbiome Analysis on metagenomics results from sequencing data samples. In particular, it supports analyses on the PathoScope generated report files. PathoStat provides various functionalities including Relative Abundance charts, Diversity estimates and plots, tests of Differential Abundance, Time Series visualization, and Core OTU analysis.' diff --git a/recipes/bioconductor-pathrender/build.sh b/recipes/bioconductor-pathrender/build.sh new file mode 100644 index 00000000000000..da43ce21683122 --- /dev/null +++ b/recipes/bioconductor-pathrender/build.sh @@ -0,0 +1,4 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-pathrender/meta.yaml b/recipes/bioconductor-pathrender/meta.yaml new file mode 100644 index 00000000000000..c4156b17b184d4 --- /dev/null +++ b/recipes/bioconductor-pathrender/meta.yaml @@ -0,0 +1,41 @@ +{% set version = "1.46.0" %} +{% set name = "pathRender" %} +{% set bioc = "3.6" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + fn: '{{ name }}_{{ version }}.tar.gz' + url: + - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: 7799606f8be32f984e3eac7a3beaa80d207bfa16e1ee3308bfec07c7f4b20587 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ +requirements: + build: + - bioconductor-annotationdbi + - bioconductor-cmap + - bioconductor-graph + - bioconductor-rgraphviz + - r-base + - r-rcolorbrewer + run: + - bioconductor-annotationdbi + - bioconductor-cmap + - bioconductor-graph + - bioconductor-rgraphviz + - r-base + - r-rcolorbrewer +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: LGPL + summary: 'build graphs from pathway databases, render them by Rgraphviz.' diff --git a/recipes/bioconductor-pathvar/build.sh b/recipes/bioconductor-pathvar/build.sh new file mode 100644 index 00000000000000..da43ce21683122 --- /dev/null +++ b/recipes/bioconductor-pathvar/build.sh @@ -0,0 +1,4 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-pathvar/meta.yaml b/recipes/bioconductor-pathvar/meta.yaml new file mode 100644 index 00000000000000..60d41ece809339 --- /dev/null +++ b/recipes/bioconductor-pathvar/meta.yaml @@ -0,0 +1,43 @@ +{% set version = "1.8.0" %} +{% set name = "pathVar" %} +{% set bioc = "3.6" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + fn: '{{ name }}_{{ version }}.tar.gz' + url: + - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: 06068a120838bcaa26f55a2d50ee93a8a25d85ec5cf6b0ef56d8e557352105d1 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ +requirements: + build: + - r-base + - r-data.table + - r-emt + - r-ggplot2 + - r-gridextra + - r-matching + - r-mclust + run: + - r-base + - r-data.table + - r-emt + - r-ggplot2 + - r-gridextra + - r-matching + - r-mclust +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: 'LGPL (>= 2.0)' + summary: 'This package contains the functions to find the pathways that have significantly different variability than a reference gene set. It also finds the categories from this pathway that are significant where each category is a cluster of genes. The genes are separated into clusters by their level of variability.' diff --git a/recipes/bioconductor-pbase/build.sh b/recipes/bioconductor-pbase/build.sh new file mode 100644 index 00000000000000..da43ce21683122 --- /dev/null +++ b/recipes/bioconductor-pbase/build.sh @@ -0,0 +1,4 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-pbase/meta.yaml b/recipes/bioconductor-pbase/meta.yaml new file mode 100644 index 00000000000000..93d18527e04466 --- /dev/null +++ b/recipes/bioconductor-pbase/meta.yaml @@ -0,0 +1,70 @@ +{% set version = "0.18.0" %} +{% set name = "Pbase" %} +{% set bioc = "3.6" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + fn: '{{ name }}_{{ version }}.tar.gz' + url: + - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: 3d846d81f7ec04b52aabe2c8d98d787c8144f8f3c33bb603ca1937f46b0dca9f +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ +requirements: + build: + - bioconductor-annotationfilter + - bioconductor-biobase + - bioconductor-biocgenerics + - bioconductor-biocparallel + - bioconductor-biomart + - bioconductor-biostrings + - 'bioconductor-cleaver >=1.3.6' + - 'bioconductor-ensembldb >=1.99.13' + - bioconductor-genomicranges + - bioconductor-gviz + - bioconductor-iranges + - 'bioconductor-msnbase >=1.15.5' + - bioconductor-mzid + - 'bioconductor-mzr >=1.99.1' + - bioconductor-pviz + - bioconductor-rtracklayer + - bioconductor-s4vectors + - r-base + - r-rcpp + - gcc # [linux] + - llvm # [osx] + run: + - bioconductor-annotationfilter + - bioconductor-biobase + - bioconductor-biocgenerics + - bioconductor-biocparallel + - bioconductor-biomart + - bioconductor-biostrings + - 'bioconductor-cleaver >=1.3.6' + - 'bioconductor-ensembldb >=1.99.13' + - bioconductor-genomicranges + - bioconductor-gviz + - bioconductor-iranges + - 'bioconductor-msnbase >=1.15.5' + - bioconductor-mzid + - 'bioconductor-mzr >=1.99.1' + - bioconductor-pviz + - bioconductor-rtracklayer + - bioconductor-s4vectors + - r-base + - r-rcpp + - libcxx # [osx] +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: GPL-3 + summary: 'A set of classes and functions to investigate and understand protein sequence data in the context of a proteomics experiment.' diff --git a/recipes/bioconductor-pcagopromoter/build.sh b/recipes/bioconductor-pcagopromoter/build.sh new file mode 100644 index 00000000000000..da43ce21683122 --- /dev/null +++ b/recipes/bioconductor-pcagopromoter/build.sh @@ -0,0 +1,4 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-pcagopromoter/meta.yaml b/recipes/bioconductor-pcagopromoter/meta.yaml new file mode 100644 index 00000000000000..e239861e030a52 --- /dev/null +++ b/recipes/bioconductor-pcagopromoter/meta.yaml @@ -0,0 +1,37 @@ +{% set version = "1.22.0" %} +{% set name = "pcaGoPromoter" %} +{% set bioc = "3.6" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + fn: '{{ name }}_{{ version }}.tar.gz' + url: + - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: 5fcfb0cf2e97e063642675540ea426c2492d22013f1579872ed30a708cb6e10c +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ +requirements: + build: + - bioconductor-annotationdbi + - bioconductor-biostrings + - r-base + - r-ellipse + run: + - bioconductor-annotationdbi + - bioconductor-biostrings + - r-base + - r-ellipse +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: 'GPL (>= 2)' + summary: 'This package contains functions to ease the analyses of DNA micro arrays. It utilizes principal component analysis as the initial multivariate analysis, followed by functional interpretation of the principal component dimensions with overrepresentation analysis for GO terms and regulatory interpretations using overrepresentation analysis of predicted transcription factor binding sites with the primo algorithm.' diff --git a/recipes/bioconductor-pcpheno/build.sh b/recipes/bioconductor-pcpheno/build.sh new file mode 100644 index 00000000000000..da43ce21683122 --- /dev/null +++ b/recipes/bioconductor-pcpheno/build.sh @@ -0,0 +1,4 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-pcpheno/meta.yaml b/recipes/bioconductor-pcpheno/meta.yaml new file mode 100644 index 00000000000000..ee9cf1cfa667a0 --- /dev/null +++ b/recipes/bioconductor-pcpheno/meta.yaml @@ -0,0 +1,55 @@ +{% set version = "1.40.0" %} +{% set name = "PCpheno" %} +{% set bioc = "3.6" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + fn: '{{ name }}_{{ version }}.tar.gz' + url: + - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: 51390c27f53cefb769b725bfbd3cacdb02a242b1e8e1a3b628fcb8884d08fce9 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ +requirements: + build: + - 'bioconductor-annotate >=1.17.4' + - bioconductor-annotationdbi + - bioconductor-biobase + - bioconductor-category + - bioconductor-go.db + - bioconductor-graph + - bioconductor-gseabase + - bioconductor-kegg.db + - bioconductor-ppidata + - bioconductor-ppistats + - 'bioconductor-scisi >=1.3.0' + - bioconductor-slgi + - r-base + run: + - 'bioconductor-annotate >=1.17.4' + - bioconductor-annotationdbi + - bioconductor-biobase + - bioconductor-category + - bioconductor-go.db + - bioconductor-graph + - bioconductor-gseabase + - bioconductor-kegg.db + - bioconductor-ppidata + - bioconductor-ppistats + - 'bioconductor-scisi >=1.3.0' + - bioconductor-slgi + - r-base +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Tools to integrate, annotate, and link phenotypes to cellular organizational units such as protein complexes and pathways.' diff --git a/recipes/bioconductor-phastcons100way.ucsc.hg19/meta.yaml b/recipes/bioconductor-phastcons100way.ucsc.hg19/meta.yaml new file mode 100644 index 00000000000000..250ae47c9dc97f --- /dev/null +++ b/recipes/bioconductor-phastcons100way.ucsc.hg19/meta.yaml @@ -0,0 +1,42 @@ +{% set version = "3.6.0" %} +{% set name = "phastCons100way.UCSC.hg19" %} +{% set bioc = "3.6" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + fn: '{{ name }}_{{ version }}.tar.gz' + url: + - 'http://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: d562071ea6a9a9f65e43241f3721f95f6d3543d44c6e94ba5ff7df3376d6f625 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ +requirements: + build: + - bioconductor-bsgenome + - bioconductor-genomicranges + - 'bioconductor-genomicscores >=1.0.0' + - bioconductor-iranges + - bioconductor-s4vectors + - r-base + run: + - bioconductor-bsgenome + - bioconductor-genomicranges + - 'bioconductor-genomicscores >=1.0.0' + - bioconductor-iranges + - bioconductor-s4vectors + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'http://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Store UCSC phastCons conservation scores for the human genome (hg19) calculated from multiple alignments with other 99 vertebrate species.' diff --git a/recipes/bioconductor-phastcons100way.ucsc.hg19/post-link.sh b/recipes/bioconductor-phastcons100way.ucsc.hg19/post-link.sh new file mode 100644 index 00000000000000..64086feb1b61c4 --- /dev/null +++ b/recipes/bioconductor-phastcons100way.ucsc.hg19/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="phastCons100way.UCSC.hg19_3.6.0.tar.gz" +URLS=( + "http://bioconductor.org/packages/3.6/data/annotation/src/contrib/phastCons100way.UCSC.hg19_3.6.0.tar.gz" + "https://bioarchive.galaxyproject.org/phastCons100way.UCSC.hg19_3.6.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-phastcons100way.ucsc.hg19/bioconductor-phastcons100way.ucsc.hg19_3.6.0_src_all.tar.gz" +) +MD5="62955c9b6b2d13c0e7b7870b213dbff1" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING \ No newline at end of file diff --git a/recipes/bioconductor-phastcons100way.ucsc.hg19/pre-unlink.sh b/recipes/bioconductor-phastcons100way.ucsc.hg19/pre-unlink.sh new file mode 100644 index 00000000000000..0d32f08a8b7049 --- /dev/null +++ b/recipes/bioconductor-phastcons100way.ucsc.hg19/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ phastCons100way.UCSC.hg19 diff --git a/recipes/bioconductor-proloc/build.sh b/recipes/bioconductor-proloc/build.sh new file mode 100644 index 00000000000000..da43ce21683122 --- /dev/null +++ b/recipes/bioconductor-proloc/build.sh @@ -0,0 +1,4 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-proloc/meta.yaml b/recipes/bioconductor-proloc/meta.yaml new file mode 100644 index 00000000000000..f84dff918991d8 --- /dev/null +++ b/recipes/bioconductor-proloc/meta.yaml @@ -0,0 +1,94 @@ +{% set version = "1.18.0" %} +{% set name = "pRoloc" %} +{% set bioc = "3.6" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + fn: '{{ name }}_{{ version }}.tar.gz' + url: + - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: 8039b509b59ab4a9ba4182e5e4a322de9e1a52ff08a5fce5997d9dcadd65d86b +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ +requirements: + build: + - bioconductor-biobase + - bioconductor-biocgenerics + - bioconductor-biocparallel + - bioconductor-biomart + - 'bioconductor-mlinterfaces >=1.37.1' + - 'bioconductor-msnbase >=1.19.20' + - r-base + - r-caret + - r-class + - r-dendextend + - r-e1071 + - r-fnn + - r-ggplot2 + - r-gtools + - r-hexbin + - r-kernlab + - r-knitr + - r-lattice + - r-mass + - 'r-mclust >=4.3' + - r-mvtnorm + - r-nnet + - r-plyr + - r-proxy + - r-randomforest + - r-rcolorbrewer + - 'r-rcpp >=0.10.3' + - r-rcpparmadillo + - 'r-rtsne >=0.13' + - r-sampling + - r-scales + - gcc # [linux] + - llvm # [osx] + run: + - bioconductor-biobase + - bioconductor-biocgenerics + - bioconductor-biocparallel + - bioconductor-biomart + - 'bioconductor-mlinterfaces >=1.37.1' + - 'bioconductor-msnbase >=1.19.20' + - r-base + - r-caret + - r-class + - r-dendextend + - r-e1071 + - r-fnn + - r-ggplot2 + - r-gtools + - r-hexbin + - r-kernlab + - r-knitr + - r-lattice + - r-mass + - 'r-mclust >=4.3' + - r-mvtnorm + - r-nnet + - r-plyr + - r-proxy + - r-randomforest + - r-rcolorbrewer + - 'r-rcpp >=0.10.3' + - r-rcpparmadillo + - 'r-rtsne >=0.13' + - r-sampling + - r-scales + - libcxx # [osx] +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: GPL-2 + summary: 'The pRoloc package implements machine learning and visualisation methods for the analysis and interogation of quantitiative mass spectrometry data to reliably infer protein sub-cellular localisation.' diff --git a/recipes/bioconductor-prolocgui/build.sh b/recipes/bioconductor-prolocgui/build.sh new file mode 100644 index 00000000000000..da43ce21683122 --- /dev/null +++ b/recipes/bioconductor-prolocgui/build.sh @@ -0,0 +1,4 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-prolocgui/meta.yaml b/recipes/bioconductor-prolocgui/meta.yaml new file mode 100644 index 00000000000000..3709583ece43da --- /dev/null +++ b/recipes/bioconductor-prolocgui/meta.yaml @@ -0,0 +1,47 @@ +{% set version = "1.12.0" %} +{% set name = "pRolocGUI" %} +{% set bioc = "3.6" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + fn: '{{ name }}_{{ version }}.tar.gz' + url: + - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: fcc718947eed8d7e5be79c8580fec0049c241879fc9dd1db5b1c413eedd98f34 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ +requirements: + build: + - bioconductor-biobase + - 'bioconductor-msnbase >=2.1.11' + - 'bioconductor-proloc >=1.11.1' + - r-base + - r-dplyr + - 'r-dt >=0.1.40' + - r-ggplot2 + - r-scales + - 'r-shiny >=0.9.1' + run: + - bioconductor-biobase + - 'bioconductor-msnbase >=2.1.11' + - 'bioconductor-proloc >=1.11.1' + - r-base + - r-dplyr + - 'r-dt >=0.1.40' + - r-ggplot2 + - r-scales + - 'r-shiny >=0.9.1' +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: GPL-2 + summary: 'The package pRolocGUI comprises functions to interactively visualise organelle (spatial) proteomics data on the basis of pRoloc, pRolocdata and shiny.' diff --git a/recipes/bioconductor-qsea/build.sh b/recipes/bioconductor-qsea/build.sh new file mode 100644 index 00000000000000..da43ce21683122 --- /dev/null +++ b/recipes/bioconductor-qsea/build.sh @@ -0,0 +1,4 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-qsea/meta.yaml b/recipes/bioconductor-qsea/meta.yaml new file mode 100644 index 00000000000000..d1cc120fb76a1f --- /dev/null +++ b/recipes/bioconductor-qsea/meta.yaml @@ -0,0 +1,60 @@ +{% set version = "1.4.0" %} +{% set name = "qsea" %} +{% set bioc = "3.6" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + fn: '{{ name }}_{{ version }}.tar.gz' + url: + - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + sha256: 999dc5eaaaccf34f5f338ca1f78b7af4a0ada168b056d36af3f3d34a4caade01 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ +requirements: + build: + - bioconductor-biocgenerics + - bioconductor-biocparallel + - bioconductor-biostrings + - bioconductor-bsgenome + - bioconductor-genomeinfodb + - bioconductor-genomicranges + - bioconductor-hmmcopy + - bioconductor-iranges + - bioconductor-limma + - bioconductor-rsamtools + - bioconductor-rtracklayer + - r-base + - r-gtools + - r-zoo + - gcc # [linux] + - llvm # [osx] + run: + - bioconductor-biocgenerics + - bioconductor-biocparallel + - bioconductor-biostrings + - bioconductor-bsgenome + - bioconductor-genomeinfodb + - bioconductor-genomicranges + - bioconductor-hmmcopy + - bioconductor-iranges + - bioconductor-limma + - bioconductor-rsamtools + - bioconductor-rtracklayer + - r-base + - r-gtools + - r-zoo + - libcxx # [osx] +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: 'GPL (>=2)' + summary: 'qsea (quantitative sequencing enrichment analysis) was developed as the successor of the MEDIPS package for analyzing data derived from methylated DNA immunoprecipitation (MeDIP) experiments followed by sequencing (MeDIP-seq). However, qsea provides several functionalities for the analysis of other kinds of quantitative sequencing data (e.g. ChIP-seq, MBD-seq, CMS-seq and others) including calculation of differential enrichment between groups of samples.' diff --git a/recipes/bioconductor-quartpac/build.sh b/recipes/bioconductor-quartpac/build.sh new file mode 100644 index 00000000000000..da43ce21683122 --- /dev/null +++ b/recipes/bioconductor-quartpac/build.sh @@ -0,0 +1,4 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-quartpac/meta.yaml b/recipes/bioconductor-quartpac/meta.yaml new file mode 100644 index 00000000000000..8be30a653abed5 --- /dev/null +++ b/recipes/bioconductor-quartpac/meta.yaml @@ -0,0 +1,39 @@ +{% set version = "1.10.0" %} +{% set name = "QuartPAC" %} +{% set bioc = "3.6" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + fn: '{{ name }}_{{ version }}.tar.gz' + url: + - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: f991280bd845f866f289bde3c138ac053a50ee665518ac6cb05c698e9fa4ebd0 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ +requirements: + build: + - bioconductor-graphpac + - bioconductor-ipac + - bioconductor-spacepac + - r-base + - r-data.table + run: + - bioconductor-graphpac + - bioconductor-ipac + - bioconductor-spacepac + - r-base + - r-data.table +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: GPL-2 + summary: 'Identifies clustering of somatic mutations in proteins over the entire quaternary structure.' diff --git a/recipes/bioconductor-quaternaryprod/build.sh b/recipes/bioconductor-quaternaryprod/build.sh new file mode 100644 index 00000000000000..da43ce21683122 --- /dev/null +++ b/recipes/bioconductor-quaternaryprod/build.sh @@ -0,0 +1,4 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-quaternaryprod/meta.yaml b/recipes/bioconductor-quaternaryprod/meta.yaml new file mode 100644 index 00000000000000..45e41b56e88fa8 --- /dev/null +++ b/recipes/bioconductor-quaternaryprod/meta.yaml @@ -0,0 +1,40 @@ +{% set version = "1.6.0" %} +{% set name = "QuaternaryProd" %} +{% set bioc = "3.6" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + fn: '{{ name }}_{{ version }}.tar.gz' + url: + - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: 54eef0c74b8a77e29e9f747bb069223776ec20c1b8f5333763278c0998a52196 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ +requirements: + build: + - r-base + - r-dplyr + - 'r-rcpp >=0.11.3' + - r-rlist + - gcc # [linux] + - llvm # [osx] + run: + - r-base + - r-dplyr + - 'r-rcpp >=0.11.3' + - r-rlist + - libcxx # [osx] +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: 'GPL (>=3)' + summary: 'QuaternaryProd is an R package that performs causal reasoning on biological networks, including publicly available networks such as STRINGdb. QuaternaryProd is an open-sorce alternative to commercial products such as Quiagen and Inginuity pathway analysis. For a given a set of differentially expressed genes, QuaternaryProd computes the significance of upstream regulators in the network by performing causal reasoning using the Quaternary Dot Product Scoring Statistic (Quaternary Statistic), Ternary Dot product Scoring Statistic (Ternary Statistic) and Fisher''s exact test. The Quaternary Statistic handles signed, unsigned and ambiguous edges in the network. Ambiguity arises when the direction of causality is unknown, or when the source node (e.g., a protein) has edges with conflicting signs for the same target gene. On the other hand, the Ternary Statistic provides causal reasoning using the signed and unambiguous edges only. The Vignette provides more details on the Quaternary Statistic and illustrates an example of how to perform causal reasoning using STRINGdb.' diff --git a/recipes/bioconductor-rarevariantvis/build.sh b/recipes/bioconductor-rarevariantvis/build.sh new file mode 100644 index 00000000000000..da43ce21683122 --- /dev/null +++ b/recipes/bioconductor-rarevariantvis/build.sh @@ -0,0 +1,4 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-rarevariantvis/meta.yaml b/recipes/bioconductor-rarevariantvis/meta.yaml new file mode 100644 index 00000000000000..b75f3314a83df3 --- /dev/null +++ b/recipes/bioconductor-rarevariantvis/meta.yaml @@ -0,0 +1,61 @@ +{% set version = "2.6.0" %} +{% set name = "RareVariantVis" %} +{% set bioc = "3.6" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + fn: '{{ name }}_{{ version }}.tar.gz' + url: + - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: 573fb6f7091499f1e27e21fa0621f55d959470eb4a54f49e6f09b99d358e35b0 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ +requirements: + build: + - bioconductor-biocgenerics + - bioconductor-bsgenome + - bioconductor-bsgenome.hsapiens.ucsc.hg19 + - bioconductor-genomeinfodb + - bioconductor-genomicfeatures + - bioconductor-genomicranges + - bioconductor-genomicscores + - bioconductor-iranges + - bioconductor-phastcons100way.ucsc.hg19 + - bioconductor-s4vectors + - bioconductor-summarizedexperiment + - bioconductor-txdb.hsapiens.ucsc.hg19.knowngene + - bioconductor-variantannotation + - r-base + - r-googlevis + - r-gtools + run: + - bioconductor-biocgenerics + - bioconductor-bsgenome + - bioconductor-bsgenome.hsapiens.ucsc.hg19 + - bioconductor-genomeinfodb + - bioconductor-genomicfeatures + - bioconductor-genomicranges + - bioconductor-genomicscores + - bioconductor-iranges + - bioconductor-phastcons100way.ucsc.hg19 + - bioconductor-s4vectors + - bioconductor-summarizedexperiment + - bioconductor-txdb.hsapiens.ucsc.hg19.knowngene + - bioconductor-variantannotation + - r-base + - r-googlevis + - r-gtools +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Second version of RareVariantVis package aims to provide comprehensive information about rare variants for your genome data. It annotates, filters and presents genomic variants (especially rare ones) in a global, per chromosome way. For discovered rare variants CRISPR guide RNAs are designed, so the user can plan further functional studies. Large structural variants, including copy number variants are also supported. Package accepts variants directly from variant caller - for example GATK or Speedseq. Output of package are lists of variants together with adequate visualization. Visualization of variants is performed in two ways - standard that outputs png figures and interactive that uses JavaScript d3 package. Interactive visualization allows to analyze trio/family data, for example in search for causative variants in rare Mendelian diseases, in point-and-click interface. The package includes homozygous region caller and allows to analyse whole human genomes in less than 30 minutes on a desktop computer. RareVariantVis disclosed novel causes of several rare monogenic disorders, including one with non-coding causative variant - keratolythic winter erythema.' diff --git a/recipes/bioconductor-rariant/build.sh b/recipes/bioconductor-rariant/build.sh new file mode 100644 index 00000000000000..da43ce21683122 --- /dev/null +++ b/recipes/bioconductor-rariant/build.sh @@ -0,0 +1,4 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-rariant/meta.yaml b/recipes/bioconductor-rariant/meta.yaml new file mode 100644 index 00000000000000..e4bcb5ed10e308 --- /dev/null +++ b/recipes/bioconductor-rariant/meta.yaml @@ -0,0 +1,59 @@ +{% set version = "1.14.0" %} +{% set name = "Rariant" %} +{% set bioc = "3.6" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + fn: '{{ name }}_{{ version }}.tar.gz' + url: + - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: 648ae2d5e7ef8aa5698b99dd9895dba688f7f4b4bcd6ac1a2df1bfb6dd13dccd +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ +requirements: + build: + - bioconductor-exomecopy + - bioconductor-genomeinfodb + - bioconductor-genomicranges + - bioconductor-ggbio + - bioconductor-iranges + - bioconductor-rsamtools + - bioconductor-s4vectors + - bioconductor-somaticsignatures + - bioconductor-variantannotation + - r-base + - r-dplyr + - r-ggplot2 + - r-reshape2 + - r-shiny + - r-vgam + run: + - bioconductor-exomecopy + - bioconductor-genomeinfodb + - bioconductor-genomicranges + - bioconductor-ggbio + - bioconductor-iranges + - bioconductor-rsamtools + - bioconductor-s4vectors + - bioconductor-somaticsignatures + - bioconductor-variantannotation + - r-base + - r-dplyr + - r-ggplot2 + - r-reshape2 + - r-shiny + - r-vgam +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: GPL-3 + summary: 'The ''Rariant'' package identifies single nucleotide variants from sequencing data based on the difference of binomially distributed mismatch rates between matched samples.' diff --git a/recipes/bioconductor-scde/build.sh b/recipes/bioconductor-scde/build.sh new file mode 100644 index 00000000000000..da43ce21683122 --- /dev/null +++ b/recipes/bioconductor-scde/build.sh @@ -0,0 +1,4 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-scde/meta.yaml b/recipes/bioconductor-scde/meta.yaml new file mode 100644 index 00000000000000..0d7a870630e197 --- /dev/null +++ b/recipes/bioconductor-scde/meta.yaml @@ -0,0 +1,71 @@ +{% set version = "2.6.0" %} +{% set name = "scde" %} +{% set bioc = "3.6" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + fn: '{{ name }}_{{ version }}.tar.gz' + url: + - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' + sha256: 226c6ac1699c507546144313027b844280092e311da1fb4cb10b288d6854aa33 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ +requirements: + build: + - bioconductor-biocparallel + - bioconductor-edger + - bioconductor-pcamethods + - r-base + - r-cairo + - r-extremes + - r-flexmix + - r-mass + - r-mgcv + - r-nnet + - r-quantreg + - r-rcolorbrewer + - 'r-rcpp >=0.10.4' + - 'r-rcpparmadillo >=0.5.400.2.0' + - r-rjson + - r-rmtstat + - r-rook + - gcc # [linux] + - llvm # [osx] + - xorg-libxrender 0.9.* + - xorg-libsm 1.2.* + - xorg-libxext 1.3.* + run: + - bioconductor-biocparallel + - bioconductor-edger + - bioconductor-pcamethods + - r-base + - r-cairo + - r-extremes + - r-flexmix + - r-mass + - r-mgcv + - r-nnet + - r-quantreg + - r-rcolorbrewer + - 'r-rcpp >=0.10.4' + - 'r-rcpparmadillo >=0.5.400.2.0' + - r-rjson + - r-rmtstat + - r-rook + - xorg-libxrender 0.9.* + - xorg-libsm 1.2.* + - xorg-libxext 1.3.* + - libcxx # [osx] +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: GPL-2 + summary: 'The scde package implements a set of statistical methods for analyzing single-cell RNA-seq data. scde fits individual error models for single-cell RNA-seq measurements. These models can then be used for assessment of differential expression between groups of cells, as well as other types of analysis. The scde package also contains the pagoda framework which applies pathway and gene set overdispersion analysis to identify and characterize putative cell subpopulations based on transcriptional signatures. The overall approach to the differential expression analysis is detailed in the following publication: "Bayesian approach to single-cell differential expression analysis" (Kharchenko PV, Silberstein L, Scadden DT, Nature Methods, doi: 10.1038/nmeth.2967). The overall approach to subpopulation identification and characterization is detailed in the following pre-print: "Characterizing transcriptional heterogeneity through pathway and gene set overdispersion analysis" (Fan J, Salathia N, Liu R, Kaeser G, Yung Y, Herman J, Kaper F, Fan JB, Zhang K, Chun J, and Kharchenko PV, Nature Methods, doi:10.1038/nmeth.3734).' diff --git a/recipes/bioconductor-simpintlists/meta.yaml b/recipes/bioconductor-simpintlists/meta.yaml new file mode 100644 index 00000000000000..bbf440db9a14ff --- /dev/null +++ b/recipes/bioconductor-simpintlists/meta.yaml @@ -0,0 +1,32 @@ +{% set version = "1.14.0" %} +{% set name = "simpIntLists" %} +{% set bioc = "3.6" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + fn: '{{ name }}_{{ version }}.tar.gz' + url: + - 'http://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: 74576f1b355473e76fd8f402a0e2f674821b8deaa3d3381187fc6d3ffa62b5e9 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ +requirements: + build: + - r-base + run: + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'http://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' + license: 'GPL (>= 2)' + summary: 'The package contains BioGRID interactions for arabidopsis(thale cress), c.elegans, fruit fly, human, mouse, yeast( budding yeast ) and S.pombe (fission yeast) . Entrez ids, official names and unique ids can be used to find proteins. The format of interactions are lists. For each gene/protein, there is an entry in the list with "name" containing name of the gene/protein and "interactors" containing the list of genes/proteins interacting with it.' diff --git a/recipes/bioconductor-simpintlists/post-link.sh b/recipes/bioconductor-simpintlists/post-link.sh new file mode 100644 index 00000000000000..abc34406da8e7c --- /dev/null +++ b/recipes/bioconductor-simpintlists/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="simpIntLists_1.14.0.tar.gz" +URLS=( + "http://bioconductor.org/packages/3.6/data/experiment/src/contrib/simpIntLists_1.14.0.tar.gz" + "https://bioarchive.galaxyproject.org/simpIntLists_1.14.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-simpintlists/bioconductor-simpintlists_1.14.0_src_all.tar.gz" +) +MD5="38c2b32e4e24ca6b2761abf5a55e1d88" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING \ No newline at end of file diff --git a/recipes/bioconductor-simpintlists/pre-unlink.sh b/recipes/bioconductor-simpintlists/pre-unlink.sh new file mode 100644 index 00000000000000..286d62f42fe742 --- /dev/null +++ b/recipes/bioconductor-simpintlists/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ simpIntLists diff --git a/recipes/bioconductor-spacepac/build.sh b/recipes/bioconductor-spacepac/build.sh new file mode 100644 index 00000000000000..da43ce21683122 --- /dev/null +++ b/recipes/bioconductor-spacepac/build.sh @@ -0,0 +1,4 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-spacepac/meta.yaml b/recipes/bioconductor-spacepac/meta.yaml new file mode 100644 index 00000000000000..0be1e48bc2331d --- /dev/null +++ b/recipes/bioconductor-spacepac/meta.yaml @@ -0,0 +1,33 @@ +{% set version = "1.16.0" %} +{% set name = "SpacePAC" %} +{% set bioc = "3.6" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + fn: '{{ name }}_{{ version }}.tar.gz' + url: + - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: d6cc73719fb06dec064fac3fb91f88c077e90ef573fc2e58eed4d83f8df988b5 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ +requirements: + build: + - bioconductor-ipac + - r-base + run: + - bioconductor-ipac + - r-base +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: GPL-2 + summary: 'Identifies clustering of somatic mutations in proteins via a simulation approach while considering the protein''s tertiary structure.' diff --git a/recipes/bioconductor-stemhypoxia/meta.yaml b/recipes/bioconductor-stemhypoxia/meta.yaml new file mode 100644 index 00000000000000..73e65b70db61c7 --- /dev/null +++ b/recipes/bioconductor-stemhypoxia/meta.yaml @@ -0,0 +1,32 @@ +{% set version = "1.14.0" %} +{% set name = "stemHypoxia" %} +{% set bioc = "3.6" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + fn: '{{ name }}_{{ version }}.tar.gz' + url: + - 'http://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: 883e0099b7dafeb1d58e254315b228346b5f7d5afba360f0ebf99db44277d650 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ +requirements: + build: + - r-base + run: + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'http://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' + license: 'GPL (>=2)' + summary: 'Expression profiling using microarray technology to prove if ''Hypoxia Promotes Efficient Differentiation of Human Embryonic Stem Cells to Functional Endothelium'' by Prado-Lopez et al. (2010) Stem Cells 28:407-418. Full data available at Gene Expression Omnibus series GSE37761.' diff --git a/recipes/bioconductor-stemhypoxia/post-link.sh b/recipes/bioconductor-stemhypoxia/post-link.sh new file mode 100644 index 00000000000000..e0cbfd5b6d9559 --- /dev/null +++ b/recipes/bioconductor-stemhypoxia/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="stemHypoxia_1.14.0.tar.gz" +URLS=( + "http://bioconductor.org/packages/3.6/data/experiment/src/contrib/stemHypoxia_1.14.0.tar.gz" + "https://bioarchive.galaxyproject.org/stemHypoxia_1.14.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-stemhypoxia/bioconductor-stemhypoxia_1.14.0_src_all.tar.gz" +) +MD5="ce1e542ac7f851642c8f55e25da1312a" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING \ No newline at end of file diff --git a/recipes/bioconductor-stemhypoxia/pre-unlink.sh b/recipes/bioconductor-stemhypoxia/pre-unlink.sh new file mode 100644 index 00000000000000..c78b4ebf8530b0 --- /dev/null +++ b/recipes/bioconductor-stemhypoxia/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ stemHypoxia diff --git a/recipes/bioconductor-vanillaice/build.sh b/recipes/bioconductor-vanillaice/build.sh new file mode 100644 index 00000000000000..da43ce21683122 --- /dev/null +++ b/recipes/bioconductor-vanillaice/build.sh @@ -0,0 +1,4 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-vanillaice/meta.yaml b/recipes/bioconductor-vanillaice/meta.yaml new file mode 100644 index 00000000000000..68e7c515ab005f --- /dev/null +++ b/recipes/bioconductor-vanillaice/meta.yaml @@ -0,0 +1,62 @@ +{% set version = "1.40.0" %} +{% set name = "VanillaICE" %} +{% set bioc = "3.6" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + fn: '{{ name }}_{{ version }}.tar.gz' + url: + - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: e2d6f62714c6da9341072bb89c6a17b6fddd6769dc695cff40c594b89da05c93 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ +requirements: + build: + - bioconductor-biobase + - 'bioconductor-biocgenerics >=0.13.6' + - bioconductor-bsgenome.hsapiens.ucsc.hg18 + - bioconductor-crlmm + - 'bioconductor-genomeinfodb >=1.11.4' + - 'bioconductor-genomicranges >=1.27.6' + - 'bioconductor-iranges >=1.14.0' + - 'bioconductor-oligoclasses >=1.31.1' + - 'bioconductor-s4vectors >=0.9.25' + - 'bioconductor-summarizedexperiment >=1.5.3' + - r-base + - r-data.table + - r-foreach + - r-lattice + - r-matrixstats + - gcc # [linux] + - llvm # [osx] + run: + - bioconductor-biobase + - 'bioconductor-biocgenerics >=0.13.6' + - bioconductor-bsgenome.hsapiens.ucsc.hg18 + - bioconductor-crlmm + - 'bioconductor-genomeinfodb >=1.11.4' + - 'bioconductor-genomicranges >=1.27.6' + - 'bioconductor-iranges >=1.14.0' + - 'bioconductor-oligoclasses >=1.31.1' + - 'bioconductor-s4vectors >=0.9.25' + - 'bioconductor-summarizedexperiment >=1.5.3' + - r-base + - r-data.table + - r-foreach + - r-lattice + - r-matrixstats + - libcxx # [osx] +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: LGPL-2 + summary: 'Hidden Markov Models for characterizing chromosomal alterations in high throughput SNP arrays.' diff --git a/recipes/bioconductor-watermelon/build.sh b/recipes/bioconductor-watermelon/build.sh new file mode 100644 index 00000000000000..da43ce21683122 --- /dev/null +++ b/recipes/bioconductor-watermelon/build.sh @@ -0,0 +1,4 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-watermelon/meta.yaml b/recipes/bioconductor-watermelon/meta.yaml new file mode 100644 index 00000000000000..784913878c64ba --- /dev/null +++ b/recipes/bioconductor-watermelon/meta.yaml @@ -0,0 +1,47 @@ +{% set version = "1.22.0" %} +{% set name = "wateRmelon" %} +{% set bioc = "3.6" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + fn: '{{ name }}_{{ version }}.tar.gz' + url: + - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: b0d82f5016e87a12cd7568391a6ae0684a11a1b198c1a22fe56db6ad26e78380 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ +requirements: + build: + - bioconductor-biobase + - bioconductor-illuminahumanmethylation450kanno.ilmn12.hg19 + - bioconductor-illuminaio + - bioconductor-limma + - bioconductor-lumi + - bioconductor-methylumi + - bioconductor-roc + - r-base + - r-matrixstats + run: + - bioconductor-biobase + - bioconductor-illuminahumanmethylation450kanno.ilmn12.hg19 + - bioconductor-illuminaio + - bioconductor-limma + - bioconductor-lumi + - bioconductor-methylumi + - bioconductor-roc + - r-base + - r-matrixstats +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: GPL-3 + summary: '15 flavours of betas and three performance metrics, with methods for objects produced by methylumi and minfi packages.' diff --git a/recipes/bioconductor-wavetiling/build.sh b/recipes/bioconductor-wavetiling/build.sh new file mode 100644 index 00000000000000..da43ce21683122 --- /dev/null +++ b/recipes/bioconductor-wavetiling/build.sh @@ -0,0 +1,4 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-wavetiling/meta.yaml b/recipes/bioconductor-wavetiling/meta.yaml new file mode 100644 index 00000000000000..f351dd44fb6821 --- /dev/null +++ b/recipes/bioconductor-wavetiling/meta.yaml @@ -0,0 +1,54 @@ +{% set version = "1.20.0" %} +{% set name = "waveTiling" %} +{% set bioc = "3.6" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + fn: '{{ name }}_{{ version }}.tar.gz' + url: + - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: 4f9e350f0cc50ad17bbefdf8063808c84271a529b2325d4bf85959b911299fb6 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ +requirements: + build: + - bioconductor-affy + - bioconductor-biobase + - bioconductor-biostrings + - bioconductor-genomegraphs + - bioconductor-genomicranges + - bioconductor-iranges + - bioconductor-oligo + - bioconductor-oligoclasses + - bioconductor-preprocesscore + - r-base + - r-waveslim + - gcc # [linux] + - llvm # [osx] + run: + - bioconductor-affy + - bioconductor-biobase + - bioconductor-biostrings + - bioconductor-genomegraphs + - bioconductor-genomicranges + - bioconductor-iranges + - bioconductor-oligo + - bioconductor-oligoclasses + - bioconductor-preprocesscore + - r-base + - r-waveslim + - libcxx # [osx] +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: 'GPL (>=2)' + summary: 'This package is designed to conduct transcriptome analysis for tiling arrays based on fast wavelet-based functional models.' diff --git a/recipes/bioconductor-yeastcc/meta.yaml b/recipes/bioconductor-yeastcc/meta.yaml new file mode 100644 index 00000000000000..25122262037f10 --- /dev/null +++ b/recipes/bioconductor-yeastcc/meta.yaml @@ -0,0 +1,34 @@ +{% set version = "1.18.0" %} +{% set name = "yeastCC" %} +{% set bioc = "3.6" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + fn: '{{ name }}_{{ version }}.tar.gz' + url: + - 'http://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + sha256: d166f00c91828632439753a814f6c63237efda363a3d12b5bc7c1161a39da0e2 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ +requirements: + build: + - 'bioconductor-biobase >=2.5.5' + - r-base + run: + - 'bioconductor-biobase >=2.5.5' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'http://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'ExpressionSet for Spellman et al. (1998) yeast cell cycle microarray experiment' diff --git a/recipes/bioconductor-yeastcc/post-link.sh b/recipes/bioconductor-yeastcc/post-link.sh new file mode 100644 index 00000000000000..07c2425ad12daa --- /dev/null +++ b/recipes/bioconductor-yeastcc/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="yeastCC_1.18.0.tar.gz" +URLS=( + "http://bioconductor.org/packages/3.6/data/experiment/src/contrib/yeastCC_1.18.0.tar.gz" + "https://bioarchive.galaxyproject.org/yeastCC_1.18.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-yeastcc/bioconductor-yeastcc_1.18.0_src_all.tar.gz" +) +MD5="676bd01ca703f018cd36a8b7a2f37989" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING \ No newline at end of file diff --git a/recipes/bioconductor-yeastcc/pre-unlink.sh b/recipes/bioconductor-yeastcc/pre-unlink.sh new file mode 100644 index 00000000000000..a65428df919758 --- /dev/null +++ b/recipes/bioconductor-yeastcc/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ yeastCC diff --git a/recipes/biolite-tools/meta.yaml b/recipes/biolite-tools/meta.yaml index 96c5084614959a..a7cdcd9a4fd91d 100644 --- a/recipes/biolite-tools/meta.yaml +++ b/recipes/biolite-tools/meta.yaml @@ -9,6 +9,9 @@ source: url: https://bitbucket.org/caseywdunn/biolite/downloads/biolite-tools-{{ version }}.tar.gz sha256: b2e08caa65d1bf0914a910fa2e90fa5757d0e2ddd0f2e4ec41dbd5682dab3093 +build: + number: 1 + requirements: build: - zlib {{ CONDA_ZLIB }}* diff --git a/recipes/bis-snp/bis-snp.sh b/recipes/bis-snp/bis-snp.sh new file mode 100755 index 00000000000000..6375d74942d6a4 --- /dev/null +++ b/recipes/bis-snp/bis-snp.sh @@ -0,0 +1,64 @@ +#!/bin/bash +# Bis-SNP executable shell script (modified from the Picard executable shell script) +set -eu -o pipefail + +set -o pipefail +export LC_ALL=en_US.UTF-8 + +# Find original directory of bash script, resolving symlinks +# http://stackoverflow.com/questions/59895/can-a-bash-script-tell-what-directory-its-stored-in/246128#246128 +SOURCE="${BASH_SOURCE[0]}" +while [ -h "$SOURCE" ]; do # resolve $SOURCE until the file is no longer a symlink + DIR="$( cd -P "$( dirname "$SOURCE" )" && pwd )" + SOURCE="$(readlink "$SOURCE")" + [[ $SOURCE != /* ]] && SOURCE="$DIR/$SOURCE" # if $SOURCE was a relative symlink, we need to resolve it relative to the path where the symlink file was located +done +DIR="$( cd -P "$( dirname "$SOURCE" )" && pwd )" + +JAR_DIR=$DIR +ENV_PREFIX="$(dirname $(dirname $DIR))" +# Use Java installed with Anaconda to ensure correct version +java="$ENV_PREFIX/bin/java" + +# if JAVA_HOME is set (non-empty), use it. Otherwise keep "java" +if [ -n "${JAVA_HOME:=}" ]; then + if [ -e "$JAVA_HOME/bin/java" ]; then + java="$JAVA_HOME/bin/java" + fi +fi + +# extract memory and system property Java arguments from the list of provided arguments +# http://java.dzone.com/articles/better-java-shell-script +default_jvm_mem_opts="-Xms512m -Xmx1g" +jvm_mem_opts="" +jvm_prop_opts="" +pass_args="" +for arg in "$@"; do + case $arg in + '-D'*) + jvm_prop_opts="$jvm_prop_opts $arg" + ;; + '-XX'*) + jvm_prop_opts="$jvm_prop_opts $arg" + ;; + '-Xm'*) + jvm_mem_opts="$jvm_mem_opts $arg" + ;; + *) + pass_args="$pass_args $arg" + ;; + esac +done + +if [ "$jvm_mem_opts" == "" ]; then + jvm_mem_opts="$default_jvm_mem_opts" +fi + +pass_arr=($pass_args) +if [[ ${pass_arr[0]:=} == org* ]] +then + eval "$java" $jvm_mem_opts $jvm_prop_opts -cp "$JAR_DIR/BisSNP.jar" $pass_args +else + eval "$java" $jvm_mem_opts $jvm_prop_opts -jar "$JAR_DIR/BisSNP.jar" $pass_args +fi +exit diff --git a/recipes/bis-snp/build.sh b/recipes/bis-snp/build.sh new file mode 100644 index 00000000000000..787ffe150ac5d7 --- /dev/null +++ b/recipes/bis-snp/build.sh @@ -0,0 +1,13 @@ +#!/bin/bash + +TGT="$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM" +[ -d "$TGT" ] || mkdir -p "$TGT" +[ -d "${PREFIX}/bin" ] || mkdir -p "${PREFIX}/bin" + +cd "${SRC_DIR}" +cp -rvp . "${TGT}" + +cp $RECIPE_DIR/bis-snp.sh $TGT/bis-snp +ln -s $TGT/bis-snp $PREFIX/bin +ln -s $TGT/BisSNP-${PKG_VERSION}.jar $TGT/BisSNP.jar +chmod 0755 "${PREFIX}/bin/bis-snp" diff --git a/recipes/bis-snp/meta.yaml b/recipes/bis-snp/meta.yaml new file mode 100644 index 00000000000000..fd04f41dff7492 --- /dev/null +++ b/recipes/bis-snp/meta.yaml @@ -0,0 +1,26 @@ +{% set version = "0.82.2" %} + +package: + name: bis-snp + version: {{ version }} + +source: + fn: BisSNP-{{ version }}.jar + url: https://downloads.sourceforge.net/project/bissnp/BisSNP-{{ version }}/BisSNP-{{ version }}.jar + sha256: f15358c89bfdaff04c407ec382940c70cfa00857e88f7e917aa4ba11345f4e52 + +build: + number: 0 + +requirements: + run: + - openjdk 7.0.161 + +test: + commands: + - "bis-snp 2>&1 | grep usage:" + +about: + home: "http://people.csail.mit.edu/dnaase/bissnp2011/" + license: MIT + summary: "Bisulfite-seq/NOMe-seq SNPs & cytosine methylation caller" diff --git a/recipes/blasr_libcpp/meta.yaml b/recipes/blasr_libcpp/meta.yaml index d5030bf5ddacda..b4bc8337f3e724 100644 --- a/recipes/blasr_libcpp/meta.yaml +++ b/recipes/blasr_libcpp/meta.yaml @@ -6,7 +6,7 @@ package: version: {{ version }} build: - number: 0 + number: 1 skip: True # [not py27 or osx] string: boost{{CONDA_BOOST}}_{{PKG_BUILDNUM}} @@ -18,15 +18,15 @@ requirements: build: - llvm # [osx] - gcc # [linux] - - hdf5 + - hdf5 {{ CONDA_HDF5 }}* - python - - htslib + - htslib {{ CONDA_HTSLIB }}* - pbbam - boost {{CONDA_BOOST}}* run: - libgcc # [linux] - - hdf5 + - hdf5 {{ CONDA_HDF5 }}* - boost {{CONDA_BOOST}}* test: @@ -42,4 +42,3 @@ about: home: https://github.com/PacificBiosciences/{{ name }} license: BSD-3-Clause-Clear summary: Blasr_libcpp is a library used by blasr and other executables such as samtoh5, loadPulses for analyzing PacBio sequences - diff --git a/recipes/blat/meta.yaml b/recipes/blat/meta.yaml index 551de3b962f0dd..9b748ee7c35c38 100644 --- a/recipes/blat/meta.yaml +++ b/recipes/blat/meta.yaml @@ -8,15 +8,15 @@ source: md5: 16e546b8843b85e0b0f2fa603cd78724 build: - number: 1 + number: 2 requirements: build: - libpng - - zlib + - zlib {{CONDA_ZLIB}}* run: - libpng - - zlib + - zlib {{CONDA_ZLIB}}* about: home: https://genome.ucsc.edu/FAQ/FAQblat.html license: Free for academic, nonprofit and personal use diff --git a/recipes/bowtie2/meta.yaml b/recipes/bowtie2/meta.yaml index 1d6296cc243c70..e3306ff5d2bace 100644 --- a/recipes/bowtie2/meta.yaml +++ b/recipes/bowtie2/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "2.3.4" %} +{% set version = "2.3.4.1" %} package: @@ -8,7 +8,7 @@ package: source: fn: bowtie2-{{ version }}-source.zip url: http://downloads.sourceforge.net/project/bowtie-bio/bowtie2/{{ version }}/bowtie2-{{ version }}-source.zip - sha256: 51101a0bc180393c48e94e7fd2f5afcaece9eb50d4b2514abdbdbb7509417db2 + sha256: a1efef603b91ecc11cfdb822087ae00ecf2dd922e03c85eea1ed7f8230c119dc patches: - bowtie2.patch diff --git a/recipes/breakdancer/build.sh b/recipes/breakdancer/build.sh index 0a170727ab74eb..f0c9cb0e1c3a13 100644 --- a/recipes/breakdancer/build.sh +++ b/recipes/breakdancer/build.sh @@ -12,6 +12,6 @@ make make install # Make bam2cfg.pl work from bin; it needs some modules from lib. -BAM2CFG_LIB=${PREFIX}/lib/breakdancer-maxunstable +BAM2CFG_LIB=`dirname $( find ${PREFIX}/lib -name "bam2cfg.pl" )` ${PREFIX}/bin/sed -i'' "s@use AlnParser;@use lib \"${BAM2CFG_LIB}\";\nuse AlnParser;@" ${BAM2CFG_LIB}/bam2cfg.pl ln -s ${BAM2CFG_LIB}/bam2cfg.pl ${PREFIX}/bin diff --git a/recipes/breakdancer/meta.yaml b/recipes/breakdancer/meta.yaml index 1df7147f2c5307..eee79fe806112a 100644 --- a/recipes/breakdancer/meta.yaml +++ b/recipes/breakdancer/meta.yaml @@ -11,12 +11,12 @@ about: summary: SV detection from paired end reads mapping build: - number: 1 + number: 2 skip: True # [not py27] requirements: build: - - python >=2.7,<3 + - python - perl - cmake >=2.8 - gcc @@ -32,8 +32,8 @@ requirements: test: commands: - - 'breakdancer-max 2>&1 | grep "Usage: breakdancer-max" > /dev/null' - - 'bam2cfg.pl 2>&1 | grep "Usage" > /dev/null' + - 'breakdancer-max 2>&1 | grep "Usage: breakdancer-max"' + - bam2cfg.pl 2>&1 | grep "Usage" source: fn: {{ name }}-{{ version }}.tar.gz @@ -43,5 +43,5 @@ source: - builddeps.patch # This patch is applied during the build via builddeps.patch. # The reason is that samtools is a tarball within the breakdancer tarball and - # needs to be extracted first. + # needs to be extracted first. #- samtools.patch diff --git a/recipes/breseq/meta.yaml b/recipes/breseq/meta.yaml index bdf69bae1e96cd..33d039cdee06bc 100644 --- a/recipes/breseq/meta.yaml +++ b/recipes/breseq/meta.yaml @@ -6,7 +6,7 @@ package: version: {{ version }} build: - number: 1 + number: 2 source: fn: {{ name|lower }}_{{ version }}.tar.gz @@ -15,15 +15,15 @@ source: requirements: build: - - gcc # [not osx] - - llvm # [osx] - - zlib + - gcc # [not osx] + - llvm # [osx] + - zlib {{CONDA_ZLIB}}* run: - - libgcc # [not osx] - - zlib - - r-base - - bowtie2 >=2.0.0,!=2.0.3,!=2.0.4,!=2.3.1 + - libgcc # [not osx] + - zlib {{CONDA_ZLIB}}* + - r-base + - bowtie2 >=2.0.0,!=2.0.3,!=2.0.4,!=2.3.1 test: commands: diff --git a/recipes/bwa/0.5.9/meta.yaml b/recipes/bwa/0.5.9/meta.yaml index 7a54bb554de49a..09b724fdbc622f 100644 --- a/recipes/bwa/0.5.9/meta.yaml +++ b/recipes/bwa/0.5.9/meta.yaml @@ -1,22 +1,30 @@ +{% set version = "0.5.9" %} +{% set sha256 = "0a4404af1261714b14585476e36ad2359ff4806224adc7d864c6231553b1a88a" %} + package: name: bwa - version: "0.5.9" + version: {{ version }} build: - number: 0 + number: 1 source: - fn: bwa-0.5.9.tar.bz2 - url: http://downloads.sourceforge.net/project/bio-bwa/bwa-0.5.9.tar.bz2 - md5: b60719d7f6bc49fd39cbc4e0b6bd787e + fn: bwa-{{ version }}.tar.bz2 + url: http://downloads.sourceforge.net/project/bio-bwa/bwa-{{ version }}.tar.bz2 + sha256: {{ sha256 }} requirements: build: - - gcc - - zlib + - gcc # [not osx] + - llvm # [osx] + - zlib {{CONDA_ZLIB}}* run: - - libgcc - - zlib + - libgcc # [not osx] + - zlib {{CONDA_ZLIB}}* + +test: + commands: + - bwa 2>&1 | grep "index sequences in the" about: home: http://bio-bwa.sourceforge.net diff --git a/recipes/bwa/0.6.2/meta.yaml b/recipes/bwa/0.6.2/meta.yaml index 9217d013fb69e0..dd295f586772d9 100644 --- a/recipes/bwa/0.6.2/meta.yaml +++ b/recipes/bwa/0.6.2/meta.yaml @@ -1,22 +1,30 @@ +{% set version = "0.6.2" %} +{% set sha256 = "8783e5640d8e4ae028e048c56db1d6b4adff6234d1047bd4f98247ffc3be69e6" %} + package: name: bwa - version: "0.6.2" + version: {{ version }} build: - number: 0 + number: 1 source: - fn: bwa-0.6.2.tar.bz2 - url: http://downloads.sourceforge.net/project/bio-bwa/bwa-0.6.2.tar.bz2 - md5: 5e4043769ce3436f6098ec67f6e02332 + fn: bwa-{{ version }}.tar.bz2 + url: http://downloads.sourceforge.net/project/bio-bwa/bwa-{{ version }}.tar.bz2 + sha256: {{ sha256 }} requirements: build: - - gcc - - zlib + - gcc # [not osx] + - llvm # [osx] + - zlib {{CONDA_ZLIB}}* run: - - libgcc - - zlib + - libgcc # [not osx] + - zlib {{CONDA_ZLIB}}* + +test: + commands: + - bwa 2>&1 | grep "index sequences in the" about: home: http://bio-bwa.sourceforge.net diff --git a/recipes/bwa/0.7.3a/meta.yaml b/recipes/bwa/0.7.3a/meta.yaml index efca6714612dda..d566cbff642c8b 100644 --- a/recipes/bwa/0.7.3a/meta.yaml +++ b/recipes/bwa/0.7.3a/meta.yaml @@ -1,26 +1,30 @@ +{% set version = "0.7.3a" %} +{% set sha256 = "5093e39b83f64b9bb348a86d4fd129abc4797c5b4472bc110e16fc67ab920e56" %} + package: name: bwa - version: "0.7.3a" + version: {{ version }} build: - number: 0 + number: 1 source: - fn: bwa-0.7.3a.tar.bz2 - url: http://downloads.sourceforge.net/project/bio-bwa/bwa-0.7.3a.tar.bz2 - md5: 7ed9f5d750d26f5bf91cee1fa6f65df2 + fn: bwa-{{ version }}.tar.bz2 + url: http://downloads.sourceforge.net/project/bio-bwa/bwa-{{ version }}.tar.bz2 + sha256: {{ sha256 }} requirements: build: - - gcc - - zlib + - gcc # [not osx] + - llvm # [osx] + - zlib {{CONDA_ZLIB}}* run: - - libgcc - - zlib + - libgcc # [not osx] + - zlib {{CONDA_ZLIB}}* test: commands: - - bwa 2>&1 | grep "index sequences" + - bwa 2>&1 | grep "index sequences in the" about: home: http://bio-bwa.sourceforge.net diff --git a/recipes/bwa/0.7.8/meta.yaml b/recipes/bwa/0.7.8/meta.yaml index 67fdd0ea5d476a..f3324829cb1b35 100644 --- a/recipes/bwa/0.7.8/meta.yaml +++ b/recipes/bwa/0.7.8/meta.yaml @@ -1,22 +1,30 @@ +{% set version = "0.7.8" %} +{% set sha256 = "6669dbf7486a83acc4453a3c68a7857a76f1c229e229a02a9bae638480fb0b09" %} + package: name: bwa - version: "0.7.8" + version: {{ version }} build: - number: 0 + number: 1 source: - fn: bwa-0.7.8.tar.bz2 - url: http://downloads.sourceforge.net/project/bio-bwa/bwa-0.7.8.tar.bz2 - md5: 51ca7a29907022080398b2b88207e33c + fn: bwa-{{ version }}.tar.bz2 + url: http://downloads.sourceforge.net/project/bio-bwa/bwa-{{ version }}.tar.bz2 + sha256: {{ sha256 }} requirements: build: - - gcc - - zlib + - gcc # [not osx] + - llvm # [osx] + - zlib {{CONDA_ZLIB}}* run: - - libgcc - - zlib + - libgcc # [not osx] + - zlib {{CONDA_ZLIB}}* + +test: + commands: + - bwa 2>&1 | grep "index sequences in the" about: home: http://bio-bwa.sourceforge.net diff --git a/recipes/bwa/meta.yaml b/recipes/bwa/meta.yaml index f8071094e8fa29..82bd620c7785a8 100644 --- a/recipes/bwa/meta.yaml +++ b/recipes/bwa/meta.yaml @@ -1,4 +1,5 @@ {% set version = "0.7.17" %} +{% set sha256 = "980b9591b61c60042c4a39b9e31ccaad8d17ff179d44d347997825da3fdf47fd" %} package: name: bwa @@ -7,10 +8,10 @@ package: source: fn: bwa-{{ version }}.tar.gz url: https://github.com/lh3/bwa/archive/v{{ version }}.tar.gz - sha256: 980b9591b61c60042c4a39b9e31ccaad8d17ff179d44d347997825da3fdf47fd + sha256: {{ sha256 }} build: - number: 1 + number: 2 requirements: build: diff --git a/recipes/cancerit-allelecount/build.sh b/recipes/cancerit-allelecount/build.sh index cd2f3cac4bf7f2..26898c28f757b2 100644 --- a/recipes/cancerit-allelecount/build.sh +++ b/recipes/cancerit-allelecount/build.sh @@ -1,7 +1,7 @@ #!/bin/bash set -eu -wget -O htslib-1.2.1.tar.bz2 https://github.com/samtools/htslib/releases/download/1.2.1/htslib-1.2.1.tar.bz2 +wget --ca-certificate=$PREFIX/ssl/cert.pem -O htslib-1.2.1.tar.bz2 https://github.com/samtools/htslib/releases/download/1.2.1/htslib-1.2.1.tar.bz2 tar -xjvpf htslib-1.2.1.tar.bz2 cd htslib-1.2.1 patch -p0 < $SRC_DIR/patches/htslibcramindex.diff diff --git a/recipes/cancerit-allelecount/meta.yaml b/recipes/cancerit-allelecount/meta.yaml index 28dde5885e231e..f904ed7417d8da 100644 --- a/recipes/cancerit-allelecount/meta.yaml +++ b/recipes/cancerit-allelecount/meta.yaml @@ -4,16 +4,18 @@ package: source: fn: alleleCount-v2.1.2.tar.gz url: https://github.com/cancerit/alleleCount/archive/v2.1.2.tar.gz + sha256: 2c7fd5521d4dd3353a3937949007ba8b0b0ad6025ea06f82ee351e837f1dd625 build: - number: 1 + number: 2 skip: True # [osx] requirements: build: - gcc # [linux] - llvm # [osx] - - zlib + - zlib {{CONDA_ZLIB}}* + - wget run: - - zlib + - zlib {{CONDA_ZLIB}}* test: commands: - 'alleleCounter -h' diff --git a/recipes/cansam/meta.yaml b/recipes/cansam/meta.yaml index a2dadc2dff3e30..943c9fcde17c52 100644 --- a/recipes/cansam/meta.yaml +++ b/recipes/cansam/meta.yaml @@ -9,16 +9,19 @@ source: patches: - makefile.patch +build: + number: 1 + requirements: build: - gcc - boost {{CONDA_BOOST}}* - - zlib + - zlib {{CONDA_ZLIB}}* run: - libgcc - boost {{CONDA_BOOST}}* - - zlib + - zlib {{CONDA_ZLIB}}* test: commands: diff --git a/recipes/cassiopee/meta.yaml b/recipes/cassiopee/meta.yaml index d0081314c5fbb0..e59175bb88835d 100644 --- a/recipes/cassiopee/meta.yaml +++ b/recipes/cassiopee/meta.yaml @@ -3,7 +3,7 @@ package: version: "1.0.5" build: - number: 0 + number: 1 source: fn: 1.0.5.tar.gz diff --git a/recipes/cdbtools/meta.yaml b/recipes/cdbtools/meta.yaml index ede82c10c18688..e41c83fd47d2dc 100644 --- a/recipes/cdbtools/meta.yaml +++ b/recipes/cdbtools/meta.yaml @@ -11,16 +11,16 @@ source: - zlib.patch build: - number: 1 + number: 2 skip: True # [not linux64 or osx] requirements: build: - - zlib + - zlib {{CONDA_ZLIB}}* - gcc # [linux] - llvm # [osx] run: - - zlib + - zlib {{CONDA_ZLIB}}* - libgcc # [linux] test: diff --git a/recipes/centrifuge/meta.yaml b/recipes/centrifuge/meta.yaml index f8e48abb9a1e57..5f068922d176d0 100644 --- a/recipes/centrifuge/meta.yaml +++ b/recipes/centrifuge/meta.yaml @@ -6,7 +6,7 @@ package: version: {{ version }} build: - number: 1 + number: 2 source: fn: {{ name|lower }}_{{ version }}.tar.gz @@ -17,13 +17,13 @@ requirements: build: - gcc # [not osx] - llvm # [osx] - - zlib + - zlib {{CONDA_ZLIB}}* - perl - python run: - libgcc # [not osx] - - zlib + - zlib {{CONDA_ZLIB}}* - perl - python diff --git a/recipes/cgat-scripts/meta.yaml b/recipes/cgat-scripts/meta.yaml index d071e0e2eb54bd..7bf019f84deba2 100644 --- a/recipes/cgat-scripts/meta.yaml +++ b/recipes/cgat-scripts/meta.yaml @@ -10,7 +10,7 @@ source: build: skip: True # [not py3k] - number: 0 + number: 1 entry_points: - cgat = CGAT.cgat:main @@ -43,7 +43,7 @@ requirements: - ucsc-bedgraphtobigwig 357 - ucsc-bedtobigbed 357 - ucsc-wigtobigwig 357 - - zlib 1.2.* + - zlib {{CONDA_ZLIB}}* run: # python dependencies @@ -72,7 +72,7 @@ requirements: - ucsc-bedgraphtobigwig 357 - ucsc-bedtobigbed 357 - ucsc-wigtobigwig 357 - - zlib 1.2.* + - zlib {{CONDA_ZLIB}}* test: diff --git a/recipes/cgcloud-lib/meta.yaml b/recipes/cgcloud-lib/meta.yaml index 7422035d57801c..e15bac43a2a40d 100644 --- a/recipes/cgcloud-lib/meta.yaml +++ b/recipes/cgcloud-lib/meta.yaml @@ -8,7 +8,7 @@ source: md5: 76cb2e9b3b6f716c0790bf7a55594c94 build: - number: 0 + number: 1 skip: True # [not py27] requirements: @@ -16,12 +16,12 @@ requirements: - python - setuptools - bd2k-python-lib - - boto ==2.38.0 + - boto >=2.38.0 run: - python - bd2k-python-lib - - boto ==2.38.0 + - boto >=2.38.0 test: imports: diff --git a/recipes/chewbbaca/1.0/build.sh b/recipes/chewbbaca/1.0/build.sh new file mode 100644 index 00000000000000..b0e3292f176990 --- /dev/null +++ b/recipes/chewbbaca/1.0/build.sh @@ -0,0 +1,15 @@ +DEST="$PREFIX/lib/chewBBACA" +mkdir -p "$DEST" +cp --recursive --archive --no-target-directory "$PWD" "$DEST" + +ln -s "$PREFIX/lib/chewBBACA/chewBBACA.py" "$PREFIX/bin" +ln -s "$PREFIX/lib/chewBBACA/chewBBACA.py" "$PREFIX/bin/chewbbaca" +ln -s "$PREFIX/lib/chewBBACA/utils/AutoAlleleCuration.py" "$PREFIX/bin" +ln -s "$PREFIX/lib/chewBBACA/utils/CountNumberMissingData.py" "$PREFIX/bin" +ln -s "$PREFIX/lib/chewBBACA/utils/Extract_cgAlleles.py" "$PREFIX/bin" +ln -s "$PREFIX/lib/chewBBACA/utils/ParalogPrunning.py" "$PREFIX/bin" +ln -s "$PREFIX/lib/chewBBACA/utils/RemoveGenes.py" "$PREFIX/bin" +ln -s "$PREFIX/lib/chewBBACA/utils/RemoveGenomes.py" "$PREFIX/bin" +ln -s "$PREFIX/lib/chewBBACA/utils/TestGenomeQuality.py" "$PREFIX/bin" +ln -s "$PREFIX/lib/chewBBACA/utils/assemblyStats.py" "$PREFIX/bin" +ln -s "$PREFIX/lib/chewBBACA/utils/init_schema_4_bbaca.py" "$PREFIX/bin" diff --git a/recipes/chewbbaca/1.0/meta.yaml b/recipes/chewbbaca/1.0/meta.yaml new file mode 100644 index 00000000000000..b0126330e586d5 --- /dev/null +++ b/recipes/chewbbaca/1.0/meta.yaml @@ -0,0 +1,37 @@ +{% set name = "chewBBACA" %} +{% set version = "1.0" %} + +package: + name: {{ name|lower }} + version: {{ version }} + +source: + url: https://github.com/B-UMMI/chewBBACA/archive/{{ version }}.tar.gz + sha256: c4a34c3ecd780cacfdabbb116cba36ced11cba36fefdf4ca9bea9ecd3c918d71 + +build: + skip: True # [osx or py3k] + number: 0 + +requirements: + build: + - python + + run: + - python + - numpy 1.13.1 + - scipy >=0.13.3 + - plotly 1.12.* + - biopython 1.70 + - prodigal >=2.6.0 + - blast >=2.5.0 + +test: + commands: + - chewBBACA.py -h + +about: + home: https://github.com/B-UMMI/chewBBACA + license: GPL-3.0 + license_file: LICENSE + summary: Whole genome and core genome MultiLocus Sequence Typing. diff --git a/recipes/chewbbaca/build.sh b/recipes/chewbbaca/build.sh index b0e3292f176990..5227f51eca79f9 100644 --- a/recipes/chewbbaca/build.sh +++ b/recipes/chewbbaca/build.sh @@ -1,15 +1,3 @@ -DEST="$PREFIX/lib/chewBBACA" -mkdir -p "$DEST" -cp --recursive --archive --no-target-directory "$PWD" "$DEST" +#!/bin/bash -ln -s "$PREFIX/lib/chewBBACA/chewBBACA.py" "$PREFIX/bin" -ln -s "$PREFIX/lib/chewBBACA/chewBBACA.py" "$PREFIX/bin/chewbbaca" -ln -s "$PREFIX/lib/chewBBACA/utils/AutoAlleleCuration.py" "$PREFIX/bin" -ln -s "$PREFIX/lib/chewBBACA/utils/CountNumberMissingData.py" "$PREFIX/bin" -ln -s "$PREFIX/lib/chewBBACA/utils/Extract_cgAlleles.py" "$PREFIX/bin" -ln -s "$PREFIX/lib/chewBBACA/utils/ParalogPrunning.py" "$PREFIX/bin" -ln -s "$PREFIX/lib/chewBBACA/utils/RemoveGenes.py" "$PREFIX/bin" -ln -s "$PREFIX/lib/chewBBACA/utils/RemoveGenomes.py" "$PREFIX/bin" -ln -s "$PREFIX/lib/chewBBACA/utils/TestGenomeQuality.py" "$PREFIX/bin" -ln -s "$PREFIX/lib/chewBBACA/utils/assemblyStats.py" "$PREFIX/bin" -ln -s "$PREFIX/lib/chewBBACA/utils/init_schema_4_bbaca.py" "$PREFIX/bin" +$PYTHON setup.py install --single-version-externally-managed --record record.txt diff --git a/recipes/chewbbaca/meta.yaml b/recipes/chewbbaca/meta.yaml index b0126330e586d5..de6b93f64d7b22 100644 --- a/recipes/chewbbaca/meta.yaml +++ b/recipes/chewbbaca/meta.yaml @@ -1,37 +1,56 @@ -{% set name = "chewBBACA" %} -{% set version = "1.0" %} +{% set name='chewBBACA' %} +{% set version='2.0.6' %} package: - name: {{ name|lower }} - version: {{ version }} + name: {{ name|lower }} + version: {{ version }} source: - url: https://github.com/B-UMMI/chewBBACA/archive/{{ version }}.tar.gz - sha256: c4a34c3ecd780cacfdabbb116cba36ced11cba36fefdf4ca9bea9ecd3c918d71 + fn: {{ name }}-{{ version }}.tar.gz + url: https://pypi.python.org/packages/a8/ac/d099d8004dd855763d9834a3171a58fa543bd0c45f86f530971294fed719/{{ name }}-{{ version }}.tar.gz + md5: 975cb3798b65b8ae5f3190279129b30f build: - skip: True # [osx or py3k] - number: 0 + skip: True # [ py27 ] + entry_points: + - chewBBACA.py = CHEWBBACA.chewBBACA:main + build: 0 requirements: - build: - - python - - run: - - python - - numpy 1.13.1 - - scipy >=0.13.3 - - plotly 1.12.* - - biopython 1.70 - - prodigal >=2.6.0 - - blast >=2.5.0 + build: + - python + - setuptools + - numpy >=1.14.0 + - scipy >=0.13.3 + - biopython >=1.70 + - plotly >=1.12.9 + - sparqlwrapper >=1.7.6 + run: + - python + - numpy >=1.14.0 + - scipy >=0.13.3 + - biopython >=1.70 + - plotly >=1.12.9 + - sparqlwrapper >=1.7.6 + - blast >=2.5.0 + - prodigal >=2.6.0 + - clustalw >=2.1 + - mafft test: - commands: - - chewBBACA.py -h + imports: + - CHEWBBACA + - CHEWBBACA.SchemaEvaluator + - CHEWBBACA.allelecall + - CHEWBBACA.createschema + - CHEWBBACA.utils + + commands: + - chewBBACA.py --help about: home: https://github.com/B-UMMI/chewBBACA license: GPL-3.0 - license_file: LICENSE - summary: Whole genome and core genome MultiLocus Sequence Typing. + summary: 'A complete suite for gene-by-gene schema creation and strain identification' + license_family: GPL3 + description: 'chewBBACA is a comprehensive pipeline including a set of functions for the creation and validation of whole genome and core genome MultiLocus Sequence Typing (wg/cgMLST) schemas, providing an allele calling algorithm based on Blast Score Ratio that can be run in multiprocessor settings and a set of functions to visualize and validate allele variation in the loci.' diff --git a/recipes/clever-toolkit/meta.yaml b/recipes/clever-toolkit/meta.yaml index d0af48876af4e5..b1b4b6f25cca07 100644 --- a/recipes/clever-toolkit/meta.yaml +++ b/recipes/clever-toolkit/meta.yaml @@ -5,7 +5,7 @@ package: version: {{ version }} build: - number: 3 + number: 4 string: py{{CONDA_PY}}_boost{{CONDA_BOOST}}_{{PKG_BUILDNUM}} skip: True # [osx or py2k] @@ -19,12 +19,12 @@ requirements: - gcc - boost {{CONDA_BOOST}}* - cmake - - zlib + - zlib {{CONDA_ZLIB}}* run: - libgcc - python - boost {{CONDA_BOOST}}* - - zlib + - zlib {{CONDA_ZLIB}}* - bedtools 2.26.* - samtools 1.* - bcftools 1.* diff --git a/recipes/cmv/build.sh b/recipes/cmv/build.sh index c468578a5bcdb4..306f58b13bf156 100644 --- a/recipes/cmv/build.sh +++ b/recipes/cmv/build.sh @@ -1,12 +1,12 @@ #!/bin/bash -export LIBRARY_PATH="${PREFIX}/lib" -export LD_LIBRARY_PATH="${PREFIX}/lib" +export LIBRARY_PATH="${PREFIX}/lib:/usr/lib:/usr/lib64" +export LD_LIBRARY_PATH="${PREFIX}/lib:/usr/lib:/usr/lib64" export LDFLAGS="-L${PREFIX}/lib" export CPPFLAGS="-I${PREFIX}/include" -stack setup +stack setup --local-bin-path ${PREFIX}/bin stack update -stack install --extra-include-dirs ${PREFIX}/include --local-bin-path ${PREFIX}/bin +stack install --local-bin-path ${PREFIX}/bin #cleanup rm -r .stack-work diff --git a/recipes/cmv/meta.yaml b/recipes/cmv/meta.yaml index 170e99e82b6d77..069453b812e993 100644 --- a/recipes/cmv/meta.yaml +++ b/recipes/cmv/meta.yaml @@ -12,31 +12,35 @@ source: md5: {{ md5 }} build: - number: 0 + number: 1 skip: True # [osx] requirements: build: - - stack >=1.5.1 - - gmp >=5.0.1,<7 + - stack >=1.6.5 + - gmp {{CONDA_GMP}}* - cairo - pango - - zlib + - zlib {{CONDA_ZLIB}}* - perl - xorg-libxrender - xorg-libsm - xorg-libxext - gcc + - libgcc + - libxml2 run: - - gmp >=5.0.1,<7 + - gmp {{CONDA_GMP}}* - libgcc + - pthread-stubs - cairo - pango - - zlib + - zlib {{CONDA_ZLIB}}* - xorg-libxrender - xorg-libsm - xorg-libxext + - libxml2 test: commands: diff --git a/recipes/cogent/meta.yaml b/recipes/cogent/meta.yaml index 59d07571ae47f3..e66878280db633 100644 --- a/recipes/cogent/meta.yaml +++ b/recipes/cogent/meta.yaml @@ -8,14 +8,14 @@ source: md5: ecdfa0bc89e0c04c9d4d39cac9984498 build: - number: 0 + number: 1 skip: True [py3k or osx] requirements: build: - python - numpy >=1.3 - - zlib + - zlib {{CONDA_ZLIB}}* - matplotlib >=1.1.0 - mpi4py >=1.0 # [not osx] - mysql-python >=1.2.2 # [not osx] @@ -24,7 +24,7 @@ requirements: run: - python - numpy >=1.3 - - zlib + - zlib {{CONDA_ZLIB}}* - matplotlib >=1.1.0 - mpi4py >=1.0 # [not osx] - mysql-python >=1.2.2 # [not osx] diff --git a/recipes/collectl/meta.yaml b/recipes/collectl/meta.yaml index 80a7569c45c2a1..655a7462fbdb6a 100644 --- a/recipes/collectl/meta.yaml +++ b/recipes/collectl/meta.yaml @@ -9,15 +9,15 @@ source: - usrenvbin.patch build: - number: 1 + number: 2 requirements: build: - perl-threaded - - zlib + - zlib {{CONDA_ZLIB}}* run: - perl-threaded - - zlib + - zlib {{CONDA_ZLIB}}* test: commands: diff --git a/recipes/combined-pvalues/meta.yaml b/recipes/combined-pvalues/meta.yaml index 7946436acd7193..1171ebdb7e4fe6 100644 --- a/recipes/combined-pvalues/meta.yaml +++ b/recipes/combined-pvalues/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "0.46" %} +{% set version = "0.48" %} package: name: combined-pvalues @@ -6,7 +6,7 @@ package: source: url: https://github.com/brentp/combined-pvalues/archive/v{{ version }}.tar.gz - md5: 807d3adb4bc8d61a0e7dbe7248b202cd + md5: 2ed642df0222a36dfce13e98c35f1b9f build: skip: True # [not py27] diff --git a/recipes/cooler/meta.yaml b/recipes/cooler/meta.yaml index 71c49fc98602b2..63183240a20ef9 100644 --- a/recipes/cooler/meta.yaml +++ b/recipes/cooler/meta.yaml @@ -10,7 +10,7 @@ source: md5: 4f09de27e1070a86cc7f522b452e6c03 build: - number: 0 + number: 1 entry_points: - cooler = cooler.cli:cli @@ -18,9 +18,10 @@ requirements: build: - python - setuptools + - zlib {{CONDA_ZLIB}}* run: - - zlib + - zlib {{CONDA_ZLIB}}* - hdf5 - python - six diff --git a/recipes/coprarna/meta.yaml b/recipes/coprarna/meta.yaml index b3a4cd2b039a42..77903db8f1f3b6 100644 --- a/recipes/coprarna/meta.yaml +++ b/recipes/coprarna/meta.yaml @@ -1,6 +1,6 @@ {% set name = "coprarna" %} -{% set version = "2.1.2" %} -{% set md5 = "3fe51843e255bb8c6ee4d322f04c09b9" %} +{% set version = "2.1.3" %} +{% set md5 = "974ebdc320b1fe55f38e02a581284ccc" %} package: name: {{ name }} diff --git a/recipes/coreutils/meta.yaml b/recipes/coreutils/meta.yaml index e99c9629f82c3a..e0528be1262a67 100644 --- a/recipes/coreutils/meta.yaml +++ b/recipes/coreutils/meta.yaml @@ -8,12 +8,14 @@ source: sha256: 031a9842298864ed0d7ae87e008759465c8b4716ed4bf97d723fe8ced5145e94 build: - number: 0 + number: 1 requirements: build: - gcc # [linux] - llvm # [osx] + run: + - libgcc # [linux] test: commands: diff --git a/recipes/csvtk/meta.yaml b/recipes/csvtk/meta.yaml index 3626bbceb3656c..c83370046b488d 100644 --- a/recipes/csvtk/meta.yaml +++ b/recipes/csvtk/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "0.12.0" %} +{% set version = "0.13.0" %} package: name: csvtk @@ -16,15 +16,15 @@ build: source: fn: csvtk_v{{ version }}_osx.tar.gz # [osx] url: https://github.com/shenwei356/csvtk/releases/download/v{{ version }}/csvtk_darwin_amd64.tar.gz # [osx] - md5: d06f54861e70565931e9d16a25ebb228 # [osx] + md5: 77e87397c1c70ec2fc72efa162e945bf # [osx] fn: csvtk_v{{ version }}_linux.tar.gz # [linux] url: https://github.com/shenwei356/csvtk/releases/download/v{{ version }}/csvtk_linux_386.tar.gz # [linux] - md5: 354993c9f7e0fff88eb1c5ff495f6e97 # [linux] + md5: d6c3ef0c6696001682d150c40b8380b6 # [linux] fn: csvtk_v{{ version }}_linux64.tar.gz # [linux64] url: https://github.com/shenwei356/csvtk/releases/download/v{{ version }}/csvtk_linux_amd64.tar.gz # [linux64] - md5: 7db96ea13822b9f658644354198b8dfa # [linux64] + md5: caefdb6909d0e2de1c19eecb0a40aeab # [linux64] test: commands: diff --git a/recipes/cutadapt/meta.yaml b/recipes/cutadapt/meta.yaml index eba50f5cb0e255..d2fa4a3181bec0 100644 --- a/recipes/cutadapt/meta.yaml +++ b/recipes/cutadapt/meta.yaml @@ -1,6 +1,6 @@ package: name: cutadapt - version: '1.15' + version: '1.16' about: home: https://cutadapt.readthedocs.io/ @@ -8,9 +8,9 @@ about: summary: 'trim adapters from high-throughput sequencing reads' source: - fn: cutadapt-1.15.tar.gz - url: https://pypi.python.org/packages/5a/89/a041e0a108bef64b1347e9b7126d813e61f0ce028d3db830fb7b77aab1ab/cutadapt-1.15.tar.gz - md5: 50baff135228644e8c68e90e2bd4e953 + fn: cutadapt-1.16.tar.gz + url: https://pypi.python.org/packages/68/73/2ae48245bbf6d84a24bdf29540ed01669f09c5d21c26258f2ce07e13c767/cutadapt-1.16.tar.gz + md5: 222d062207e2a3a2a0760caa83bf14ff build: number: 0 diff --git a/recipes/cwltest/meta.yaml b/recipes/cwltest/meta.yaml index 94ba76dc478f47..b701de67406afa 100644 --- a/recipes/cwltest/meta.yaml +++ b/recipes/cwltest/meta.yaml @@ -1,11 +1,12 @@ +{% set version = "1.0.20180209171722" %} package: name: cwltest - version: '1.0.20170214185319' + version: {{ version }} source: - fn: cwltest-1.0.20170214185319.tar.gz - url: https://pypi.python.org/packages/07/b0/c7b2c65152471274e496d1b99635955ba3d51ff389cfca06ec11127412ee/cwltest-1.0.20170214185319.tar.gz - md5: 0f4cd403e1cc08a450437c4ab5c5218e + fn: cwltest-{{ version }}.tar.gz + url: https://pypi.io/packages/source/c/cwltest/cwltest-{{ version }}.tar.gz + md5: 9ddcc22e76b86492cf2a2a20b67c829a build: @@ -17,16 +18,20 @@ requirements: - python - setuptools - schema-salad - - typing + - mistune >=0.7.3,<0.8 + - typing >=3.5.3,<3.6 - junit-xml - futures + - subprocess32 run: - python - schema-salad - - typing + - mistune >=0.7.3,<0.8 + - typing >=3.5.3,<3.6 - junit-xml - futures + - subprocess32 test: imports: diff --git a/recipes/cwltool/meta.yaml b/recipes/cwltool/meta.yaml index 08429c3b5112d7..2768557a3d5f69 100644 --- a/recipes/cwltool/meta.yaml +++ b/recipes/cwltool/meta.yaml @@ -1,4 +1,4 @@ -{% set version="1.0.20170928192020" %} +{% set version="1.0.20180130110340" %} package: name: cwltool @@ -7,7 +7,7 @@ package: source: fn: cwltool-{{ version }}.tar.gz url: https://pypi.io/packages/source/c/cwltool/cwltool-{{ version }}.tar.gz - md5: d4b5de52b19366175cab6e606825cf7e + md5: c89765e94c8eeeb5c0f61906575a8dec build: number: 0 @@ -19,7 +19,7 @@ requirements: - setuptools - requests - shellescape - - cwltest + - cwltest >=1.0.20180209171722 # schema-salad and pinned deps - schema-salad >=2.6.20170927145003,<3.0 - cachecontrol >=0.11.7,<0.12 @@ -33,7 +33,7 @@ requirements: - python - requests - shellescape - - cwltest + - cwltest >=1.0.20180209171722 # schema-salad and pinned deps - schema-salad >=2.6.20170927145003,<3.0 - cachecontrol >=0.11.7,<0.12 diff --git a/recipes/cyvcf2/0.7.2/meta.yaml b/recipes/cyvcf2/0.7.2/meta.yaml index 0fa1ed1d176932..d41cf6ae75d263 100644 --- a/recipes/cyvcf2/0.7.2/meta.yaml +++ b/recipes/cyvcf2/0.7.2/meta.yaml @@ -11,7 +11,7 @@ source: md5: bd42bb44534db93b52ee2e97836abb6c build: - number: 0 + number: 1 requirements: build: @@ -20,7 +20,7 @@ requirements: - cython - numpy - gcc - - zlib + - zlib {{CONDA_ZLIB}}* - cython run: @@ -30,7 +30,7 @@ requirements: - seaborn - pandas - libgcc - - zlib + - zlib {{CONDA_ZLIB}}* test: imports: diff --git a/recipes/cyvcf2/meta.yaml b/recipes/cyvcf2/meta.yaml index 3a781e804aa772..44029d90bc43cf 100644 --- a/recipes/cyvcf2/meta.yaml +++ b/recipes/cyvcf2/meta.yaml @@ -12,7 +12,7 @@ source: sha256: {{ sha256hash }} build: - number: 0 + number: 1 requirements: build: diff --git a/recipes/dazz_db/meta.yaml b/recipes/dazz_db/meta.yaml index 18394d09cd4787..1c223d34ab0cd7 100644 --- a/recipes/dazz_db/meta.yaml +++ b/recipes/dazz_db/meta.yaml @@ -3,13 +3,13 @@ package: version: "1.0p2" build: - number: 0 + number: 1 + source: fn: dazz_db_V1.0p2.tar.gz sha256: 3e98d10454b12bf0bcba1cdec226882e8214a3040472cbfaec0f9b589099d730 url: https://github.com/thegenemyers/DAZZ_DB/archive/8ab7daf27123a3dfd17189af168ebe22b343170f.tar.gz - requirements: build: - gcc # [not osx] diff --git a/recipes/dbg2olc/meta.yaml b/recipes/dbg2olc/meta.yaml index 4cbc7875f7e9b3..0ffc1fc85fe8f2 100644 --- a/recipes/dbg2olc/meta.yaml +++ b/recipes/dbg2olc/meta.yaml @@ -6,7 +6,7 @@ package: version: {{ version }} build: - number: 0 + number: 1 script: "mkdir -p $PREFIX/bin; g++ -O3 -o DBG2OLC *.cpp; mv DBG2OLC $PREFIX/bin" source: @@ -16,16 +16,16 @@ source: requirements: build: - - gcc # [not osx] - - llvm # [osx] - - zlib + - gcc # [not osx] + - llvm # [osx] + - zlib {{CONDA_ZLIB}}* run: - - libgcc # [not osx] - - zlib - - sparseassembler - - sparc - - assemblyutility + - libgcc # [not osx] + - zlib {{CONDA_ZLIB}}* + - sparseassembler + - sparc + - assemblyutility test: commands: diff --git a/recipes/dcmtk/meta.yaml b/recipes/dcmtk/meta.yaml index f527d9319105bd..128c833ea3363a 100644 --- a/recipes/dcmtk/meta.yaml +++ b/recipes/dcmtk/meta.yaml @@ -9,19 +9,19 @@ source: fn: dcmtk-{{ DCMTK_VERSION }}_{{ DCMTK_VERSION_DATE }}.tar.gz url: http://dicom.offis.de/download/dcmtk/snapshot/old/dcmtk-{{ DCMTK_VERSION }}_{{ DCMTK_VERSION_DATE }}.tar.gz sha1: 9daa6b64767443a60d5cb8946905e4e7003d1658 - + build: - number: 4 - + number: 5 + requirements: build: - cmake - - gcc >=4.7 [linux] + - gcc >=4.7 - openssl - libpng - libtiff - libxml2 - - zlib + - zlib {{CONDA_ZLIB}}* - jpeg run: - openssl @@ -29,8 +29,8 @@ requirements: - libtiff - jpeg - libxml2 - - zlib - - libgcc # [linux] + - zlib {{CONDA_ZLIB}}* + - libgcc test: commands: @@ -42,7 +42,7 @@ test: - dcmseg_tests - dcmsr_tests - drttest - - ofstd_tests + #- ofstd_tests about: home: http://dicom.offis.de diff --git a/recipes/ddocent/meta.yaml b/recipes/ddocent/meta.yaml index cbb5da5e0438dc..b7c4445244e8ab 100644 --- a/recipes/ddocent/meta.yaml +++ b/recipes/ddocent/meta.yaml @@ -1,13 +1,17 @@ package: name: ddocent version: '2.2.25' + source: fn: v2.2.25.zip sha256: 134a47e4f5703b91483efd338cae8d3e972d160e6a606e27cb1f5fccc71874e6 url: https://github.com/jpuritz/dDocent/archive/v2.2.25.zip + build: - number: 0 + number: 1 skip: True # [osx] + string: bamtools{{CONDA_BAMTOOLS}}_{{PKG_BUILDNUM}} + requirements: build: - gcc # [unix] @@ -28,7 +32,7 @@ requirements: - vcflib - gnuplot - parallel - - bamtools + - bamtools {{ CONDA_BAMTOOLS }}* - openjdk - pear - unzip @@ -51,7 +55,7 @@ requirements: - vcflib - gnuplot - parallel - - bamtools + - bamtools {{ CONDA_BAMTOOLS }}* - openjdk - pear - unzip diff --git a/recipes/debwt/meta.yaml b/recipes/debwt/meta.yaml index 93b2171a7ee146..8611ee866bc008 100644 --- a/recipes/debwt/meta.yaml +++ b/recipes/debwt/meta.yaml @@ -3,7 +3,7 @@ package: version: "1.0.1" build: - number: 0 + number: 1 source: git_url: https://github.com/DixianZhu/deBWT.git @@ -12,10 +12,10 @@ source: requirements: build: - gcc - - zlib + - zlib {{CONDA_ZLIB}}* run: - libgcc - - zlib + - zlib {{CONDA_ZLIB}}* test: commands: diff --git a/recipes/deepvariant/meta.yaml b/recipes/deepvariant/meta.yaml index b757decf9957d7..9d3514234ed806 100644 --- a/recipes/deepvariant/meta.yaml +++ b/recipes/deepvariant/meta.yaml @@ -19,7 +19,7 @@ source: md5: 0e3e34e4f5cbfb6d0f3007656a6a2632 build: - number: 0 + number: 1 skip: true # [osx or not py27] requirements: @@ -27,6 +27,7 @@ requirements: - python - unzip - zip + - zlib {{CONDA_ZLIB}}* - curl # Needed for non-binary build # - google-cloud-sdk @@ -52,7 +53,7 @@ requirements: - six - crcmod - parallel - + test: commands: # Pre-built binaries need GLIBC 2.16 and 2.23 (htslib) so fail diff --git a/recipes/delly/meta.yaml b/recipes/delly/meta.yaml index 70db1753637d70..cdfbd8333ac4a8 100644 --- a/recipes/delly/meta.yaml +++ b/recipes/delly/meta.yaml @@ -11,7 +11,7 @@ source: - Makefile.patch build: - number: 0 + number: 1 string: boost{{CONDA_BOOST}}_{{PKG_BUILDNUM}} skip: True # [osx] diff --git a/recipes/denovogear/meta.yaml b/recipes/denovogear/meta.yaml index 85c17da323e2e9..2ab7b39ef3a164 100644 --- a/recipes/denovogear/meta.yaml +++ b/recipes/denovogear/meta.yaml @@ -3,7 +3,7 @@ package: version: "1.1.1" build: - number: 0 + number: 1 skip: True # [osx] string: boost{{CONDA_BOOST}}_{{PKG_BUILDNUM}} @@ -14,19 +14,19 @@ source: requirements: build: - - cmake - - gcc - - boost {{CONDA_BOOST}}* - - eigen - - zlib - - htslib + - cmake + - gcc + - boost {{CONDA_BOOST}}* + - eigen + - zlib {{CONDA_ZLIB}}* + - htslib {{CONDA_HTSLIB}}* run: - - libgcc - - boost {{CONDA_BOOST}}* - - eigen - - zlib - - htslib + - libgcc + - boost {{CONDA_BOOST}}* + - eigen + - zlib {{CONDA_ZLIB}}* + - htslib {{CONDA_HTSLIB}}* test: commands: diff --git a/recipes/detonate/build.sh b/recipes/detonate/build.sh index 7f148a7ae90ba0..a54133965e8e19 100644 --- a/recipes/detonate/build.sh +++ b/recipes/detonate/build.sh @@ -11,7 +11,7 @@ export CFLAGS="$CPPFLAGS" export CFLAGS_EXTRA="${LDFLAGS} ${CPPFLAGS}" -find -name Makefile | xargs -I {} sed -i.bak 's/-lcurses/-lncurses/g' {} +find -name Makefile | xargs -I {} sed -i.bak 's/-lcurses/-lncurses -ltinfo/g' {} make diff --git a/recipes/detonate/meta.yaml b/recipes/detonate/meta.yaml index 355ec458204c61..13a07f7dd27ff0 100644 --- a/recipes/detonate/meta.yaml +++ b/recipes/detonate/meta.yaml @@ -17,7 +17,7 @@ source: # - rsem-eval.Makefile.patch build: - number: 1 + number: 2 string: boost{{CONDA_BOOST}}_{{PKG_BUILDNUM}} package: diff --git a/recipes/diamond/0.8.26/meta.yaml b/recipes/diamond/0.8.26/meta.yaml index 0f8ee0198a5904..e9492528294d4c 100644 --- a/recipes/diamond/0.8.26/meta.yaml +++ b/recipes/diamond/0.8.26/meta.yaml @@ -11,7 +11,7 @@ source: md5: {{ md5 }} build: - number: 0 + number: 1 skip: False # We pin on gcc version to avoid gcc-5 dual ABI issues depending on boost. @@ -20,10 +20,10 @@ requirements: - gcc # [unix] - llvm # [osx] - cmake - - zlib + - zlib {{CONDA_ZLIB}}* run: - libgcc # [unix] - - zlib + - zlib {{CONDA_ZLIB}}* test: commands: diff --git a/recipes/diamond/0.8.27/meta.yaml b/recipes/diamond/0.8.27/meta.yaml index cd76b5dd470b95..0356e5ef002e82 100644 --- a/recipes/diamond/0.8.27/meta.yaml +++ b/recipes/diamond/0.8.27/meta.yaml @@ -11,7 +11,7 @@ source: md5: {{ md5 }} build: - number: 0 + number: 1 skip: False # We pin on gcc version to avoid gcc-5 dual ABI issues depending on boost. @@ -20,10 +20,10 @@ requirements: - gcc # [unix] - llvm # [osx] - cmake - - zlib + - zlib {{CONDA_ZLIB}}* run: - libgcc # [unix] - - zlib + - zlib {{CONDA_ZLIB}}* test: commands: diff --git a/recipes/diamond/0.8.28/meta.yaml b/recipes/diamond/0.8.28/meta.yaml index f8ccc92fc688b8..857e3535ca5baa 100644 --- a/recipes/diamond/0.8.28/meta.yaml +++ b/recipes/diamond/0.8.28/meta.yaml @@ -11,7 +11,7 @@ source: md5: {{ md5 }} build: - number: 0 + number: 1 skip: False # We pin on gcc version to avoid gcc-5 dual ABI issues depending on boost. @@ -20,10 +20,10 @@ requirements: - gcc # [unix] - llvm # [osx] - cmake - - zlib + - zlib {{CONDA_ZLIB}}* run: - libgcc # [unix] - - zlib + - zlib {{CONDA_ZLIB}}* test: commands: diff --git a/recipes/diamond/0.8.29/meta.yaml b/recipes/diamond/0.8.29/meta.yaml index 2c26114336ebe5..5ca6e0974ac9f1 100644 --- a/recipes/diamond/0.8.29/meta.yaml +++ b/recipes/diamond/0.8.29/meta.yaml @@ -11,7 +11,7 @@ source: md5: {{ md5 }} build: - number: 0 + number: 1 skip: False # We pin on gcc version to avoid gcc-5 dual ABI issues depending on boost. @@ -20,10 +20,10 @@ requirements: - gcc # [unix] - llvm # [osx] - cmake - - zlib + - zlib {{CONDA_ZLIB}}* run: - libgcc # [unix] - - zlib + - zlib {{CONDA_ZLIB}}* test: commands: diff --git a/recipes/diamond/0.8.30/meta.yaml b/recipes/diamond/0.8.30/meta.yaml index 1d5ecc725ae734..7cb2e6ea50ecda 100644 --- a/recipes/diamond/0.8.30/meta.yaml +++ b/recipes/diamond/0.8.30/meta.yaml @@ -11,7 +11,7 @@ source: md5: {{ md5 }} build: - number: 0 + number: 1 skip: False # We pin on gcc version to avoid gcc-5 dual ABI issues depending on boost. @@ -20,10 +20,10 @@ requirements: - gcc # [unix] - llvm # [osx] - cmake - - zlib + - zlib {{CONDA_ZLIB}}* run: - libgcc # [unix] - - zlib + - zlib {{CONDA_ZLIB}}* test: commands: diff --git a/recipes/diamond/0.8.31/meta.yaml b/recipes/diamond/0.8.31/meta.yaml index 6c206013d09de0..f88d277871d962 100644 --- a/recipes/diamond/0.8.31/meta.yaml +++ b/recipes/diamond/0.8.31/meta.yaml @@ -11,7 +11,7 @@ source: md5: {{ md5 }} build: - number: 0 + number: 1 skip: False # We pin on gcc version to avoid gcc-5 dual ABI issues depending on boost. @@ -20,10 +20,10 @@ requirements: - gcc # [unix] - llvm # [osx] - cmake - - zlib + - zlib {{CONDA_ZLIB}}* run: - libgcc # [unix] - - zlib + - zlib {{CONDA_ZLIB}}* test: commands: diff --git a/recipes/diamond/0.8.36/meta.yaml b/recipes/diamond/0.8.36/meta.yaml index b955b510f5a849..9d87d63a9283e1 100644 --- a/recipes/diamond/0.8.36/meta.yaml +++ b/recipes/diamond/0.8.36/meta.yaml @@ -11,7 +11,7 @@ source: md5: {{ md5 }} build: - number: 0 + number: 1 skip: False # We pin on gcc version to avoid gcc-5 dual ABI issues depending on boost. @@ -20,10 +20,10 @@ requirements: - gcc # [unix] - llvm # [osx] - cmake - - zlib + - zlib {{CONDA_ZLIB}}* run: - libgcc # [unix] - - zlib + - zlib {{CONDA_ZLIB}}* test: commands: diff --git a/recipes/diamond/0.9.10/meta.yaml b/recipes/diamond/0.9.10/meta.yaml index 8e43fd12fedf93..118322cac939e5 100644 --- a/recipes/diamond/0.9.10/meta.yaml +++ b/recipes/diamond/0.9.10/meta.yaml @@ -12,7 +12,7 @@ source: sha256: {{ sha256 }} build: - number: 0 + number: 1 skip: False requirements: @@ -20,10 +20,10 @@ requirements: - gcc # [unix] - llvm # [osx] - cmake - - zlib + - zlib {{CONDA_ZLIB}}* run: - libgcc # [unix] - - zlib + - zlib {{CONDA_ZLIB}}* test: commands: diff --git a/recipes/diamond/meta.yaml b/recipes/diamond/meta.yaml index 27b46b481699d6..7ed3a363e5c352 100644 --- a/recipes/diamond/meta.yaml +++ b/recipes/diamond/meta.yaml @@ -12,7 +12,7 @@ source: sha256: {{ sha256 }} build: - number: 0 + number: 1 skip: False requirements: diff --git a/recipes/dimspy/1.0.0/build.sh b/recipes/dimspy/1.0.0/build.sh new file mode 100644 index 00000000000000..3786386a73c834 --- /dev/null +++ b/recipes/dimspy/1.0.0/build.sh @@ -0,0 +1,3 @@ +#!/bin/bash + +$PYTHON setup.py install --single-version-externally-managed --record=record.txt diff --git a/recipes/dimspy/1.0.0/meta.yaml b/recipes/dimspy/1.0.0/meta.yaml new file mode 100644 index 00000000000000..a181b84b9ecf61 --- /dev/null +++ b/recipes/dimspy/1.0.0/meta.yaml @@ -0,0 +1,49 @@ +package: + name: dimspy + version: "1.0.0" + +source: + fn: dimspy-1.0.0.tar.gz + url: https://pypi.python.org/packages/41/e4/d050d2bfea7029cf79a877b4f9a05b4b1a1dfbd059699dbb49c570001982/dimspy-1.0.0.tar.gz + md5: 8e77008cf521541ef3a8778f4ec697bb + +build: + skip: True # [py3k] + number: 0 + entry_points: + - dimspy = dimspy.__main__:main + +requirements: + build: + - python + - setuptools + - numpy + - scipy + - fastcluster + - pymzml + - h5py + - pythonnet + run: + - python + - numpy + - scipy + - fastcluster + - pymzml + - h5py + - pythonnet + +test: + imports: + - dimspy + - dimspy.models + - dimspy.portals + - dimspy.process + + commands: + - dimspy --help + +about: + home: https://github.com/computational-metabolomics/dimspy + license: GPLv3 + summary: 'Python package for data processing of direct-infusion mass spectrometry-based metabolomics and lipidomics data' + license_family: GPL3 diff --git a/recipes/dimspy/meta.yaml b/recipes/dimspy/meta.yaml index a181b84b9ecf61..a6eb7855fbe9e9 100644 --- a/recipes/dimspy/meta.yaml +++ b/recipes/dimspy/meta.yaml @@ -1,11 +1,11 @@ package: name: dimspy - version: "1.0.0" + version: "1.1.0" source: - fn: dimspy-1.0.0.tar.gz - url: https://pypi.python.org/packages/41/e4/d050d2bfea7029cf79a877b4f9a05b4b1a1dfbd059699dbb49c570001982/dimspy-1.0.0.tar.gz - md5: 8e77008cf521541ef3a8778f4ec697bb + fn: dimspy-1.1.0.tar.gz + url: https://pypi.python.org/packages/ec/fb/5f8870de75f787c6e63dbe968600095ad0c1866aa13174247f9a15cbe454/dimspy-1.1.0.tar.gz + md5: fa743170874747a7bb8ab8a70443e084 build: skip: True # [py3k] diff --git a/recipes/disco/1.0/meta.yaml b/recipes/disco/1.0/meta.yaml index eaca7a7e22bc04..4712c5283d5d35 100644 --- a/recipes/disco/1.0/meta.yaml +++ b/recipes/disco/1.0/meta.yaml @@ -12,19 +12,18 @@ source: md5: {{ md5 }} build: - number: 0 - skip: False + number: 1 requirements: build: - gcc - openmpi >=1.8 - - zlib + - zlib {{CONDA_ZLIB}}* run: - libgcc # [not osx] - openmpi >=1.8 - - zlib + - zlib {{CONDA_ZLIB}}* test: commands: diff --git a/recipes/disco/1.2/meta.yaml b/recipes/disco/1.2/meta.yaml index b45bfc669d9ecf..166a532b71feee 100644 --- a/recipes/disco/1.2/meta.yaml +++ b/recipes/disco/1.2/meta.yaml @@ -12,8 +12,7 @@ source: md5: {{ md5 }} build: - number: 0 - skip: False + number: 1 requirements: build: diff --git a/recipes/discosnp/meta.yaml b/recipes/discosnp/meta.yaml index 7ce3abb8c7a8c9..92e70796a59a53 100644 --- a/recipes/discosnp/meta.yaml +++ b/recipes/discosnp/meta.yaml @@ -8,7 +8,7 @@ source: md5: "dfc35f6f5b83e7f661f5acbcb3c03bad" build: - number: 4 + number: 5 requirements: build: diff --git a/recipes/discovar-denovo/meta.yaml b/recipes/discovar-denovo/meta.yaml index 5cb14edea528af..55ce74ddb9a088 100644 --- a/recipes/discovar-denovo/meta.yaml +++ b/recipes/discovar-denovo/meta.yaml @@ -4,7 +4,7 @@ about: summary: 'Suitable for de novo assembly of large and small genomes.' build: - number: 0 + number: 1 skip: True # [osx] package: @@ -15,11 +15,11 @@ requirements: build: - gcc - jemalloc - - zlib + - zlib {{CONDA_ZLIB}}* run: - libgcc - jemalloc - - zlib + - zlib {{CONDA_ZLIB}}* source: fn: discovardenovo-52488.tar.gz diff --git a/recipes/disty/meta.yaml b/recipes/disty/meta.yaml index 14a4be0b0d40e9..f99ad2fa035d46 100644 --- a/recipes/disty/meta.yaml +++ b/recipes/disty/meta.yaml @@ -11,17 +11,17 @@ source: sha256: {{ sha256 }} build: - number: 0 + number: 1 requirements: build: - gcc # [not osx] - llvm # [osx] - - zlib ==1.2.8 + - zlib {{CONDA_ZLIB}}* - libgcc # [not osx] run: - - zlib ==1.2.8 + - zlib {{CONDA_ZLIB}}* - libgcc # [not osx] test: diff --git a/recipes/downpore/build.sh b/recipes/downpore/build.sh old mode 100644 new mode 100755 index a28d171516c883..2d80e2225bd3e0 --- a/recipes/downpore/build.sh +++ b/recipes/downpore/build.sh @@ -3,7 +3,7 @@ mkdir -p $PREFIX/bin mkdir -p src/github.com/jteutenberg/downpore -mv commands data seeds sequence trim util downpore.go src/github.com/jteutenberg/downpore +mv commands data overlap seeds sequence trim util downpore.go src/github.com/jteutenberg/downpore cd src/github.com/jteutenberg/downpore export GOPATH="$SRC_DIR/" diff --git a/recipes/downpore/meta.yaml b/recipes/downpore/meta.yaml index 01960ebbaafeec..95dd6c8adb3f5a 100644 --- a/recipes/downpore/meta.yaml +++ b/recipes/downpore/meta.yaml @@ -1,13 +1,13 @@ -{% set version = "0.1.1" %} +{% set version = "0.2" %} package: name: downpore version: {{ version }} source: - url: https://github.com/jteutenberg/downpore/archive/v{{ version }}.tar.gz - fn: downpore_{{ version }}.tar.gz - sha256: 8ab03431a57ca8acd022ca9cd3ebe14561bf1708cab53cbf9ff1a31acf737278 + url: https://github.com/jteutenberg/downpore/archive/0.2.tar.gz + fn: downpore-{{ version }}.tar.gz + sha256: c9c488fde56c80e6e5a75be70cfa285f6be519aaa92a66513d177860babb0153 build: number: 0 diff --git a/recipes/dsk/meta.yaml b/recipes/dsk/meta.yaml index 580a8b05e328fd..1c4268324e5a60 100644 --- a/recipes/dsk/meta.yaml +++ b/recipes/dsk/meta.yaml @@ -10,19 +10,19 @@ source: - install_paths.patch build: - number: 0 + number: 1 requirements: build: - cmake - gcc # [linux] - llvm # [osx] - - zlib + - zlib {{CONDA_ZLIB}}* - cppunit run: - libgcc # [linux] - - zlib + - zlib {{CONDA_ZLIB}}* test: commands: diff --git a/recipes/dsrc/meta.yaml b/recipes/dsrc/meta.yaml index 30516ca651bf85..05e5c098cc82d1 100644 --- a/recipes/dsrc/meta.yaml +++ b/recipes/dsrc/meta.yaml @@ -8,18 +8,18 @@ source: build: skip: True # [osx] - number: 1 + number: 2 string: boost{{CONDA_BOOST}}_{{PKG_BUILDNUM}} requirements: build: - gcc # [linux] - llvm # [osx] - - zlib + - zlib {{CONDA_ZLIB}}* - boost {{CONDA_BOOST}}* # [linux] run: - libgcc # [linux] - - zlib + - zlib {{CONDA_ZLIB}}* - boost {{CONDA_BOOST}}* # [linux] # dsrc -h returns an error so we need some data to test. diff --git a/recipes/dwgsim/meta.yaml b/recipes/dwgsim/meta.yaml index 08a820df5143c5..7ac8828d947716 100644 --- a/recipes/dwgsim/meta.yaml +++ b/recipes/dwgsim/meta.yaml @@ -5,7 +5,7 @@ about: summary: 'Whole Genome Simulator for Next-Generation Sequencing' build: - number: 3 + number: 4 package: name: dwgsim @@ -15,11 +15,11 @@ requirements: build: - gcc # [not osx] - llvm # [osx] - - zlib + - zlib {{CONDA_ZLIB}}* - ncurses run: - libgcc # [not osx] - - zlib + - zlib {{CONDA_ZLIB}}* - ncurses test: diff --git a/recipes/ecopcr/meta.yaml b/recipes/ecopcr/meta.yaml index b323333f5f4ccb..7d6f55c61f090e 100644 --- a/recipes/ecopcr/meta.yaml +++ b/recipes/ecopcr/meta.yaml @@ -6,7 +6,7 @@ package: version: {{ version }} build: - number: 0 + number: 1 skip: True # [not py27] source: @@ -17,15 +17,15 @@ source: requirements: build: - - gcc # [not osx] - - llvm # [osx] - - zlib + - gcc # [not osx] + - llvm # [osx] + - zlib {{CONDA_ZLIB}}* run: - - python - - libgcc [not osx] - - zlib - - reportlab + - python + - libgcc [not osx] + - zlib {{CONDA_ZLIB}}* + - reportlab test: commands: diff --git a/recipes/ecoprimers/meta.yaml b/recipes/ecoprimers/meta.yaml index fcb5939298060b..09d4084dccc969 100644 --- a/recipes/ecoprimers/meta.yaml +++ b/recipes/ecoprimers/meta.yaml @@ -6,23 +6,21 @@ package: version: {{ version }} build: - number: 0 + number: 1 source: fn: {{ name|lower }}_{{ version }}.tar.gz url: https://git.metabarcoding.org/obitools/ecoprimers/uploads/37c37c8d4dd62f53d66dae7a7f7b2318/ecoPrimers.tar.gz md5: 4c6bcb67f622fdf7dc8b9cc4860d1520 - requirements: build: - - gcc # [not osx] - - llvm # [osx] - - zlib - + - gcc # [not osx] + - llvm # [osx] + - zlib {{CONDA_ZLIB}}* run: - - libgcc [not osx] - - zlib + - libgcc [not osx] + - zlib {{CONDA_ZLIB}}* test: commands: @@ -32,4 +30,3 @@ about: home: https://git.metabarcoding.org/obitools/ecoprimers/wikis/home license: CeCill v2 summary: ecoPrimers is a software that finds primers from a set of sequence. - diff --git a/recipes/edlib/1.0.0/build.sh b/recipes/edlib/1.0.0/build.sh deleted file mode 100644 index ac6046fe733557..00000000000000 --- a/recipes/edlib/1.0.0/build.sh +++ /dev/null @@ -1,8 +0,0 @@ -#!/bin/bash - -cmake -D CMAKE_BUILD_TYPE=Release . -make VERBOSE=1 -make install DESTDIR=$PREFIX - -cp bin/aligner $PREFIX/bin/ - diff --git a/recipes/edlib/1.0.0/meta.yaml b/recipes/edlib/1.0.0/meta.yaml deleted file mode 100644 index 7582044f7a140e..00000000000000 --- a/recipes/edlib/1.0.0/meta.yaml +++ /dev/null @@ -1,30 +0,0 @@ -package: - name: edlib - version: "1.0.0" - -build: - number: 0 - -source: - fn: v1.0.0.tar.gz - url: https://github.com/Martinsos/edlib/archive/v1.0.0.tar.gz - -requirements: - build: - - gcc # [not osx] - - llvm # [osx] - - libgcc # [not osx] - - cmake - - run: - - libgcc # [not osx] - -test: - commands: - - echo ">" > test.fa && echo "AC" >> test.fa && aligner test.fa test.fa - -about: - home: https://github.com/Martinsos/edlib/ - license: MIT - summary: C/C++ library and program for sequence alignment using edit (Levenshtein) distance - diff --git a/recipes/edlib/1.1.2/build.sh b/recipes/edlib/1.1.2/build.sh deleted file mode 100644 index f6b2463ac5025c..00000000000000 --- a/recipes/edlib/1.1.2/build.sh +++ /dev/null @@ -1,8 +0,0 @@ -#!/bin/bash - -cmake -D CMAKE_BUILD_TYPE=Release . -make VERBOSE=1 -make install DESTDIR=$PREFIX - -cp bin/edlib-aligner $PREFIX/bin/ - diff --git a/recipes/edlib/1.1.2/meta.yaml b/recipes/edlib/1.1.2/meta.yaml deleted file mode 100644 index cf0214c2a729ab..00000000000000 --- a/recipes/edlib/1.1.2/meta.yaml +++ /dev/null @@ -1,33 +0,0 @@ -{% set version = "1.1.2" %} -{% set sha256 = "931cd09c3b47c431fd7b9adfc80b4cd742b1fbbb25218df33b54c2b6296b0b14" %} - -package: - name: edlib - version: {{ version }} - -build: - number: 0 - -source: - fn: v{{ version }}.tar.gz - url: https://github.com/Martinsos/edlib/archive/v{{ version }}.tar.gz - sha256: {{ sha256 }} - -requirements: - build: - - gcc # [not osx] - - llvm # [osx] - - libgcc # [not osx] - - cmake - - run: - - libgcc # [not osx] - -test: - commands: - - echo ">" > test.fa && echo "AC" >> test.fa && edlib-aligner test.fa test.fa - -about: - home: https://github.com/Martinsos/edlib/ - license: MIT - summary: C/C++ library and program for sequence alignment using edit (Levenshtein) distance diff --git a/recipes/edlib/1.2.0/build.sh b/recipes/edlib/1.2.0/build.sh deleted file mode 100644 index f6b2463ac5025c..00000000000000 --- a/recipes/edlib/1.2.0/build.sh +++ /dev/null @@ -1,8 +0,0 @@ -#!/bin/bash - -cmake -D CMAKE_BUILD_TYPE=Release . -make VERBOSE=1 -make install DESTDIR=$PREFIX - -cp bin/edlib-aligner $PREFIX/bin/ - diff --git a/recipes/edlib/1.2.0/meta.yaml b/recipes/edlib/1.2.0/meta.yaml deleted file mode 100644 index 126e9c208e7a1c..00000000000000 --- a/recipes/edlib/1.2.0/meta.yaml +++ /dev/null @@ -1,33 +0,0 @@ -{% set version = "1.2.0" %} -{% set sha256 = "83a34c52900f81bd847c2f18d3d07b87751a41cc75dedd5d7ba68e39cc849d9c" %} - -package: - name: edlib - version: {{ version }} - -build: - number: 0 - -source: - fn: v{{ version }}.tar.gz - url: https://github.com/Martinsos/edlib/archive/v{{ version }}.tar.gz - sha256: {{ sha256 }} - -requirements: - build: - - gcc # [not osx] - - llvm # [osx] - - libgcc # [not osx] - - cmake - - run: - - libgcc # [not osx] - -test: - commands: - - echo ">" > test.fa && echo "AC" >> test.fa && edlib-aligner test.fa test.fa - -about: - home: https://github.com/Martinsos/edlib/ - license: MIT - summary: C/C++ library and program for sequence alignment using edit (Levenshtein) distance diff --git a/recipes/edlib/meta.yaml b/recipes/edlib/meta.yaml index 817b2d186be675..972bee115b09a4 100644 --- a/recipes/edlib/meta.yaml +++ b/recipes/edlib/meta.yaml @@ -1,5 +1,5 @@ -{% set version = "1.2.1" %} -{% set sha256 = "ed9de53fb78cff1bd035469819130326bdedd474d44e65d12fc202f05ddf7587" %} +{% set version = "1.2.3" %} +{% set sha256 = "c8b2049daeff2717fb24e3e0a161aec9d9e146f37f67ab2cfda60500208399d2" %} package: name: edlib @@ -9,7 +9,7 @@ build: number: 0 source: - fn: v{{ version }}.tar.gz + fn: edlib-{{ version }}.tar.gz url: https://github.com/Martinsos/edlib/archive/v{{ version }}.tar.gz sha256: {{ sha256 }} @@ -31,3 +31,6 @@ about: home: https://github.com/Martinsos/edlib/ license: MIT summary: C/C++ library and program for sequence alignment using edit (Levenshtein) distance + +extra: + notes: From version 1.1.0 onward, the `aligner` executable has been renamed to `edlib-aligner`. diff --git a/recipes/embassy-phylip/meta.yaml b/recipes/embassy-phylip/meta.yaml index 3843f6bf5792e6..faefc1f2f3167f 100644 --- a/recipes/embassy-phylip/meta.yaml +++ b/recipes/embassy-phylip/meta.yaml @@ -3,7 +3,7 @@ package: version: "3.69.650" build: - number: 0 + number: 1 source: fn: PHYLIPNEW-3.69.650.tar.gz @@ -15,10 +15,10 @@ requirements: - gcc # [linux] - llvm # [osx] - python - - zlib + - zlib {{CONDA_ZLIB}}* - emboss run: - - zlib + - zlib {{CONDA_ZLIB}}* - emboss about: diff --git a/recipes/emboss/meta.yaml b/recipes/emboss/meta.yaml index 968f76e0175850..5edbc5fa65d5f8 100644 --- a/recipes/emboss/meta.yaml +++ b/recipes/emboss/meta.yaml @@ -3,7 +3,7 @@ package: version: "6.5.7" build: - number: 2 + number: 3 source: fn: EMBOSS-6.5.7.tar.gz @@ -12,21 +12,21 @@ source: requirements: build: - - gcc # [linux] - - llvm # [osx] - - python - - zlib + - gcc # [linux] + - llvm # [osx] + - python + - zlib {{CONDA_ZLIB}}* run: - - zlib + - zlib {{CONDA_ZLIB}}* about: home: http://emboss.open-bio.org/ license: GPL - summary: The European Molecular Biology Open Software Suite + summary: The European Molecular Biology Open Software Suite test: commands: - # test a few tools + # test a few tools - needle --help - transeq --help - sixpack --help diff --git a/recipes/emirge/meta.yaml b/recipes/emirge/meta.yaml index a5b439e40b8d68..a543fc4c53353b 100644 --- a/recipes/emirge/meta.yaml +++ b/recipes/emirge/meta.yaml @@ -12,14 +12,14 @@ source: sha256: {{ sha256 }} build: - number: 0 + number: 1 skip: True # [ py3k ] script: python setup.py install --single-version-externally-managed --record record.txt requirements: build: - cython - - zlib + - zlib {{CONDA_ZLIB}}* - gcc # [linux] - llvm # [osx] - python @@ -27,7 +27,7 @@ requirements: - numpy run: - - zlib + - zlib {{CONDA_ZLIB}}* - libgcc # [linux] - python - numpy diff --git a/recipes/ensembl-vep/meta.yaml b/recipes/ensembl-vep/meta.yaml index cd114fedcb6651..9d8e9295be1272 100644 --- a/recipes/ensembl-vep/meta.yaml +++ b/recipes/ensembl-vep/meta.yaml @@ -10,7 +10,7 @@ source: sha256: b1624ccf77f57d87678e053819acfe10108db73d8dbd0b5f2e821c1e97922034 build: - number: 0 + number: 1 skip: True # [osx] string: "htslib{{CONDA_HTSLIB}}_{{PKG_BUILDNUM}}" diff --git a/recipes/eqtlbma/meta.yaml b/recipes/eqtlbma/meta.yaml index af0cbd3ecdbc71..d8d1c1fab0bb1f 100644 --- a/recipes/eqtlbma/meta.yaml +++ b/recipes/eqtlbma/meta.yaml @@ -10,7 +10,7 @@ source: - utils_script.patch build: - number: 1 + number: 2 requirements: build: @@ -18,14 +18,14 @@ requirements: - autoconf 2.69 pl5.* - automake 1.15 pl5.* - libtool - - gsl >=1.15,<2.0 - - zlib + - gsl {{CONDA_GSL}}* + - zlib {{CONDA_ZLIB}}* - texinfo run: - libgcc - - gsl >=1.15,<2.0 - - zlib + - gsl {{CONDA_GSL}}* + - zlib {{CONDA_ZLIB}}* - r-base - r-mass - bioconductor-genomicranges diff --git a/recipes/erne/meta.yaml b/recipes/erne/meta.yaml index e591eb6f7cb2eb..a0d4e4208ebe0b 100644 --- a/recipes/erne/meta.yaml +++ b/recipes/erne/meta.yaml @@ -13,7 +13,7 @@ source: - osxfixes.patch # [osx] build: - number: 0 + number: 1 string: boost{{CONDA_BOOST}}_{{PKG_BUILDNUM}} # [linux] requirements: @@ -24,16 +24,16 @@ requirements: - libcxx # [osx] - boost ==1.63.0 # [osx] - boost {{CONDA_BOOST}}* # [linux] - - zlib - - bzip2 + - zlib {{CONDA_ZLIB}}* + - bzip2 {{CONDA_BZIP2}}* run: - libgcc # [linux] - libcxx # [osx] - boost {{CONDA_BOOST}}* # [linux] - boost ==1.63.0 # [osx] - - zlib - - bzip2 + - zlib {{CONDA_ZLIB}}* + - bzip2 {{CONDA_BZIP2}}* test: commands: diff --git a/recipes/extractpirs/meta.yaml b/recipes/extractpirs/meta.yaml index 266a7b0f5712a4..b16e043aeb678f 100644 --- a/recipes/extractpirs/meta.yaml +++ b/recipes/extractpirs/meta.yaml @@ -8,15 +8,17 @@ source: md5: de81232195f6e2eeed17a3ac028a02b6 build: - number: 0 + number: 1 skip: True # [osx] requirements: build: - - libgcc + - gcc # [not osx] + - llvm # [osx] + - zlib {{CONDA_ZLIB}}* run: - - zlib - - libgcc + - libgcc # [not osx] + - zlib {{CONDA_ZLIB}}* about: home: https://mathgen.stats.ox.ac.uk/genetics_software/shapeit/shapeit.html diff --git a/recipes/fasta3/meta.yaml b/recipes/fasta3/meta.yaml index 6c6a141764a92a..5a4512c423d5a7 100644 --- a/recipes/fasta3/meta.yaml +++ b/recipes/fasta3/meta.yaml @@ -14,7 +14,7 @@ source: - libpath.patch build: - number: 1 + number: 2 skip: True # [osx] requirements: diff --git a/recipes/fastool/meta.yaml b/recipes/fastool/meta.yaml index d734dd97f66e98..6aa5f668b48c99 100644 --- a/recipes/fastool/meta.yaml +++ b/recipes/fastool/meta.yaml @@ -8,15 +8,15 @@ source: sha256: f86f02fced9479b77d6d27a442b66e66f0c55d40d5ad2ddd91a752de57024540 build: - number: 1 + number: 2 requirements: build: - gcc - - zlib + - zlib {{CONDA_ZLIB}}* run: - libgcc - - zlib + - zlib {{CONDA_ZLIB}}* test: commands: diff --git a/recipes/fastp/meta.yaml b/recipes/fastp/meta.yaml index d81c3306810205..730d9bdc41cc9e 100644 --- a/recipes/fastp/meta.yaml +++ b/recipes/fastp/meta.yaml @@ -1,4 +1,4 @@ -{% set version="0.12.2" %} +{% set version="0.12.3" %} package: name: fastp version: {{ version }} @@ -6,7 +6,7 @@ package: source: fn: fastp-{{ version }}.tar.gz url: https://github.com/OpenGene/fastp/archive/v{{ version }}.tar.gz - md5: 399b62c276abd27ae6165d1d4a36b6ba + md5: 20bd3c3ccfd0121cee329b0c8cca960e build: number: 0 diff --git a/recipes/fastq_tools/meta.yaml b/recipes/fastq_tools/meta.yaml index cfb21827c467b6..b27de341f166b3 100644 --- a/recipes/fastq_tools/meta.yaml +++ b/recipes/fastq_tools/meta.yaml @@ -9,7 +9,7 @@ source: md5: 8d6f3d5e26ac3fd6f07543fdf572404c build: - number: 0 + number: 1 requirements: build: diff --git a/recipes/fermi/meta.yaml b/recipes/fermi/meta.yaml index 7a59f492c69070..cc62c9b3452304 100644 --- a/recipes/fermi/meta.yaml +++ b/recipes/fermi/meta.yaml @@ -3,7 +3,7 @@ package: version: "1.1_r751_beta" build: - number: 1 + number: 2 source: fn: fermi_1.1-r751-beta.tar.gz @@ -12,14 +12,13 @@ source: requirements: build: - - gcc # [not osx] - - llvm # [osx] - - zlib + - gcc + - zlib {{CONDA_ZLIB}}* run: - - libgcc # [not osx] - - perl-threaded - - zlib + - libgcc + - perl + - zlib {{CONDA_ZLIB}}* test: commands: @@ -29,4 +28,3 @@ about: home: https://github.com/lh3/fermi license: Unknown summary: A WGS de novo assembler based on the FMD-index for large genomes - diff --git a/recipes/fermi2/meta.yaml b/recipes/fermi2/meta.yaml index 2526c5737ccba2..e68661b3a147f6 100644 --- a/recipes/fermi2/meta.yaml +++ b/recipes/fermi2/meta.yaml @@ -3,7 +3,7 @@ package: version: "r193" build: - number: 0 + number: 1 source: fn: fermi2_r193.tar.gz @@ -14,14 +14,14 @@ requirements: build: - gcc # [not osx] - llvm # [osx] - - zlib + - zlib {{CONDA_ZLIB}}* run: - libgcc # [not osx] - bfc - ropebwt2 - perl - - zlib + - zlib {{CONDA_ZLIB}}* test: commands: diff --git a/recipes/fermikit/meta.yaml b/recipes/fermikit/meta.yaml index 6f4deee590db42..65533fd03245a4 100644 --- a/recipes/fermikit/meta.yaml +++ b/recipes/fermikit/meta.yaml @@ -3,7 +3,7 @@ package: version: "0.14.dev1" build: - number: 0 + number: 1 source: fn: fermikit-0.14.dev1.tar.bz2 @@ -12,22 +12,22 @@ source: requirements: build: - - gcc # [not osx] - - llvm # [osx] - - perl # For shasum checking - - zlib + - gcc # [not osx] + - llvm # [osx] + - perl # For shasum checking + - zlib {{CONDA_ZLIB}}* run: - - libgcc # [not osx] - - perl - - zlib - - bfc ==r181 - - bwa ==0.7.15 - - fermi2 ==r193 - - htsbox ==r327 - - ropebwt2 ==r187 - - seqtk ==r82 - - trimadap ==r10 + - libgcc # [not osx] + - perl + - zlib {{CONDA_ZLIB}}* + - bfc ==r181 + - bwa ==0.7.15 + - fermi2 ==r193 + - htsbox ==r327 + - ropebwt2 ==r187 + - seqtk ==r82 + - trimadap ==r10 test: source_files: diff --git a/recipes/filtlong/meta.yaml b/recipes/filtlong/meta.yaml index 81ca2ebffa1e7a..84b898c4dc108c 100644 --- a/recipes/filtlong/meta.yaml +++ b/recipes/filtlong/meta.yaml @@ -12,7 +12,7 @@ source: sha256: {{ sha256 }} build: - number: 0 + number: 1 requirements: build: diff --git a/recipes/flashlfq/meta.yaml b/recipes/flashlfq/meta.yaml index 85d3b9013b5059..6cc3fba424d51d 100644 --- a/recipes/flashlfq/meta.yaml +++ b/recipes/flashlfq/meta.yaml @@ -1,10 +1,10 @@ {% set name = "flashlfq" %} -{% set version = "0.1.100" %} +{% set version = "0.1.101" %} source: fn: FlashLFQ.zip url: https://github.com/smith-chem-wisc/FlashLFQ/releases/download/{{ version }}/FlashLFQ.zip - sha256: ef6c9b7208df55775ff906ce3c43eddbff9cc6773747cc0ce8f42c03432e5487 + sha256: 804cd6dba1debcec34378ae239eb5ea29bc82de4e3c18232ce6a9521a3fe5943 package: name: {{ name }} diff --git a/recipes/flexbar/2.5.0/meta.yaml b/recipes/flexbar/2.5.0/meta.yaml index f85b19f1fe508a..a95aea95c236ee 100644 --- a/recipes/flexbar/2.5.0/meta.yaml +++ b/recipes/flexbar/2.5.0/meta.yaml @@ -11,7 +11,7 @@ source: sha256: "{{ sha256 }}" build: - number: 0 + number: 1 skip: True # [osx] requirements: @@ -21,13 +21,13 @@ requirements: - cmake - tbb - seqan-library ==1.4.2 - - bzip2 + - bzip2 {{CONDA_BZIP2}}* - zlib {{CONDA_ZLIB}}* run: - libgcc # [not osx] - tbb - seqan-library ==1.4.2 - - bzip2 + - bzip2 {{CONDA_BZIP2}}* - zlib {{CONDA_ZLIB}}* test: diff --git a/recipes/flye/meta.yaml b/recipes/flye/meta.yaml index ec25e8489d7a3b..32187bbc34d835 100644 --- a/recipes/flye/meta.yaml +++ b/recipes/flye/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "2.3.1" %} +{% set version = "2.3.2" %} package: name: flye @@ -7,7 +7,7 @@ package: source: fn: flye-{{ version }}.tar.gz url: https://github.com/fenderglass/Flye/archive/{{ version }}.tar.gz - sha256: 61f45ffc5e30817c872a831133c0b102290024748b8026f1ed8a9e74a115cada + sha256: 52ca4cd3962a4c96380ede7839aa189d9c8e2b1e8703516abb5e3d40686e0d71 build: number: 0 diff --git a/recipes/fqtools/meta.yaml b/recipes/fqtools/meta.yaml index aaea3ba3a8cf65..599d9b66b94612 100644 --- a/recipes/fqtools/meta.yaml +++ b/recipes/fqtools/meta.yaml @@ -7,7 +7,7 @@ package: version: {{ version }} build: - number: 1 + number: 2 source: fn: {{ name|lower }}_{{ version }}.tar.gz @@ -18,12 +18,12 @@ requirements: build: - gcc # [not osx] - llvm # [osx] - - zlib - - htslib + - zlib {{CONDA_ZLIB}}* + - htslib {{ CONDA_HTSLIB }}* run: - libgcc # [not osx] - - zlib - - htslib + - zlib {{CONDA_ZLIB}}* + - htslib {{ CONDA_HTSLIB }}* test: commands: diff --git a/recipes/freebayes/meta.yaml b/recipes/freebayes/meta.yaml index 3102b4994057e7..6b4138b4419b5f 100644 --- a/recipes/freebayes/meta.yaml +++ b/recipes/freebayes/meta.yaml @@ -9,7 +9,7 @@ source: - qcfail.diff build: - number: 2 + number: 3 skip: true # [osx] string: "htslib{{ CONDA_HTSLIB }}_{{ PKG_BUILDNUM }}" @@ -28,7 +28,7 @@ requirements: - libgcc # [not osx] - htslib {{ CONDA_HTSLIB }}* - parallel - + test: commands: - freebayes --version diff --git a/recipes/fusion-inspector/meta.yaml b/recipes/fusion-inspector/meta.yaml index 3cd7089351cb2a..3f896477d4874e 100644 --- a/recipes/fusion-inspector/meta.yaml +++ b/recipes/fusion-inspector/meta.yaml @@ -1,6 +1,6 @@ {% set name = "fusion-inspector" %} {% set version = "1.1.0" %} -{% set build = "1" %} +{% set build = "2" %} package: name: {{ name }} diff --git a/recipes/fwdpp/0.5.3/meta.yaml b/recipes/fwdpp/0.5.3/meta.yaml index 33c1c6917f1179..3241b25058cdef 100644 --- a/recipes/fwdpp/0.5.3/meta.yaml +++ b/recipes/fwdpp/0.5.3/meta.yaml @@ -10,24 +10,29 @@ requirements: #b/c libsequence was built that way. #O/W we end up with "missing symbol" #errors. - #These requirements are solely + #These requirements are solely #to get the examples/unit tests #compiled. - - gcc - - zlib + - gcc + - zlib {{CONDA_ZLIB}}* - gsl {{CONDA_GSL}}* - libsequence - boost >=1.60.0 + run: + - libgcc build: - number: 0 + number: 1 + package: name: fwdpp version: '0.5.3' + test: commands: - fwdppConfig --version | grep 0.5.3 > /dev/null + source: - fn: 0.5.3.tar.gz + fn: 0.5.3.tar.gz url: http://github.com/molpopgen/fwdpp/archive/0.5.3.tar.gz md5: 09a00eb8fa1d54c953b5cb4e52a85a1c diff --git a/recipes/fwdpp/0.5.4/meta.yaml b/recipes/fwdpp/0.5.4/meta.yaml index d91338cd707349..89be993f687426 100644 --- a/recipes/fwdpp/0.5.4/meta.yaml +++ b/recipes/fwdpp/0.5.4/meta.yaml @@ -10,24 +10,29 @@ requirements: #b/c libsequence was built that way. #O/W we end up with "missing symbol" #errors. - #These requirements are solely + #These requirements are solely #to get the examples/unit tests #compiled. - - gcc - - zlib + - gcc + - zlib {{CONDA_ZLIB}}* - gsl {{CONDA_GSL}}* - libsequence - boost >=1.60.0 + run: + - libgcc build: - number: 2 + number: 3 + package: name: fwdpp version: '0.5.4' + test: commands: - fwdppConfig --version | grep 0.5.4 > /dev/null + source: - fn: 0.5.4.tar.gz + fn: 0.5.4.tar.gz url: http://github.com/molpopgen/fwdpp/archive/0.5.4.tar.gz md5: 36efa5cf0ff3730b154a2c73ec8f390b diff --git a/recipes/fwdpp/meta.yaml b/recipes/fwdpp/meta.yaml index dce3d15e8fe07a..d51263de76f21b 100644 --- a/recipes/fwdpp/meta.yaml +++ b/recipes/fwdpp/meta.yaml @@ -8,23 +8,24 @@ requirements: build: - gcc # [not osx] - llvm # [osx] - - zlib + - zlib {{CONDA_ZLIB}}* - gsl {{CONDA_GSL}}* - boost >=1.60.0 - run: - #Minimal requirement to test fwdppConfig - libgcc # [not osx] build: - number: 0 + number: 1 + package: name: fwdpp version: '0.5.7' + test: commands: - fwdppConfig --version | grep 0.5.7 > /dev/null + source: - fn: 0.5.7.tar.gz + fn: 0.5.7.tar.gz url: http://github.com/molpopgen/fwdpp/archive/0.5.7.tar.gz - md5: 3ee0e8439f10dd9f370821537ca3ae5e + md5: 3ee0e8439f10dd9f370821537ca3ae5e diff --git a/recipes/fwdpy11/meta.yaml b/recipes/fwdpy11/meta.yaml index 1b830c45ed9572..cdfd1bfdbd2ae4 100644 --- a/recipes/fwdpy11/meta.yaml +++ b/recipes/fwdpy11/meta.yaml @@ -1,11 +1,11 @@ package: name: fwdpy11 - version: "0.1.3.post1" + version: "0.1.3.post3" source: - fn: fwdpy11-0.1.3.post1.tar.gz - url: https://pypi.python.org/packages/b9/ed/56afc2a56799d1e8c541463bb8c26d6ce1c811c113db584dd1239b925216/fwdpy11-0.1.3.post1.tar.gz - md5: 0d05a5c871f2651b339c88bf0e16f077 + fn: fwdpy11-0.1.3.post3.tar.gz + url: https://pypi.python.org/packages/e8/b5/252158a60600daa00be281557360b9b627151cd779879df7db31847c3f57/fwdpy11-0.1.3.post3.tar.gz + md5: c92090691417c04828d36e7f4b410d13 build: skip: True # [py27] diff --git a/recipes/gap2seq/2.0/meta.yaml b/recipes/gap2seq/2.0/meta.yaml index cb76065747fbf8..e3c31779f1351d 100644 --- a/recipes/gap2seq/2.0/meta.yaml +++ b/recipes/gap2seq/2.0/meta.yaml @@ -3,7 +3,7 @@ package: version: "2.0" build: - number: 6 + number: 7 string: boost{{CONDA_BOOST}}_{{PKG_BUILDNUM}} source: @@ -24,7 +24,7 @@ requirements: - libcxx # [osx] - boost ==1.63.0 # [osx] # general build - - zlib + - zlib {{CONDA_ZLIB}}* - cmake - make run: @@ -35,7 +35,7 @@ requirements: - libcxx # [osx] - boost ==1.63.0 # [osx] # general run - - zlib + - zlib {{CONDA_ZLIB}}* test: commands: - GapMerger 2>&1 | grep "USAGE for" > /dev/null diff --git a/recipes/gap2seq/meta.yaml b/recipes/gap2seq/meta.yaml index 1331a734b662d8..e565456f77b0b1 100644 --- a/recipes/gap2seq/meta.yaml +++ b/recipes/gap2seq/meta.yaml @@ -7,7 +7,7 @@ package: version: {{ version }} build: - number: 2 + number: 3 string: boost{{CONDA_BOOST}}_zlib{{CONDA_ZLIB}}_{{PKG_BUILDNUM}} source: diff --git a/recipes/gat/meta.yaml b/recipes/gat/meta.yaml index 29558c0bac8aa7..c055fddcb22cc8 100644 --- a/recipes/gat/meta.yaml +++ b/recipes/gat/meta.yaml @@ -9,12 +9,12 @@ source: md5: c0271d7235eddfdc912afa1ee4b7d278 build: - number: 0 + number: 1 requirements: build: - python - - zlib + - zlib {{CONDA_ZLIB}}* - gcc # [not osx] - llvm # [osx] - setuptools >=1.1 @@ -25,7 +25,7 @@ requirements: run: - python - - zlib + - zlib {{CONDA_ZLIB}}* - cython >=0.19 - numpy >=1.7 - scipy >=0.11 diff --git a/recipes/gatk4/meta.yaml b/recipes/gatk4/meta.yaml index be6e0c78bf1a38..f956512d3a6868 100644 --- a/recipes/gatk4/meta.yaml +++ b/recipes/gatk4/meta.yaml @@ -1,4 +1,4 @@ -{% set version="4.0.1.2" %} +{% set version="4.0.2.0" %} about: home: https://www.broadinstitute.org/gatk/ @@ -15,7 +15,7 @@ build: source: fn: gatk-{{ version }}.zip url: https://github.com/broadinstitute/gatk/releases/download/{{ version }}/gatk-{{ version }}.zip - sha256: d667c08ec44f4dc2029d00ca16cfcfe7850ae9bfdcdd6e35f3048b8e7e83647b + sha256: 71557fc8d86653a48dc96ca280972fd7889841b458ec4ee94e88291bf92fd4e7 requirements: build: diff --git a/recipes/gdc-client/meta.yaml b/recipes/gdc-client/meta.yaml index 291b8ce1d764a5..cf35b5fa552298 100644 --- a/recipes/gdc-client/meta.yaml +++ b/recipes/gdc-client/meta.yaml @@ -5,7 +5,7 @@ package: version: {{ version }} build: - number: 0 + number: 1 skip: true # [py3k] source: diff --git a/recipes/genblastg/meta.yaml b/recipes/genblastg/meta.yaml index d351595cbe0e72..6eb8838d5f3d07 100644 --- a/recipes/genblastg/meta.yaml +++ b/recipes/genblastg/meta.yaml @@ -6,7 +6,7 @@ about: produced by local sequence alignment programs such as BLAST and WU-BLAST and identify groups of HSPs.' build: - number: 0 + number: 1 package: name: genblastg @@ -14,18 +14,18 @@ package: requirements: build: - - gcc # [linux] - - llvm # [osx] - - zlib + - gcc # [linux] + - llvm # [osx] + - zlib {{CONDA_ZLIB}}* run: - - libgcc # [linux] - - zlib - - blast + - libgcc # [linux] + - zlib {{CONDA_ZLIB}}* + - blast source: fn: genblast_v138.zip url: http://genome.sfu.ca/genblast/latest/genblast_v139.zip test: - commands: - - genblastG + commands: + - genblastG diff --git a/recipes/genehunter/3.0/meta.yaml b/recipes/genehunter/3.0/meta.yaml index 66c7e46e28e229..4510275ef26101 100644 --- a/recipes/genehunter/3.0/meta.yaml +++ b/recipes/genehunter/3.0/meta.yaml @@ -5,16 +5,10 @@ package: source: fn: ghm-3.0.tgz url: https://www.helmholtz-muenchen.de/fileadmin/GENEPI/downloads/ghm-3.0.tar.gz - md5: cd7400bbab7f5460fd45b300f57ba659 - # - # TODO: OSX - # - #patches: - # - osx-makefile.patch # [osx] - + md5: cd7400bbab7f5460fd45b300f57ba659 build: - number: 0 + number: 1 skip: True # [osx] requirements: @@ -25,6 +19,7 @@ requirements: run: - libgcc # [linux] + - zlib {{CONDA_ZLIB}}* test: commands: diff --git a/recipes/genehunter/3.1/meta.yaml b/recipes/genehunter/3.1/meta.yaml index d41562567fa04d..c6d9fe8269d1f2 100644 --- a/recipes/genehunter/3.1/meta.yaml +++ b/recipes/genehunter/3.1/meta.yaml @@ -6,15 +6,9 @@ source: fn: ghm-3.1.tgz url: https://www.helmholtz-muenchen.de/fileadmin/GENEPI/downloads/ghm-3.1.tgz md5: 0cfdc1aa80e7501f4766fa9537f96897 - # - # TODO: OSX - # - #patches: - # - osx-makefile.patch # [osx] - build: - number: 0 + number: 1 skip: True # [osx] requirements: @@ -25,7 +19,7 @@ requirements: run: - libgcc # [linux] - + - zlib {{CONDA_ZLIB}}* test: commands: - echo "q" | ghm diff --git a/recipes/gmap/2014.12.23/meta.yaml b/recipes/gmap/2014.12.23/meta.yaml index 1bfaec81893d9a..6d28cdcf341eb1 100644 --- a/recipes/gmap/2014.12.23/meta.yaml +++ b/recipes/gmap/2014.12.23/meta.yaml @@ -8,16 +8,16 @@ source: requirements: build: - perl - - zlib + - zlib {{CONDA_ZLIB}}* run: - perl - - zlib + - zlib {{CONDA_ZLIB}}* about: home: http://research-pub.gene.com/gmap/ license: Non-commercial summary: Genomic mapping and alignment program for mRNA and EST sequences build: - number: 3 + number: 4 skip: True # [osx] binary_has_prefix_files: - bin/atoiindex diff --git a/recipes/gmap/2015.12.31/meta.yaml b/recipes/gmap/2015.12.31/meta.yaml index e94dab25b2e597..cf5f11d117757b 100644 --- a/recipes/gmap/2015.12.31/meta.yaml +++ b/recipes/gmap/2015.12.31/meta.yaml @@ -10,19 +10,19 @@ requirements: - gcc # [linux] - llvm # [osx] - perl - - zlib - - bzip2 + - zlib {{CONDA_ZLIB}}* + - bzip2 {{CONDA_BZIP2}}* run: - libgcc # [linux] - perl - - zlib - - bzip2 + - zlib {{CONDA_ZLIB}}* + - bzip2 {{CONDA_BZIP2}}* about: home: http://research-pub.gene.com/gmap/ license: Non-commercial summary: Genomic mapping and alignment program for mRNA and EST sequences build: - number: 0 + number: 1 binary_has_prefix_files: - bin/atoiindex - bin/cmetindex diff --git a/recipes/gmap/2017.05.08/meta.yaml b/recipes/gmap/2017.05.08/meta.yaml index ebf3f48fbab77b..329af4f0bec0f9 100644 --- a/recipes/gmap/2017.05.08/meta.yaml +++ b/recipes/gmap/2017.05.08/meta.yaml @@ -10,19 +10,19 @@ requirements: - gcc # [linux] - llvm # [osx] - perl - - zlib - - bzip2 + - zlib {{CONDA_ZLIB}}* + - bzip2 {{CONDA_BZIP2}}* run: - libgcc # [linux] - perl - - zlib - - bzip2 + - zlib {{CONDA_ZLIB}}* + - bzip2 {{CONDA_BZIP2}}* about: home: http://research-pub.gene.com/gmap/ license: Non-commercial summary: Genomic mapping and alignment program for mRNA and EST sequences build: - number: 0 + number: 1 binary_has_prefix_files: - bin/atoiindex - bin/cmetindex diff --git a/recipes/gmap/2017.09.30/meta.yaml b/recipes/gmap/2017.09.30/meta.yaml index f6837b5a201ab0..08a309714ab8cd 100644 --- a/recipes/gmap/2017.09.30/meta.yaml +++ b/recipes/gmap/2017.09.30/meta.yaml @@ -10,19 +10,19 @@ requirements: - gcc # [linux] - llvm # [osx] - perl - - zlib - - bzip2 + - zlib {{CONDA_ZLIB}}* + - bzip2 {{CONDA_BZIP2}}* run: - libgcc # [linux] - perl - - zlib - - bzip2 + - zlib {{CONDA_ZLIB}}* + - bzip2 {{CONDA_BZIP2}}* about: home: http://research-pub.gene.com/gmap/ license: Non-commercial summary: Genomic mapping and alignment program for mRNA and EST sequences build: - number: 0 + number: 1 binary_has_prefix_files: - bin/atoiindex - bin/cmetindex diff --git a/recipes/gmap/meta.yaml b/recipes/gmap/meta.yaml index 77cab7b9507c6b..cd8ece74130c21 100644 --- a/recipes/gmap/meta.yaml +++ b/recipes/gmap/meta.yaml @@ -22,7 +22,7 @@ about: license: Non-commercial summary: Genomic mapping and alignment program for mRNA and EST sequences build: - number: 0 + number: 1 binary_has_prefix_files: - bin/atoiindex - bin/cmetindex diff --git a/recipes/gnu-wget/build.sh b/recipes/gnu-wget/build.sh deleted file mode 100644 index 400c26721127b2..00000000000000 --- a/recipes/gnu-wget/build.sh +++ /dev/null @@ -1,13 +0,0 @@ -#!/bin/sh -set -euo pipefail - -export CFLAGS="-I$PREFIX/include" -export LDFLAGS="-L$PREFIX/lib" -export CPATH=${PREFIX}/include - -./configure --prefix=$PREFIX \ - --enable-threads=posix \ - --with-ssl=openssl - -make -make install diff --git a/recipes/gnu-wget/meta.yaml b/recipes/gnu-wget/meta.yaml deleted file mode 100644 index 3b0cf8229c5383..00000000000000 --- a/recipes/gnu-wget/meta.yaml +++ /dev/null @@ -1,39 +0,0 @@ -package: - name: gnu-wget - version: '1.18' - -source: - fn: wget-1.18.tar.xz - url: http://ftp.gnu.org/gnu/wget/wget-1.18.tar.xz - md5: af9ca95a4bb8ac4a9bf10aeae66fa5ec - -build: - number: 2 - -requirements: - build: - - gcc # [not osx] - - llvm # [osx] - # The configure script requires Python 3 for Wget's test suite. The recipe - # does not run the tests, but the configure check cannot be turned off. - - python >=3 - - zlib - - openssl - - pkg-config - - pcre - - run: - - libgcc # [not osx] - - zlib - - openssl - - pcre - -test: - commands: - - wget --help - -about: - home: http://www.gnu.org/software/wget/ - license: GPLv3 - summary: 'Retrieve files using HTTP, HTTPS and FTP' - diff --git a/recipes/gqt/meta.yaml b/recipes/gqt/meta.yaml index 7691863b0a5595..a2e57756e6ca59 100644 --- a/recipes/gqt/meta.yaml +++ b/recipes/gqt/meta.yaml @@ -13,7 +13,7 @@ source: - src-makefile.patch build: - number: 0 + number: 1 requirements: build: @@ -21,12 +21,12 @@ requirements: - llvm # [osx] - flex - sqlite - - htslib + - htslib {{ CONDA_HTSLIB }}* run: - libgcc # [not osx] - sqlite - - htslib + - htslib {{ CONDA_HTSLIB }}* test: commands: diff --git a/recipes/grabix/meta.yaml b/recipes/grabix/meta.yaml index 064c231d46e770..7b8f7650974492 100644 --- a/recipes/grabix/meta.yaml +++ b/recipes/grabix/meta.yaml @@ -4,7 +4,7 @@ package: version: "0.1.8" build: - number: 2 + number: 3 skip: False source: diff --git a/recipes/graphmap/build.sh b/recipes/graphmap/build.sh index c7aa10a93ab2b3..f8299953f8ad21 100644 --- a/recipes/graphmap/build.sh +++ b/recipes/graphmap/build.sh @@ -6,13 +6,12 @@ export CPATH=${PREFIX}/include mkdir -p $PREFIX/bin - cd $SRC_DIR/codebase -wget -O seqlib.tar.gz https://github.com/isovic/seqlib/archive/d980be7.tar.gz +wget --no-check-certificate -O seqlib.tar.gz https://github.com/isovic/seqlib/archive/d980be7.tar.gz tar -xvf seqlib.tar.gz -C seqlib --strip-components 1 -wget -O argumentparser.tar.gz https://github.com/isovic/argumentparser/archive/72af976.tar.gz +wget --no-check-certificate -O argumentparser.tar.gz https://github.com/isovic/argumentparser/archive/72af976.tar.gz tar -xvf argumentparser.tar.gz -C argumentparser --strip-components 1 -wget -O gindex.tar.gz https://github.com/isovic/gindex/archive/b1fb5ad.tar.gz +wget --no-check-certificate -O gindex.tar.gz https://github.com/isovic/gindex/archive/b1fb5ad.tar.gz tar -xvf gindex.tar.gz -C gindex --strip-components 1 cd $SRC_DIR diff --git a/recipes/graphmap/meta.yaml b/recipes/graphmap/meta.yaml index 69139bdf53c990..1ad6e5e0eef372 100644 --- a/recipes/graphmap/meta.yaml +++ b/recipes/graphmap/meta.yaml @@ -7,7 +7,7 @@ package: version: {{ version }} build: - number: 0 + number: 1 source: fn: {{ name|lower }}_{{ version }}.tar.gz @@ -19,13 +19,13 @@ source: requirements: build: - - gnu-wget + - wget - gcc - - zlib + - zlib {{CONDA_ZLIB}}* run: - libgcc - - zlib + - zlib {{CONDA_ZLIB}}* test: commands: diff --git a/recipes/graphprot/meta.yaml b/recipes/graphprot/meta.yaml index c66578dd43e0a3..7722aae242b92a 100644 --- a/recipes/graphprot/meta.yaml +++ b/recipes/graphprot/meta.yaml @@ -11,7 +11,7 @@ source: sha256: "{{ sha256 }}" build: - number: 1 + number: 2 skip: True # [osx] requirements: diff --git a/recipes/gromacs/meta.yaml b/recipes/gromacs/meta.yaml index aa04e4f9047a77..7a9217dfe08b77 100644 --- a/recipes/gromacs/meta.yaml +++ b/recipes/gromacs/meta.yaml @@ -9,6 +9,7 @@ package: build: number: 0 + skip: True # [osx] # See http://manual.gromacs.org/documentation/ # for latest release. Note that version scheme changed from diff --git a/recipes/groot/build.sh b/recipes/groot/build.sh new file mode 100644 index 00000000000000..b346eba0bb897f --- /dev/null +++ b/recipes/groot/build.sh @@ -0,0 +1,12 @@ +#!/bin/bash +mkdir -p $PREFIX/bin +mkdir groot +mv cmd src main.go groot/ +mkdir -p src/github.com/will-rowe/ +mv groot src/github.com/will-rowe/ +cd src/github.com/will-rowe/groot + +export GOPATH="$SRC_DIR/" +go get ./... +go build -o groot main.go +mv groot $PREFIX/bin diff --git a/recipes/groot/meta.yaml b/recipes/groot/meta.yaml new file mode 100644 index 00000000000000..51e6f3d9406a8a --- /dev/null +++ b/recipes/groot/meta.yaml @@ -0,0 +1,28 @@ +{% set version = "0.2" %} + +package: + name: groot + version: {{ version }} + +source: + url: https://github.com/will-rowe/groot/archive/{{ version }}.tar.gz + fn: groot_{{ version }}.tar.gz + sha256: af04e6596e47f6fef653f6ed5cce539bd6b52ace41e16a837c9aa3d89f7a6479 + +build: + number: 0 + +requirements: + build: + - go + - mercurial + +test: + commands: + - groot + - groot version + +about: + home: https://github.com/will-rowe/groot + license: MIT + summary: A tool for resistome profiling of metagenomic samples. diff --git a/recipes/gubbins/meta.yaml b/recipes/gubbins/meta.yaml index 8519812d35a8da..c84f0df8ac0da1 100644 --- a/recipes/gubbins/meta.yaml +++ b/recipes/gubbins/meta.yaml @@ -7,7 +7,7 @@ package: version: {{ version }} build: - number: 0 + number: 1 skip: True # [py27] source: diff --git a/recipes/gvcftools/meta.yaml b/recipes/gvcftools/meta.yaml index 50f4483233d80f..3eec162ea60ff3 100644 --- a/recipes/gvcftools/meta.yaml +++ b/recipes/gvcftools/meta.yaml @@ -1,30 +1,30 @@ package: name: gvcftools version: '0.17.0' - + source: fn: gvcftools-0.17.0.tar.gz url: https://github.com/sequencing/gvcftools/releases/download/v0.17.0/gvcftools-0.17.0.tar.gz build: - number: 1 + number: 2 skip: True # [not linux] requirements: build: - gcc # [not osx] - llvm # [osx] - - zlib + - zlib {{CONDA_ZLIB}}* run: - libgcc # [not osx] - perl - - zlib + - zlib {{CONDA_ZLIB}}* test: commands: - - extract_variants -h 2>&1 | grep 'extract_variants extracts variants from a VCF file' + - extract_variants -h 2>&1 | grep "extract_variants extracts variants from a VCF file" about: home: https://sites.google.com/site/gvcftools/home diff --git a/recipes/hap.py/meta.yaml b/recipes/hap.py/meta.yaml index 1f0216da86465d..2242764a7015ab 100644 --- a/recipes/hap.py/meta.yaml +++ b/recipes/hap.py/meta.yaml @@ -9,7 +9,7 @@ source: md5: 3052070d05dc08964e355c9da57f37ea build: - number: 0 + number: 1 skip: True # [not py27 or osx] requirements: @@ -17,7 +17,7 @@ requirements: - python - setuptools - gcc - - zlib + - zlib {{CONDA_ZLIB}}* - cython - numpy - pandas @@ -31,7 +31,7 @@ requirements: - python - libgcc - cython - - zlib + - zlib {{CONDA_ZLIB}}* - numpy - pandas - pybedtools diff --git a/recipes/haploclique/1.3.1/meta.yaml b/recipes/haploclique/1.3.1/meta.yaml index 8870d5454b3867..6eab5e5b52e170 100644 --- a/recipes/haploclique/1.3.1/meta.yaml +++ b/recipes/haploclique/1.3.1/meta.yaml @@ -7,7 +7,7 @@ package: version: {{ version }} build: - number: 0 + number: 1 source: fn: {{ name }}-v{{ version }}.tar.bz2 diff --git a/recipes/hera/meta.yaml b/recipes/hera/meta.yaml index 45aad06c1604c1..d5c12061b62fe1 100644 --- a/recipes/hera/meta.yaml +++ b/recipes/hera/meta.yaml @@ -15,31 +15,31 @@ source: - hera.makefile.patch build: - number: 0 + number: 1 requirements: build: - gcc # [not osx] - llvm # [osx] - cmake - - zlib + - zlib {{CONDA_ZLIB}}* - jemalloc >=4.5.0 - - htslib - - hdf5 + - htslib {{CONDA_HTSLIB}}* + - hdf5 {{CONDA_HDF5}}* - libdivsufsort - - xz - - bzip2 + - xz {{CONDA_XZ}}* + - bzip2 {{CONDA_BZIP2}}* run: - python - libgcc # [not osx] - - zlib + - zlib {{CONDA_ZLIB}}* - jemalloc >=4.5.0 - - htslib - - hdf5 + - htslib {{CONDA_HTSLIB}}* + - hdf5 {{CONDA_HDF5}}* - libdivsufsort - - xz - - bzip2 + - xz {{CONDA_XZ}}* + - bzip2 {{CONDA_BZIP2}}* test: commands: diff --git a/recipes/hicexplorer/meta.yaml b/recipes/hicexplorer/meta.yaml index c3aede248ca310..dc6ff5684ba151 100644 --- a/recipes/hicexplorer/meta.yaml +++ b/recipes/hicexplorer/meta.yaml @@ -1,52 +1,51 @@ package: name: hicexplorer - version: '2.0' + version: '2.1alpha1' source: - fn: 2.0.tar.gz - url: https://github.com/deeptools/HiCExplorer/archive/2.0.tar.gz - sha256: 975eda994b336c5279068ec8cb9c78bda34ad958f5faef88e7b49132861a6380 + fn: 2.1-alpha.tar.gz + url: https://github.com/deeptools/HiCExplorer/archive/2.1-alpha.tar.gz + sha256: 3ff39025286115162aad4fd15421eeaa7adc35a39ab539e7db304a0abb16cd75 build: - number: 1 - skip: false + number: 0 requirements: build: - python - setuptools - - numpy 1.12.* - - scipy >=0.19.0 - - matplotlib ==2.1.1 - - pysam >=0.11.2 - - intervaltree >=2.1.0 + - numpy 1.13.* + - scipy 1.0.* + - matplotlib 2.1.* + - pysam + - intervaltree - biopython >=1.68 - - pytables >=3.3.0 - - pybigwig >=0.3.4 - - pandas >=0.20.2 - - jinja2 >=2.9.6 - - configparser >=3.5.0 # [not py>34] - - cooler >=0.7.6 - - six >=1.10.0 - - future >=0.16.0 + - pytables + - pybigwig + - pandas + - jinja2 + - configparser >=3.5.* # [not py>34] + - cooler + - six + - future + - unidecode run: - python - - pybigwig >=0.3.4 - - numpy >=1.12.* - - scipy >=0.19.0 - - matplotlib ==2.1.1 - - pysam >=0.11.2 - - intervaltree >=2.1.0 + - numpy 1.13.* + - scipy 1.0.* + - matplotlib 2.1.* + - pysam + - intervaltree - biopython >=1.68 - - pytables >=3.3.0 - - pybigwig >=0.3.4 - - pandas >=0.20.2 - - jinja2 >=2.9.6 - - configparser >=3.5.0 # [not py>34] - - cooler >=0.7.6 - - six >=1.10.0 - - future >=0.16.0 - + - pytables + - pybigwig + - pandas + - jinja2 + - configparser >=3.5.* # [not py>34] + - cooler + - six + - future + - unidecode test: imports: diff --git a/recipes/hmmcopy/meta.yaml b/recipes/hmmcopy/meta.yaml index 27d80d018f7c99..f76e0695eef4d5 100644 --- a/recipes/hmmcopy/meta.yaml +++ b/recipes/hmmcopy/meta.yaml @@ -1,12 +1,15 @@ package: name: hmmcopy version: 0.1.1 + source: fn: HMMcopy-0.1.1.zip url: http://compbio-bccrc.sites.olt.ubc.ca/files/2013/12/HMMcopy.zip md5: 205a719e7ac9b9f9ba811cdd7cbdae0a + build: - number: 0 + number: 1 + requirements: build: - gcc # [not osx] @@ -15,9 +18,11 @@ requirements: run: - libgcc # [not osx] - zlib {{CONDA_ZLIB}}* + test: commands: - readCounter -h + about: home: http://compbio.bccrc.ca/software/hmmcopy/ license: GPL-3 diff --git a/recipes/hts-nim-tools/meta.yaml b/recipes/hts-nim-tools/meta.yaml index e2f37157dc08cc..b2780f32895c75 100644 --- a/recipes/hts-nim-tools/meta.yaml +++ b/recipes/hts-nim-tools/meta.yaml @@ -13,7 +13,7 @@ source: sha256: {{ sha256hash }} build: - number: 0 + number: 1 skip: True # [osx] string: "htslib{{CONDA_HTSLIB}}_{{PKG_BUILDNUM}}" diff --git a/recipes/htsbox/meta.yaml b/recipes/htsbox/meta.yaml index 6d2112bc03f1ee..2f7cc79cd430d4 100644 --- a/recipes/htsbox/meta.yaml +++ b/recipes/htsbox/meta.yaml @@ -7,7 +7,7 @@ package: version: {{ version }} build: - number: 0 + number: 1 source: fn: htsbox_{{ version }}.tar.gz @@ -18,11 +18,11 @@ requirements: build: - gcc # [not osx] - llvm # [osx] - - zlib + - zlib {{CONDA_ZLIB}}* run: - libgcc - - zlib + - zlib {{CONDA_ZLIB}}* test: commands: @@ -32,4 +32,3 @@ about: home: https://github.com/lh3/htsbox license: Unknown summary: HTSbox is a fork of early HTSlib. It is a collection of small experimental tools manipulating HTS-related files. - diff --git a/recipes/imseq/meta.yaml b/recipes/imseq/meta.yaml index f3ee4244bd031b..cafa2398ded8ce 100644 --- a/recipes/imseq/meta.yaml +++ b/recipes/imseq/meta.yaml @@ -5,7 +5,7 @@ package: version: {{ version }} build: - number: 0 + number: 1 skip: True # [osx] source: @@ -19,11 +19,11 @@ source: requirements: build: - gcc # [not osx] - - zlib + - zlib {{CONDA_ZLIB}}* - cmake run: - libgcc # [not osx] - - zlib + - zlib {{CONDA_ZLIB}}* about: home: http://www.imtools.org/ diff --git a/recipes/intarna/build.sh b/recipes/intarna/build.sh index cee26a3e1956de..1ad22197b27ce3 100644 --- a/recipes/intarna/build.sh +++ b/recipes/intarna/build.sh @@ -22,10 +22,16 @@ export CXX=${CXX} export CXXFLAGS=${CXXFLAGS} export LDFLAGS=${LDFLAGS} +if [ `uname` == Darwin ] ; then +CONFIGURE_MULTITHREADING="--disable-multithreading" +else ## linux +CONFIGURE_MULTITHREADING="" +fi + ./configure --prefix=$PREFIX \ --with-vrna=$PREFIX \ --with-boost=$PREFIX \ - --disable-multithreading \ + $CONFIGURE_MULTITHREADING \ --disable-log-coloring \ ${extra_config_options} \ diff --git a/recipes/intarna/meta.yaml b/recipes/intarna/meta.yaml index 5299979766ba0f..3417bc8dc1cd14 100644 --- a/recipes/intarna/meta.yaml +++ b/recipes/intarna/meta.yaml @@ -8,7 +8,7 @@ about: summary: Efficient target prediction incorporating seeding and accessibility of interaction sites build: - number: 0 + number: 1 string: boost{{CONDA_BOOST}}_{{PKG_BUILDNUM}} source: @@ -18,21 +18,17 @@ source: requirements: build: - # linux build - gcc # [linux] - - boost {{CONDA_BOOST}}* # [linux] - # osx build + - boost {{CONDA_BOOST}}* - llvmdev ==3.9.1 # [osx] - libcxx # [osx] - - boost ==1.63.0 # [osx] # general requirements - viennarna >=2.4.1,<3 - doxygen run: - libgcc # [linux] - libcxx # [osx] - - boost {{CONDA_BOOST}}* # [linux] - - boost ==1.63.0 # [osx] + - boost {{ CONDA_BOOST }}* # for old interface wrapper - perl diff --git a/recipes/iqtree/1.5.3/meta.yaml b/recipes/iqtree/1.5.3/meta.yaml index 5bff17fd02b40d..55b51021146075 100644 --- a/recipes/iqtree/1.5.3/meta.yaml +++ b/recipes/iqtree/1.5.3/meta.yaml @@ -6,7 +6,7 @@ package: version: {{ version }} build: - number: 0 + number: 1 source: fn: {{ name|lower }}_{{ version }}.tar.gz @@ -15,14 +15,14 @@ source: requirements: build: - - gcc - - cmake - - eigen - - zlib + - gcc + - cmake + - eigen + - zlib {{CONDA_ZLIB}}* run: - - libgcc - - zlib + - libgcc + - zlib {{CONDA_ZLIB}}* test: commands: diff --git a/recipes/iqtree/meta.yaml b/recipes/iqtree/meta.yaml index 6e644557d67b91..486236247c50ce 100644 --- a/recipes/iqtree/meta.yaml +++ b/recipes/iqtree/meta.yaml @@ -6,7 +6,7 @@ package: version: {{ version }} build: - number: 0 + number: 1 source: fn: {{ name|lower }}_{{ version }}.tar.gz @@ -15,14 +15,14 @@ source: requirements: build: - - gcc - - cmake - - eigen - - zlib + - gcc + - cmake + - eigen + - zlib {{CONDA_ZLIB}}* run: - - libgcc - - zlib + - libgcc + - zlib {{CONDA_ZLIB}}* test: commands: diff --git a/recipes/itk/4.6.1/meta.yaml b/recipes/itk/4.6.1/meta.yaml index ef764b6f34cdbf..7b01644c728d48 100644 --- a/recipes/itk/4.6.1/meta.yaml +++ b/recipes/itk/4.6.1/meta.yaml @@ -11,7 +11,7 @@ source: md5: 2c84eae50ab2452cdad32aaadced3c37 build: - number: 0 + number: 1 requirements: build: @@ -21,11 +21,11 @@ requirements: - libtiff - libpng - jpeg - - zlib + - zlib {{CONDA_ZLIB}}* run: - python - libgcc # [not osx] - - zlib + - zlib {{CONDA_ZLIB}}* - libtiff - libpng - jpeg diff --git a/recipes/itk/meta.yaml b/recipes/itk/meta.yaml index 8ceadfa52e2b16..61469fce7a696f 100644 --- a/recipes/itk/meta.yaml +++ b/recipes/itk/meta.yaml @@ -11,7 +11,7 @@ source: md5: f7e7fb92ea3e11c78685c7977e0433d8 build: - number: 1 + number: 2 requirements: build: @@ -21,11 +21,11 @@ requirements: - libtiff - libpng - jpeg - - zlib + - zlib {{CONDA_ZLIB}}* run: - python - libgcc # [not osx] - - zlib + - zlib {{CONDA_ZLIB}}* - libtiff - libpng - jpeg diff --git a/recipes/kaiju/1.6.1/build.sh b/recipes/kaiju/1.6.1/build.sh new file mode 100755 index 00000000000000..b66ce25c2dfdcc --- /dev/null +++ b/recipes/kaiju/1.6.1/build.sh @@ -0,0 +1,22 @@ +#!/bin/bash + +mkdir -p $PREFIX/bin + +cd $SRC_DIR/src/ + +make + +cd $SRC_DIR/bin/ +cp addTaxonNames $PREFIX/bin +cp convertNR $PREFIX/bin +cp gbk2faa.pl $PREFIX/bin +cp kaiju $PREFIX/bin +cp kaiju2krona $PREFIX/bin +cp kaijup $PREFIX/bin +cp kaijuReport $PREFIX/bin +cp kaijux $PREFIX/bin +cp makeDB.sh $PREFIX/bin +cp mergeOutputs $PREFIX/bin +cp mkbwt $PREFIX/bin +cp mkfmi $PREFIX/bin +cp taxonlist.tsv $PREFIX/bin diff --git a/recipes/kaiju/1.6.1/meta.yaml b/recipes/kaiju/1.6.1/meta.yaml new file mode 100755 index 00000000000000..cf1042c76f6555 --- /dev/null +++ b/recipes/kaiju/1.6.1/meta.yaml @@ -0,0 +1,36 @@ +{% set version = "1.6.1" %} + +package: + name: kaiju + version: {{ version }} + +source: + fn: v{{ version }}.tar.gz + url: https://github.com/bioinformatics-centre/kaiju/archive/v{{ version }}.tar.gz + sha256: ee6c319ab3e58db846139810705bfe33306618d78d75d715fac623f302be9e72 + +build: + number: 0 + no_link: + - bin/makeDB.sh + +requirements: + build: + - gcc + - zlib {{ CONDA_ZLIB }}* + + run: + - libgcc + - perl + - gnu-wget >=1.16 + - zlib {{ CONDA_ZLIB }}* + +test: + commands: + - kaiju 2>&1 | grep "Kaiju {{ version }}" + +about: + home: http://kaiju.binf.ku.dk/ + license: GNU GPL v3 + summary: 'Fast and sensitive taxonomic classification for metagenomics' + license_file: LICENSE diff --git a/recipes/kaiju/build.sh b/recipes/kaiju/build.sh index b66ce25c2dfdcc..f47d2011d67e66 100755 --- a/recipes/kaiju/build.sh +++ b/recipes/kaiju/build.sh @@ -19,4 +19,5 @@ cp makeDB.sh $PREFIX/bin cp mergeOutputs $PREFIX/bin cp mkbwt $PREFIX/bin cp mkfmi $PREFIX/bin +cp convert_mar_to_kaiju.py $PREFIX/bin cp taxonlist.tsv $PREFIX/bin diff --git a/recipes/kaiju/meta.yaml b/recipes/kaiju/meta.yaml index b8621a3177d9ab..91e06187948733 100755 --- a/recipes/kaiju/meta.yaml +++ b/recipes/kaiju/meta.yaml @@ -1,12 +1,13 @@ +{% set version = "1.6.2" %} + package: name: kaiju - version: 1.5.0 + version: {{ version }} source: - fn: v1.5.0.tar.gz - url: https://github.com/bioinformatics-centre/kaiju/archive/v1.5.0.tar.gz - md5: e8effb834a7d1e2863880c60d481ecf2 - + fn: v{{ version }}.tar.gz + url: https://github.com/bioinformatics-centre/kaiju/archive/v{{ version }}.tar.gz + sha256: 474eb3d4cd619ce3dc456cb570f233d228154e64cce597eb8a294fa07b26b6cd build: number: 0 @@ -16,16 +17,17 @@ build: requirements: build: - gcc + - zlib {{ CONDA_ZLIB }}* + run: - libgcc - perl - gnu-wget >=1.16 + - zlib {{ CONDA_ZLIB }}* test: commands: - - kaiju 2>&1 | head -n 1 | grep -q '^Error:'; echo $? - -#Tool always outputs error code one so created a workaround + - kaiju 2>&1 | grep "Kaiju {{ version }}" about: home: http://kaiju.binf.ku.dk/ diff --git a/recipes/kallisto/meta.yaml b/recipes/kallisto/meta.yaml index c7df6e0a452f0e..86124ef889a01f 100644 --- a/recipes/kallisto/meta.yaml +++ b/recipes/kallisto/meta.yaml @@ -10,17 +10,17 @@ source: sha256: 2164938c2c61c04e338c4c132cf749f56d39e6f0b4c517121bca1fbc218e430e build: - number: 0 + number: 1 string: hdf5{{CONDA_HDF5}}_{{PKG_BUILDNUM}} requirements: build: - - hdf5 {{CONDA_HDF5}} + - hdf5 {{CONDA_HDF5}}* - cmake - zlib - gcc run: - - hdf5 {{CONDA_HDF5}} + - hdf5 {{CONDA_HDF5}}* - libgcc test: files: diff --git a/recipes/kat/2.3.4/meta.yaml b/recipes/kat/2.3.4/meta.yaml index d37144f858838c..b5512efcc50d64 100644 --- a/recipes/kat/2.3.4/meta.yaml +++ b/recipes/kat/2.3.4/meta.yaml @@ -18,7 +18,7 @@ about: summary: 'KAT is a suite of tools that analyse jellyfish hashes or sequence files (fasta or fastq) using kmer counts' build: - number: 0 + number: 1 string: boost{{CONDA_BOOST}}_{{PKG_BUILDNUM}} skip: True # [osx or py2k] @@ -28,7 +28,7 @@ requirements: - llvm # [osx] - libgcc # [not osx] - python - - zlib + - zlib {{CONDA_ZLIB}}* - autoconf - automake - libtool @@ -42,7 +42,7 @@ requirements: run: - python - libgcc # [not osx] - - zlib + - zlib {{CONDA_ZLIB}}* - boost {{CONDA_BOOST}}* - gnuplot - jellyfish diff --git a/recipes/kissplice/meta.yaml b/recipes/kissplice/meta.yaml index bdd4daaf9e2061..ed65b451796e31 100644 --- a/recipes/kissplice/meta.yaml +++ b/recipes/kissplice/meta.yaml @@ -8,7 +8,7 @@ source: md5: "36ef9e22a0607f0ab4516cc0d4cf9fea" build: - number: 0 + number: 1 skip: True # [py3k] requirements: diff --git a/recipes/kmc/meta.yaml b/recipes/kmc/meta.yaml index 08f0303dd6e958..4be44737a1354b 100644 --- a/recipes/kmc/meta.yaml +++ b/recipes/kmc/meta.yaml @@ -15,7 +15,7 @@ source: - 0004-kmc-no-libz-libbz2-static-link.patch build: - number: 0 + number: 1 # this recipe builds kmc without the asmlib speedup string: "noasmlib_{{ PKG_BUILDNUM }}" diff --git a/recipes/kmergenie/meta.yaml b/recipes/kmergenie/meta.yaml index f40ced35e2f67a..597273291b1ea2 100644 --- a/recipes/kmergenie/meta.yaml +++ b/recipes/kmergenie/meta.yaml @@ -7,7 +7,7 @@ package: version: {{ version }} build: - number: 1 + number: 2 skip: True # [not py27] source: @@ -20,12 +20,12 @@ requirements: - python - gcc # [linux] - llvm # [osx] - - zlib + - zlib {{ CONDA_ZLIB }}* - r-base run: - python - libgcc # [linux] - - zlib + - zlib {{ CONDA_ZLIB }}* - r-base test: diff --git a/recipes/kodoja/meta.yaml b/recipes/kodoja/meta.yaml index 71c5d231549d1c..dd48de8bef21fd 100644 --- a/recipes/kodoja/meta.yaml +++ b/recipes/kodoja/meta.yaml @@ -1,10 +1,10 @@ package: name: kodoja - version: "0.0.2" + version: "0.0.3" source: - url: https://github.com/abaizan/kodoja/archive/kodoja-v0.0.2.tar.gz - sha256: 245da0cbb2d2f3ed46a08a8bb42f1b98c8575228faa9e8d59269a265b3f3173d + url: https://github.com/abaizan/kodoja/archive/kodoja-v0.0.3.tar.gz + sha256: 526bbcff79c5c4a6edb782b9028cb71d0b77c2e957acc96f2b5672ce55ca7246 build: number: 0 diff --git a/recipes/kraken-ea/meta.yaml b/recipes/kraken-ea/meta.yaml index d235001b1babf0..03dd2bace8aa1e 100644 --- a/recipes/kraken-ea/meta.yaml +++ b/recipes/kraken-ea/meta.yaml @@ -7,17 +7,17 @@ source: md5: 34dce0103874e199a13eeed9bf20bd73 build: - number: 1 + number: 2 skip: False requirements: build: - perl - - zlib + - zlib {{CONDA_ZLIB}}* - gcc run: - - zlib + - zlib {{CONDA_ZLIB}}* - jellyfish 1.1.11 - perl - libgcc diff --git a/recipes/krakenhll/meta.yaml b/recipes/krakenhll/meta.yaml index b63954c0ea27b3..35c75f30b2beb1 100644 --- a/recipes/krakenhll/meta.yaml +++ b/recipes/krakenhll/meta.yaml @@ -29,6 +29,8 @@ requirements: run: - jellyfish 1.* - perl + - perl-libwww-perl + - perl-lwp-protocol-https - libgcc - zlib {{CONDA_ZLIB}}* diff --git a/recipes/leptonica/1.73/meta.yaml b/recipes/leptonica/1.73/meta.yaml index 92ad3b0bbb6f05..11b69115b18f5d 100644 --- a/recipes/leptonica/1.73/meta.yaml +++ b/recipes/leptonica/1.73/meta.yaml @@ -2,7 +2,7 @@ package: name: leptonica version: 1.73 build: - number: 0 + number: 1 skip: True # [osx] source: fn: leptonica-1.73.tar.gz @@ -14,10 +14,10 @@ requirements: - jpeg - libpng - libtiff - - zlib + - zlib {{CONDA_ZLIB}}* - cmake run: - - zlib + - zlib {{CONDA_ZLIB}}* - jpeg - libpng - libtiff diff --git a/recipes/libbambamc/0.5.00/meta.yaml b/recipes/libbambamc/0.5.00/meta.yaml index 0dfe0a7bf05c49..0d19490f9d9b5f 100644 --- a/recipes/libbambamc/0.5.00/meta.yaml +++ b/recipes/libbambamc/0.5.00/meta.yaml @@ -7,13 +7,16 @@ package: name: libbambamc version: 0.0.50 +build: + number: 1 + requirements: build: - gcc - - zlib + - zlib {{CONDA_ZLIB}}* run: - libgcc - - zlib + - zlib {{CONDA_ZLIB}}* source: fn: 0.0.50-release-20140430085950.tar.gz @@ -21,7 +24,11 @@ source: url: https://github.com/gt1/bambamc/archive/0.0.50-release-20140430085950.tar.gz test: - files: - - test.c + # mulled doesn't support these + #requires: + # - gcc + #files: + # - test.c commands: - - gcc -I ${PREFIX}/include -L ${PREFIX}/lib -lbambamc test.c + # - gcc -I ${PREFIX}/include -L ${PREFIX}/lib -lbambamc test.c + - test -f $PREFIX/lib/libbambamc.so diff --git a/recipes/libbigwig/meta.yaml b/recipes/libbigwig/meta.yaml index 3bd7f81d78f543..07e2a0a1525a34 100644 --- a/recipes/libbigwig/meta.yaml +++ b/recipes/libbigwig/meta.yaml @@ -6,7 +6,7 @@ package: version: {{ version }} build: - number: 0 + number: 1 source: fn: libBigWig-{{ version }}.tar.gz diff --git a/recipes/libsequence/1.8.4/build.sh b/recipes/libsequence/1.8.4/build.sh new file mode 100644 index 00000000000000..aad04ead2eea47 --- /dev/null +++ b/recipes/libsequence/1.8.4/build.sh @@ -0,0 +1,6 @@ +#!/bin/bash + +CXXFLAGS="-O3 -DNDEBUG" CPPFLAGS="-I$CONDA_PREFIX/include $CPPFLAGS" LDFLAGS="-L$CONDA_PREFIX/lib -Wl,-rpath,$PREFIX/lib $LDFLAGS" ./configure --prefix=$PREFIX +make +# make check # Fails on macosx +make install diff --git a/recipes/libsequence/1.8.4/meta.yaml b/recipes/libsequence/1.8.4/meta.yaml new file mode 100644 index 00000000000000..3902de3f309008 --- /dev/null +++ b/recipes/libsequence/1.8.4/meta.yaml @@ -0,0 +1,37 @@ +{% set version="1.8.4" %} +{% set hash="24ac822e202549175aafbeb8db8dc5daa11e3874334fc9e55d0bb4b9bc81b221" %} + +package: + name: libsequence + version: {{ version }} + +source: + fn: {{ version }}-1.tar.gz + url: http://github.com/molpopgen/libsequence/archive/{{ version }}-1.tar.gz + sha256: {{ hash }} + +build: + number: 0 + string: "htslib{{CONDA_HTSLIB}}_{{PKG_BUILDNUM}}" + +requirements: + build: + - gcc + - zlib {{ CONDA_ZLIB }}* + - tbb + - htslib {{CONDA_HTSLIB}}* + run: + - libgcc + - zlib {{ CONDA_ZLIB }}* + - tbb + - htslib {{CONDA_HTSLIB}}* + +test: + commands: + - ls -ls $PREFIX/lib/libsequence.so # [linux] + - ls -ls $PREFIX/lib/libsequence.dylib # [osx] + +about: + home: http://http://molpopgen.github.io/libsequence/ + license: GNU Lesser General Public License v2 or later (LGPLv2+) + summary: A C++ class library for evolutionary genetics diff --git a/recipes/libsequence/meta.yaml b/recipes/libsequence/meta.yaml index a3b6d41a8a0877..0bc4933487f6e3 100644 --- a/recipes/libsequence/meta.yaml +++ b/recipes/libsequence/meta.yaml @@ -1,32 +1,34 @@ -about: - home: 'https://www.github.com/molpopgen/libsequence' - license: "https://raw.githubusercontent.com/molpopgen/libsequence/master/LICENSE" - summary: "A C++ class library for evolutionary genetics (doi: 10.1093/bioinformatics/btg316)" + +package: + name: libsequence + version: '1.9.2' + +source: + fn: 1.9.2.tar.gz + url: http://github.com/molpopgen/libsequence/archive/1.9.2.tar.gz + md5: e9ac2e624ee5bf93483df01e62429530 + +build: + number: 1 + string: "htslib{{CONDA_HTSLIB}}_{{PKG_BUILDNUM}}" + requirements: build: - - gcc + - gcc - zlib {{ CONDA_ZLIB }}* - tbb - htslib {{CONDA_HTSLIB}}* - run: + run: - libgcc - zlib {{ CONDA_ZLIB }}* - tbb - htslib {{CONDA_HTSLIB}}* -build: - number: 0 - string: "htslib{{CONDA_HTSLIB}}_{{PKG_BUILDNUM}}" -package: - name: libsequence - version: '1.9.2' + test: commands: - libsequenceConfig --version | grep 1.9.2 > /dev/null + about: home: http://http://molpopgen.github.io/libsequence/ license: GNU Lesser General Public License v2 or later (LGPLv2+) summary: 'A C++ class library for evolutionary genetics.' -source: - fn: 1.9.2.tar.gz - url: http://github.com/molpopgen/libsequence/archive/1.9.2.tar.gz - md5: e9ac2e624ee5bf93483df01e62429530 diff --git a/recipes/lighter/meta.yaml b/recipes/lighter/meta.yaml index df4baeaf8b6b50..6a0785c9dd722e 100644 --- a/recipes/lighter/meta.yaml +++ b/recipes/lighter/meta.yaml @@ -7,15 +7,15 @@ source: url: https://github.com/mourisl/Lighter/archive/v1.1.1.tar.gz build: - number: 1 + number: 2 requirements: build: - gcc # [linux] - llvm # [osx] - - zlib + - zlib {{CONDA_ZLIB}}* run: - - zlib + - zlib {{CONDA_ZLIB}}* - libgcc # [linux] test: diff --git a/recipes/lordec/meta.yaml b/recipes/lordec/meta.yaml index ed7cdee9b623ce..8f3c8af8b65a08 100644 --- a/recipes/lordec/meta.yaml +++ b/recipes/lordec/meta.yaml @@ -8,7 +8,7 @@ source: md5: "6b82f9e232eb886293411e3f0d090ab0" build: - number: 0 + number: 1 requirements: build: diff --git a/recipes/lorma/meta.yaml b/recipes/lorma/meta.yaml index 2de748ce3fe3bf..844153fba6fdc9 100644 --- a/recipes/lorma/meta.yaml +++ b/recipes/lorma/meta.yaml @@ -8,7 +8,7 @@ source: md5: "3a59e427374ffbb84430528bc1430f64" build: - number: 1 + number: 2 skip: True # [osx] requirements: diff --git a/recipes/lumpy-sv/meta.yaml b/recipes/lumpy-sv/meta.yaml index 63c3f2d5701ad3..3515b476076e7c 100644 --- a/recipes/lumpy-sv/meta.yaml +++ b/recipes/lumpy-sv/meta.yaml @@ -9,16 +9,16 @@ source: sha256: 1a7a5d18875b297acaa68ee1e864ca048654ebc85348920b518dc689d2b7a3cf build: - number: 0 + number: 1 skip: True # [not py27] requirements: build: - - zlib + - zlib {{CONDA_ZLIB}}* - gcc run: - - zlib + - zlib {{CONDA_ZLIB}}* - python - samtools - gawk diff --git a/recipes/mappy/meta.yaml b/recipes/mappy/meta.yaml index ec1b0ef6798b01..b31eb85cadbcf8 100644 --- a/recipes/mappy/meta.yaml +++ b/recipes/mappy/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "2.8" %} +{% set version = "2.9" %} package: name: mappy @@ -7,10 +7,10 @@ package: source: fn: mappy-{{ version }}.tar.gz url: https://pypi.io/packages/source/m/mappy/mappy-{{ version }}.tar.gz - sha256: 7e7b26ed6c93fb6e3b9bd01df36c8ee55a4516d410057cd6ebef3a6d684f4542 + sha256: 49b2b784e4003358e1ef16d42900be73743cffd61bb91705b3fa6aebae1ccdfd build: - number: 0 + number: 1 requirements: build: diff --git a/recipes/mapsembler2/meta.yaml b/recipes/mapsembler2/meta.yaml index bf8f03a341090c..c8b3a63467c68c 100644 --- a/recipes/mapsembler2/meta.yaml +++ b/recipes/mapsembler2/meta.yaml @@ -8,7 +8,7 @@ source: md5: "2165dfa0372356aac2b0a50f53a838ff" build: - number: 1 + number: 2 requirements: build: diff --git a/recipes/mapsplice/meta.yaml b/recipes/mapsplice/meta.yaml index 92daca797178a3..9bc96509e2fbf8 100644 --- a/recipes/mapsplice/meta.yaml +++ b/recipes/mapsplice/meta.yaml @@ -19,12 +19,12 @@ build: requirements: build: - python - - zlib + - zlib {{CONDA_ZLIB}}* - ncurses {{CONDA_NCURSES}}* run: - python - - zlib + - zlib {{CONDA_ZLIB}}* - ncurses {{CONDA_NCURSES}}* test: diff --git a/recipes/mash/meta.yaml b/recipes/mash/meta.yaml index 78342cf63cb22f..b739e6b4d132ee 100644 --- a/recipes/mash/meta.yaml +++ b/recipes/mash/meta.yaml @@ -10,7 +10,7 @@ source: sha256: 7bea8cd3c266640bbd97f2e1c9d0168892915c1c14f7d03a9751bf7a3709dd01 build: - number: 0 + number: 1 string: gsl{{CONDA_GSL}}_{{PKG_BUILDNUM}} requirements: diff --git a/recipes/megagta/meta.yaml b/recipes/megagta/meta.yaml index 866d6f889ff254..0a51917bf365f0 100644 --- a/recipes/megagta/meta.yaml +++ b/recipes/megagta/meta.yaml @@ -1,9 +1,14 @@ package: name: megagta version: "0.1_alpha" + source: fn: megagta-v0.1alpha-src.tar.gz url: https://github.com/HKU-BAL/megagta/releases/download/v0.1-alpha/megagta-v0.1alpha-src.tar.gz + +build: + number: 1 + requirements: build: - automake @@ -11,20 +16,23 @@ requirements: - m4 - gcc # [linux] - llvm # [osx] - - zlib + - zlib {{CONDA_ZLIB}}* - ant run: - libgcc # [linux] - - zlib + - zlib {{CONDA_ZLIB}}* - python >=2.7,<3 - hmmer >=3.1b2 + build: skip: True # [osx] + test: requires: - python >=2.7,<3 commands: - megagta.py -v > /dev/null + about: home: https://github.com/HKU-BAL/megagta license: "GNU General Public License v3 (GPLv3" diff --git a/recipes/megahit/meta.yaml b/recipes/megahit/meta.yaml index 9b131a0e3712f7..dc96ca5c88bb7e 100644 --- a/recipes/megahit/meta.yaml +++ b/recipes/megahit/meta.yaml @@ -3,39 +3,39 @@ {% set sha256 = "d0d3965dd49c6fdaea958ef66146cb6b30b7d51acbbfe94194c437f15a424cb5" %} package: - name: {{ name }} - version: {{ version }} + name: {{ name }} + version: {{ version }} source: - fn: v{{ version }}.tar.gz - sha256: {{ sha256 }} - url: https://github.com/voutcn/{{ name }}/archive/v{{ version }}.tar.gz + fn: v{{ version }}.tar.gz + sha256: {{ sha256 }} + url: https://github.com/voutcn/{{ name }}/archive/v{{ version }}.tar.gz build: - number: 0 + number: 1 requirements: - build: - # megahit requires openpm, which is not available in clang < 3.7 - - gcc - - zlib 1.2.8 - run: - - libgcc # for gomp - - zlib 1.2.8 - - python + build: + # megahit requires openpm, which is not available in clang < 3.7 + - gcc + - zlib {{CONDA_ZLIB}}* + run: + - libgcc # for gomp + - zlib {{CONDA_ZLIB}}* + - python test: - commands: - # Run one of the examples provided with megahit to make sure the - # binaries actually work. - # The output has to be removed to prevent permission failure during - # cleanup after mulled-build. - - megahit --12 $PREFIX/share/megahit/example/readsInterleaved1.fa.gz && rm -r megahit_out + commands: + # Run one of the examples provided with megahit to make sure the + # binaries actually work. + # The output has to be removed to prevent permission failure during + # cleanup after mulled-build. + - megahit --12 $PREFIX/share/megahit/example/readsInterleaved1.fa.gz && rm -r megahit_out about: - home: https://github.com/voutcn/megahit - license: GPL3 - summary: | - MEGAHIT: An ultra-fast single-node solution for large and complex - metagenomics assembly via succinct de Bruijn graph + home: https://github.com/voutcn/megahit + license: GPL3 + summary: | + MEGAHIT: An ultra-fast single-node solution for large and complex + metagenomics assembly via succinct de Bruijn graph diff --git a/recipes/meme/4.11.1/meta.yaml b/recipes/meme/4.11.1/meta.yaml index 261095b40b2e17..580746067f4ea3 100644 --- a/recipes/meme/4.11.1/meta.yaml +++ b/recipes/meme/4.11.1/meta.yaml @@ -10,7 +10,7 @@ package: version: 4.11.1 build: - number: 2 + number: 3 skip: True # [osx or py3k] detect_binary_files_with_prefix: True diff --git a/recipes/meme/meta.yaml b/recipes/meme/meta.yaml index abb5f59c0c2534..2dc3147492b14e 100644 --- a/recipes/meme/meta.yaml +++ b/recipes/meme/meta.yaml @@ -12,7 +12,7 @@ source: - mast.patch build: - number: 0 + number: 1 detect_binary_files_with_prefix: True requirements: diff --git a/recipes/mentalist/0.1.3/build.sh b/recipes/mentalist/0.1.3/build.sh new file mode 100644 index 00000000000000..ed146fb56a1a9f --- /dev/null +++ b/recipes/mentalist/0.1.3/build.sh @@ -0,0 +1,23 @@ +#!/bin/sh + +# circumvent a bug in conda-build >=2.1.18,<3.0.10 +# https://github.com/conda/conda-build/issues/2255 +[[ -z $REQUESTS_CA_BUNDLE && ${REQUESTS_CA_BUNDLE+x} ]] && unset REQUESTS_CA_BUNDLE +[[ -z $SSL_CERT_FILE && ${SSL_CERT_FILE+x} ]] && unset SSL_CERT_FILE + + +cp -r $SRC_DIR/src/*.jl $PREFIX/bin +ln -s $PREFIX/bin/MentaLiST.jl $PREFIX/bin/mentalist +chmod +x $PREFIX/bin/mentalist + +julia -e 'Pkg.init()' +julia -e 'Pkg.add("Suppressor")' +julia -e 'Pkg.add("ArgParse")' +julia -e 'Pkg.add("Bio")' +julia -e 'Pkg.add("OpenGene")' +julia -e 'Pkg.add("Logging")' +julia -e 'Pkg.add("Lumberjack")' + +rm -f "$PREFIX"/share/julia/site/lib/v*/*.ji +rm -rf "$PREFIX"/share/julia/site/v*/METADATA +rm -f "$PREFIX"/share/julia/site/v*/META_BRANCH diff --git a/recipes/mentalist/0.1.3/meta.yaml b/recipes/mentalist/0.1.3/meta.yaml new file mode 100644 index 00000000000000..953ba5c2098573 --- /dev/null +++ b/recipes/mentalist/0.1.3/meta.yaml @@ -0,0 +1,37 @@ +{% set name = "MentaLiST" %} +{% set version = "0.1.3" %} + +package: + name: {{ name|lower }} + version: {{ version }} + +source: + fn: {{ name|lower }}-{{ version }}.tar.gz + url: https://github.com/WGS-TB/MentaLiST/archive/v{{ version }}.tar.gz + sha256: 57874e2168b48c165fc68c2bab41819259ec828e298bc54cbc3da8f3c904c63e + +build: + number: 1 + skip: True # [osx] + +requirements: + build: + - julia 0.5.2 + - hdf5 {{ CONDA_HDF5 }}* + - mpfr + - libxml2 + run: + - julia 0.5.2 + - hdf5 {{ CONDA_HDF5 }}* + - mpfr + - libxml2 + +test: + commands: + - mentalist -h + +about: + home: https://github.com/WGS-TB/MentaLiST + summary: The MLST pipeline developed by the PathOGiST research group. + license: MIT + license_file: LICENSE diff --git a/recipes/mentalist/build.sh b/recipes/mentalist/build.sh index 3a44013cd6f910..b35fa885169296 100644 --- a/recipes/mentalist/build.sh +++ b/recipes/mentalist/build.sh @@ -1,17 +1,24 @@ #!/bin/sh +# circumvent a bug in conda-build >=2.1.18,<3.0.10 +# https://github.com/conda/conda-build/issues/2255 +[[ -z $REQUESTS_CA_BUNDLE && ${REQUESTS_CA_BUNDLE+x} ]] && unset REQUESTS_CA_BUNDLE +[[ -z $SSL_CERT_FILE && ${SSL_CERT_FILE+x} ]] && unset SSL_CERT_FILE + cp -r $SRC_DIR/src/*.jl $PREFIX/bin cp -r $SRC_DIR/scripts $PREFIX ln -s $PREFIX/bin/MentaLiST.jl $PREFIX/bin/mentalist chmod +x $PREFIX/bin/mentalist julia -e 'Pkg.init()' -julia -e 'Pkg.add("Suppressor")' julia -e 'Pkg.add("ArgParse")' julia -e 'Pkg.add("Bio")' julia -e 'Pkg.add("OpenGene")' julia -e 'Pkg.add("Logging")' julia -e 'Pkg.add("Lumberjack")' +julia -e 'Pkg.add("FastaIO")' +julia -e 'Pkg.add("JLD")' +julia -e 'Pkg.add("DataStructures")' rm -f "$PREFIX"/share/julia/site/lib/v*/*.ji rm -rf "$PREFIX"/share/julia/site/v*/METADATA diff --git a/recipes/mentalist/meta.yaml b/recipes/mentalist/meta.yaml index 1444ea2170dcf7..9c2f58234d15a9 100644 --- a/recipes/mentalist/meta.yaml +++ b/recipes/mentalist/meta.yaml @@ -1,5 +1,5 @@ {% set name = "MentaLiST" %} -{% set version = "0.2.0" %} +{% set version = "0.2.1" %} package: name: {{ name|lower }} @@ -8,7 +8,7 @@ package: source: fn: {{ name|lower }}-{{ version }}.tar.gz url: https://github.com/WGS-TB/MentaLiST/archive/v{{ version }}.tar.gz - sha256: f425e9e3e3bd9fa5177a346178ceee9e8e44936624227756b5ea2bb61d5dfcb4 + sha256: a148fcd552c9ce4964dd7cc88d7771fc5bde7d94ed46e8145ba61c8a88804c92 build: number: 1 @@ -16,11 +16,11 @@ build: requirements: build: - - julia 0.5.2 + - julia 0.6.1 - hdf5 {{ CONDA_HDF5 }}* - mpfr run: - - julia 0.5.2 + - julia 0.6.1 - hdf5 {{ CONDA_HDF5 }}* - mpfr - libxml2 diff --git a/recipes/merlin/meta.yaml b/recipes/merlin/meta.yaml index 8ba59aba757999..c70dca0b370876 100644 --- a/recipes/merlin/meta.yaml +++ b/recipes/merlin/meta.yaml @@ -9,15 +9,18 @@ source: sha1: d5227276eae862506c7ed4475255c9be182585df sha256: aa3c087b1c717209389705bf2ace4c24884575014a561dff250c0be93fe1e411 +build: + number: 1 + requirements: build: - gcc # [not osx] - llvm # [osx] - - zlib + - zlib {{CONDA_ZLIB}}* run: - libgcc # [not osx] - - zlib + - zlib {{CONDA_ZLIB}}* test: commands: diff --git a/recipes/metaphlan2/2.7.5/build.sh b/recipes/metaphlan2/2.7.5/build.sh new file mode 100644 index 00000000000000..5a39ef5b574cc0 --- /dev/null +++ b/recipes/metaphlan2/2.7.5/build.sh @@ -0,0 +1,15 @@ +#!/bin/bash + +binaries="\ +metaphlan2.py \ +strainphlan.py \ +utils/extract_markers.py \ +utils/merge_metaphlan_tables.py \ +utils/metaphlan2krona.py \ +utils/metaphlan_hclust_heatmap.py +" + +mkdir -p $PREFIX/bin +for i in $binaries; do cp $i $PREFIX/bin; done +cp -r strainphlan_src $PREFIX/bin +cp "$RECIPE_DIR/download_metaphlan2_db.py" $PREFIX/bin diff --git a/recipes/metaphlan2/2.7.5/download_metaphlan2_db.py b/recipes/metaphlan2/2.7.5/download_metaphlan2_db.py new file mode 100644 index 00000000000000..edd72278995a66 --- /dev/null +++ b/recipes/metaphlan2/2.7.5/download_metaphlan2_db.py @@ -0,0 +1,94 @@ +#!/usr/bin/env python3 + +import argparse +import bz2 +import os +import requests +import shutil +import tarfile +import io + + +METAPHLAN2_URL = 'https://bitbucket.org/biobakery/metaphlan2/downloads/mpa_v20_m200.tar' + + +def download_file(url): + """Download a file from a URL + + :param url: URL of the file to download + + :return: Path to downloaded file + """ + print("Downloading %s" % url) + r = requests.get(url, stream=True) + r.raise_for_status() + + target = os.path.basename(url) + print("Saving to %s" % target) + with open(target, "wb") as fd: + for chunk in r.iter_content(chunk_size=128): + fd.write(chunk) + return target + + +def unpack_tar_archive(filepath): + """Extract files from an archive + + Given an archive (which optionally can be compressed with either gzip or + bz2), extract the files it contains and return a list of the resulting file + names and paths. + + Once all the files are extracted the archive file is deleted from the + file system. + + :param filepath: path to an archive + """ + print("Extract %s" % filepath) + with tarfile.open(filepath, "r") as t: + t.extractall(".") + print("Removing %s" % filepath) + os.remove(filepath) + + +def unpack_bz2_archive(in_filepath, out_filepath): + """Extract files from an archive + + Given an archive (which optionally can be compressed with either gzip or + bz2), extract the files it contains and return a list of the resulting file + names and paths. + + Once all the files are extracted the archive file is deleted from the + file system. + + :param in_filepath: path to a BZ2 archive + :param out_filepath: path to a output file + """ + print("Extract %s" % in_filepath) + with bz2.BZ2File(in_filepath, 'rb') as fin, open(out_filepath, "w") as fout: + with io.TextIOWrapper(fin, encoding='utf-8') as dec: + fout.write(dec.read()) + print("Removing %s" % in_filepath) + os.remove(in_filepath) + + +if __name__ == "__main__": + parser = argparse.ArgumentParser( + description='Download MetaPhlAn2 database') + parser.add_argument('--output', help="Installation directory") + args = parser.parse_args() + + if args.output: + output = args.output + else: + output = os.path.dirname(os.path.realpath(__file__)) + print(output) + + if not os.path.exists(output): + os.makedirs(output) + + metaphlan2_tarfile = download_file(METAPHLAN2_URL) + unpack_tar_archive(metaphlan2_tarfile) + unpack_bz2_archive("mpa_v20_m200.fna.bz2", "mpa_v20_m200.fna") + + shutil.move("mpa_v20_m200.pkl", output) + shutil.move("mpa_v20_m200.fna", output) diff --git a/recipes/metaphlan2/2.7.5/meta.yaml b/recipes/metaphlan2/2.7.5/meta.yaml new file mode 100644 index 00000000000000..116d6598b20175 --- /dev/null +++ b/recipes/metaphlan2/2.7.5/meta.yaml @@ -0,0 +1,52 @@ +{% set name = "metaphlan2" %} +{% set version = "2.7.5" %} +{% set md5 = "bd78cd88faf7c3a33036715fe36ba26c" %} + +source: + fn: {{ version }}.tar.gz + md5: {{ md5 }} + url: https://bitbucket.org/biobakery/metaphlan2/get/{{ version }}.tar.gz + +build: + number: 0 + skip: True #[not py27] + +package: + name: {{ name }} + version: {{ version }} + +requirements: + run: + - python + - biom-format + - numpy + - bowtie2 >=2.2.5 + - msgpack-python + - biopython + - pandas + - pysam + - matplotlib + - scipy + - requests + +test: + commands: + - metaphlan2.py -v + - metaphlan2krona.py -h + - strainphlan.py -h + - extract_markers.py -h + - merge_metaphlan_tables.py -h + - metaphlan2krona.py -h + - metaphlan_hclust_heatmap.py -h + - download_metaphlan2_db.py -h + +about: + home: https://bitbucket.org/biobakery/metaphlan2 + license: MIT + summary: > + MetaPhlAn is a computational tool for profiling the composition of microbial + communities (Bacteria, Archaea, Eukaryotes and Viruses) from metagenomic + shotgun sequencing data with species level resolution. From version 2.0 + MetaPhlAn is also able to identify specific strains (in the not-so-frequent + cases in which the sample contains a previously sequenced strains) and to + track strains across samples for all species. diff --git a/recipes/metavelvet-sl/meta.yaml b/recipes/metavelvet-sl/meta.yaml index bbea85cce30c0b..a638838a3858e4 100644 --- a/recipes/metavelvet-sl/meta.yaml +++ b/recipes/metavelvet-sl/meta.yaml @@ -15,19 +15,19 @@ source: - run-annoIS.pl.patch build: - number: 2 + number: 3 skip: True # [osx] requirements: build: - gcc - - zlib + - zlib {{CONDA_ZLIB}}* - perl - perl-app-cpanminus - perl-module-build run: - libgcc # [not osx] - - zlib + - zlib {{CONDA_ZLIB}}* - perl - perl-app-cpanminus - perl-module-build diff --git a/recipes/metavelvet/1.1.01/meta.yaml b/recipes/metavelvet/1.1.01/meta.yaml index 83ad3b36ec7f8e..c1be5cead293c8 100644 --- a/recipes/metavelvet/1.1.01/meta.yaml +++ b/recipes/metavelvet/1.1.01/meta.yaml @@ -4,7 +4,7 @@ about: summary: 'MetaVelvet : An extension of Velvet assembler to de novo metagenome assembly from short sequence reads' build: - number: 0 + number: 1 skip: True # [osx] package: @@ -15,10 +15,10 @@ requirements: build: - libgcc - gcc - - zlib + - zlib {{CONDA_ZLIB}}* run: - libgcc - - zlib + - zlib {{CONDA_ZLIB}}* - velvet - metavelvet-annois diff --git a/recipes/metavelvet/build.sh b/recipes/metavelvet/build.sh index 697f7aad5ae65e..5d364aaf26b8eb 100644 --- a/recipes/metavelvet/build.sh +++ b/recipes/metavelvet/build.sh @@ -28,7 +28,7 @@ cd perl-build rm lib/setup.sh perl ./Build.PL -./Build manifest -./Build install --installdirs site +perl ./Build manifest +perl ./Build install --installdirs site #mv * $PREFIX/bin/ diff --git a/recipes/metavelvet/meta.yaml b/recipes/metavelvet/meta.yaml index d4908ed9e39cb1..fd56cf64438c06 100644 --- a/recipes/metavelvet/meta.yaml +++ b/recipes/metavelvet/meta.yaml @@ -4,7 +4,7 @@ about: summary: 'MetaVelvet : An extension of Velvet assembler to de novo metagenome assembly from short sequence reads' build: - number: 1 + number: 2 skip: True # [osx] package: @@ -15,19 +15,20 @@ requirements: build: - libgcc - gcc - - zlib + - zlib {{CONDA_ZLIB}}* - perl-module-build - - perl-threaded + - perl run: - libgcc - - zlib - - perl-threaded + - zlib {{CONDA_ZLIB}}* + - perl - perl-module-build - velvet source: fn: metavelvet-1.2.02.tgz url: http://metavelvet.dna.bio.keio.ac.jp/src/MetaVelvet-1.2.02.tgz + sha256: 80999b1cb6b533719d258f4c3d8517cf2a72dcfadd19c088470432382a8e0ecf patches: - metavelvet.velvet.makefile.patch - run-annoIS.pl.patch diff --git a/recipes/metfrag/2.3.1/build.sh b/recipes/metfrag/2.3.1/build.sh new file mode 100755 index 00000000000000..6532b7dbd2be54 --- /dev/null +++ b/recipes/metfrag/2.3.1/build.sh @@ -0,0 +1,12 @@ +#!/bin/bash +set -eu -o pipefail + +outdir=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $outdir +mkdir -p $PREFIX/bin +cp MetFrag2.3.1-CL.jar $outdir/metfrag.jar +cp $RECIPE_DIR/metfrag.sh $outdir/metfrag +ls -l $outdir +ln -s $outdir/metfrag $PREFIX/bin +chmod 0755 "${PREFIX}/bin/metfrag" + diff --git a/recipes/metfrag/2.3.1/meta.yaml b/recipes/metfrag/2.3.1/meta.yaml new file mode 100644 index 00000000000000..477046721cebbd --- /dev/null +++ b/recipes/metfrag/2.3.1/meta.yaml @@ -0,0 +1,25 @@ +about: + home: http://c-ruttkies.github.io/MetFrag/ + license: GNU Lesser General Public License version 2.1 or later. + summary: MetFrag is a freely available software for the annotation of high precision tandem mass spectra of metabolites which is a first and critical step for the identification of a molecular structure. Candidate molecules of different databases are fragmented in silico and matched against mass to charge values. A score calculated using the fragment peak matches gives hints to the quality of the candidate spectrum assignment. + +package: + name: metfrag + version: '2.3.1' + +source: + fn: MetFrag2.3.1-CL.jar + url: http://msbi.ipb-halle.de/~cruttkie/metfrag/MetFrag2.3.1-CL.jar + sha256: 4261ea5abd023016bd99ef5fdd197eb74306586a4a1d637c87d45e36809d21f4 + +build: + number: 0 + +requirements: + run: + - openjdk >=7 + +test: + commands: + - metfrag --help + diff --git a/recipes/metfrag/2.3.1/metfrag.sh b/recipes/metfrag/2.3.1/metfrag.sh new file mode 100755 index 00000000000000..611d7f0f9f2508 --- /dev/null +++ b/recipes/metfrag/2.3.1/metfrag.sh @@ -0,0 +1,56 @@ +#!/bin/bash +# Wraps metfrag.jar +set -o pipefail + +# Find original directory of bash script, resovling symlinks +# http://stackoverflow.com/questions/59895/can-a-bash-script-tell-what-directory-its-stored-in/246128#246128 +SOURCE="${BASH_SOURCE[0]}" +while [ -h "$SOURCE" ]; do # resolve $SOURCE until the file is no longer a symlink + DIR="$( cd -P "$( dirname "$SOURCE" )" && pwd )" + SOURCE="$(readlink "$SOURCE")" + [[ $SOURCE != /* ]] && SOURCE="$DIR/$SOURCE" # if $SOURCE was a relative symlink, we need to resolve it relative to the path where the symlink file was located +done +DIR="$( cd -P "$( dirname "$SOURCE" )" && pwd )" + +JAR_DIR=$DIR +java=java +if [ -e "$JAVA_HOME/bin/java" ] +then +java="$JAVA_HOME/bin/java" +fi + +# extract memory and system property Java arguments from the list of provided arguments +# http://java.dzone.com/articles/better-java-shell-script +default_jvm_mem_opts="" +jvm_mem_opts="" +jvm_prop_opts="" +pass_args="" +for arg in "$@"; do + case $arg in + '-D'*) + jvm_prop_opts="$jvm_prop_opts $arg" + ;; + '-XX'*) + jvm_prop_opts="$jvm_prop_opts $arg" + ;; + '-Xm'*) + jvm_mem_opts="$jvm_mem_opts $arg" + ;; + *) + pass_args="$pass_args $arg" + ;; + esac +done + +if [ "$jvm_mem_opts" == "" ] && [ -z ${_JAVA_OPTIONS+x} ]; then + jvm_mem_opts="$default_jvm_mem_opts" +fi + +pass_arr=($pass_args) +if [[ ${pass_arr[0]} == org* ]] +then + eval "$java" $jvm_mem_opts $jvm_prop_opts -cp "$JAR_DIR/metfrag.jar" $pass_args +else + eval "$java" $jvm_mem_opts $jvm_prop_opts -jar "$JAR_DIR/metfrag.jar" $pass_args +fi +exit diff --git a/recipes/metfrag/build.sh b/recipes/metfrag/build.sh index 6532b7dbd2be54..300709f9d1d028 100755 --- a/recipes/metfrag/build.sh +++ b/recipes/metfrag/build.sh @@ -4,7 +4,7 @@ set -eu -o pipefail outdir=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM mkdir -p $outdir mkdir -p $PREFIX/bin -cp MetFrag2.3.1-CL.jar $outdir/metfrag.jar +cp MetFrag2.4.2-CL.jar $outdir/metfrag.jar cp $RECIPE_DIR/metfrag.sh $outdir/metfrag ls -l $outdir ln -s $outdir/metfrag $PREFIX/bin diff --git a/recipes/metfrag/meta.yaml b/recipes/metfrag/meta.yaml index 477046721cebbd..920d05596d94db 100644 --- a/recipes/metfrag/meta.yaml +++ b/recipes/metfrag/meta.yaml @@ -5,12 +5,12 @@ about: package: name: metfrag - version: '2.3.1' + version: '2.4.2' source: - fn: MetFrag2.3.1-CL.jar - url: http://msbi.ipb-halle.de/~cruttkie/metfrag/MetFrag2.3.1-CL.jar - sha256: 4261ea5abd023016bd99ef5fdd197eb74306586a4a1d637c87d45e36809d21f4 + fn: MetFrag2.4.2-CL.jar + url: http://msbi.ipb-halle.de/~cruttkie/metfrag/MetFrag2.4.2-CL.jar + sha256: fa020f4093157647bb6b13d05c8962c82358b1f076b91e22ae116359322d7b47 build: number: 0 diff --git a/recipes/methyldackel/meta.yaml b/recipes/methyldackel/meta.yaml index 1d264d60e853ca..8181e617360e63 100644 --- a/recipes/methyldackel/meta.yaml +++ b/recipes/methyldackel/meta.yaml @@ -3,7 +3,7 @@ package: version: "0.3.0" build: - number: 0 + number: 1 skip: False source: @@ -13,11 +13,11 @@ source: requirements: build: - - zlib + - zlib {{CONDA_ZLIB}}* - gcc # [not osx] - llvm # [osx] run: - - zlib + - zlib {{CONDA_ZLIB}}* - libgcc # [not osx] test: diff --git a/recipes/micro_razers/meta.yaml b/recipes/micro_razers/meta.yaml index 40fe90c70f5381..0950052ad9c008 100644 --- a/recipes/micro_razers/meta.yaml +++ b/recipes/micro_razers/meta.yaml @@ -8,7 +8,7 @@ source: sha256: df083d5939d7e73fd00bbc6bb291ac7ea7b8d446cf89a9758fdffdc0eca9ec1c build: - number: 0 + number: 1 skip: True # [osx] requirements: diff --git a/recipes/minialign/meta.yaml b/recipes/minialign/meta.yaml index a0f7493ec2a60b..45235e4fee7637 100644 --- a/recipes/minialign/meta.yaml +++ b/recipes/minialign/meta.yaml @@ -6,7 +6,7 @@ package: version: {{ version }} build: - number: 0 + number: 1 source: fn: {{ name|lower }}_{{ version }}.tar.gz @@ -15,13 +15,13 @@ source: requirements: build: - - gcc # [not osx] - - llvm # [osx] - - zlib + - gcc # [not osx] + - llvm # [osx] + - zlib {{CONDA_ZLIB}}* run: - - libgcc # [not osx] - - zlib + - libgcc # [not osx] + - zlib {{CONDA_ZLIB}}* test: commands: diff --git a/recipes/miniasm/meta.yaml b/recipes/miniasm/meta.yaml index ac751d3a9e220c..4165c1ef1fcf80 100644 --- a/recipes/miniasm/meta.yaml +++ b/recipes/miniasm/meta.yaml @@ -6,7 +6,7 @@ package: version: {{ version }} build: - number: 0 + number: 1 source: fn: {{ name|lower }}_{{ version }}.tar.gz @@ -16,11 +16,11 @@ source: requirements: build: - gcc - - zlib + - zlib {{CONDA_ZLIB}}* run: - libgcc - - zlib + - zlib {{CONDA_ZLIB}}* test: commands: diff --git a/recipes/minimap2/meta.yaml b/recipes/minimap2/meta.yaml index 7dffbff06c7930..b03dc32d53488e 100644 --- a/recipes/minimap2/meta.yaml +++ b/recipes/minimap2/meta.yaml @@ -1,6 +1,6 @@ {% set name = "minimap2" %} -{% set version = "2.8" %} -{% set hash = "844d99ad57095a2befda8fb4730275d273b3349ee7098a0d4f5165eb06b21659" %} +{% set version = "2.9" %} +{% set hash = "9366e2e92c6e7ecce09ff95a9eb68392807c6947f3f467f236d27ca29ff4ae03" %} package: name: {{ name|lower }} @@ -12,7 +12,7 @@ source: sha256: {{ hash }} build: - number: 0 + number: 1 requirements: build: diff --git a/recipes/minvar/1.2a3/meta.yaml b/recipes/minvar/1.2a3/meta.yaml index 8802995e177c38..81a0d0954bb25a 100644 --- a/recipes/minvar/1.2a3/meta.yaml +++ b/recipes/minvar/1.2a3/meta.yaml @@ -1,5 +1,5 @@ {% set version = "1.2a3" %} -{% set build = 0 %} +{% set build = 1 %} package: name: minvar diff --git a/recipes/minvar/1.2b/meta.yaml b/recipes/minvar/1.2b/meta.yaml index 64e13d16049e54..be99acfe4400ad 100644 --- a/recipes/minvar/1.2b/meta.yaml +++ b/recipes/minvar/1.2b/meta.yaml @@ -1,5 +1,5 @@ {% set version = "1.2b" %} -{% set build = 0 %} +{% set build = 1 %} package: name: minvar diff --git a/recipes/minvar/2.0/meta.yaml b/recipes/minvar/2.0/meta.yaml index bcfb53dbf74ca3..51255308e39bf5 100644 --- a/recipes/minvar/2.0/meta.yaml +++ b/recipes/minvar/2.0/meta.yaml @@ -1,5 +1,5 @@ {% set version = "2.0" %} -{% set build = 0 %} +{% set build = 1 %} package: name: minvar diff --git a/recipes/minvar/2.1.1/meta.yaml b/recipes/minvar/2.1.1/meta.yaml index 7c2203f5415126..84eccef1190331 100644 --- a/recipes/minvar/2.1.1/meta.yaml +++ b/recipes/minvar/2.1.1/meta.yaml @@ -1,5 +1,5 @@ {% set version = "2.1.1" %} -{% set build = 1 %} +{% set build = 2 %} package: name: minvar diff --git a/recipes/minvar/2.1.2/meta.yaml b/recipes/minvar/2.1.2/meta.yaml index 6e114098a0a23d..f6b6655d88233c 100644 --- a/recipes/minvar/2.1.2/meta.yaml +++ b/recipes/minvar/2.1.2/meta.yaml @@ -1,5 +1,5 @@ {% set version = "2.1.2" %} -{% set build = 0 %} +{% set build = 1 %} package: name: minvar diff --git a/recipes/minvar/2.1/meta.yaml b/recipes/minvar/2.1/meta.yaml index a93f3a0d0e84cd..40b753c1a47952 100644 --- a/recipes/minvar/2.1/meta.yaml +++ b/recipes/minvar/2.1/meta.yaml @@ -1,5 +1,5 @@ {% set version = "2.1" %} -{% set build = 0 %} +{% set build = 1 %} package: name: minvar diff --git a/recipes/molpopgen-analysis/build.sh b/recipes/molpopgen-analysis/build.sh new file mode 100644 index 00000000000000..ee10d30299e0c0 --- /dev/null +++ b/recipes/molpopgen-analysis/build.sh @@ -0,0 +1,6 @@ +#!/bin/bash + +CXXFLAGS="-O3 -DNDEBUG" CPPFLAGS="-I$PREFIX/include $CPPFLAGS" LDFLAGS="-L$PREFIX/lib -Wl,-rpath,$PREFIX/lib $LDFLAGS" ./configure --prefix=$PREFIX +make +make install + diff --git a/recipes/molpopgen-analysis/meta.yaml b/recipes/molpopgen-analysis/meta.yaml new file mode 100644 index 00000000000000..e12382828a8fb3 --- /dev/null +++ b/recipes/molpopgen-analysis/meta.yaml @@ -0,0 +1,41 @@ +{% set version="0.8.8" %} +{% set hash="f9ef9e0a90fce2c0f4fe462d6c05e22fef22df1c23b63a7c64ad7b538f6e8bb0" %} + +package: + name: molpopgen-analysis + version: {{ version }} + +source: + fn: analysis-{{ version }}.tar.gz + url: https://github.com/molpopgen/analysis/archive/{{ version }}.tar.gz + sha256: {{ hash }} + +build: + number: 0 + +requirements: + build: + - gcc + - gsl {{ CONDA_GSL }}* + - libsequence 1.8.4 + run: + - libgcc + - gsl {{ CONDA_GSL }}* + - libsequence 1.8.4 + +test: + commands: + - command -v compute + - command -v gestimator + - command -v kimura80 + - command -v polydNdS + - command -v sharedPoly + - command -v descPoly + - command -v HBKpermute + - command -v MKtest + - command -v rsq + +about: + home: https://github.com/molpopgen/analysis + license: GNU General Public License v2 (GPLv2) + summary: Programs for the (pre-NGS-era) analysis of population-genetic data diff --git a/recipes/mosaik/meta.yaml b/recipes/mosaik/meta.yaml index 310866f06cc6e6..a0111165a09364 100644 --- a/recipes/mosaik/meta.yaml +++ b/recipes/mosaik/meta.yaml @@ -17,10 +17,10 @@ source: requirements: build: - - zlib + - zlib {{CONDA_ZLIB}}* - gcc run: - - zlib + - zlib {{CONDA_ZLIB}}* - libgcc test: @@ -28,5 +28,5 @@ test: - MosaikAligner --help | grep Usage > /dev/null build: - number: 2 + number: 3 skip: False diff --git a/recipes/mosdepth/meta.yaml b/recipes/mosdepth/meta.yaml index 189c3f18831987..8dddbae9fbe059 100644 --- a/recipes/mosdepth/meta.yaml +++ b/recipes/mosdepth/meta.yaml @@ -17,7 +17,7 @@ source: - install.diff build: - number: 0 + number: 1 skip: True # [osx] string: "htslib{{CONDA_HTSLIB}}_{{PKG_BUILDNUM}}" diff --git a/recipes/mothur/1.25.0/meta.yaml b/recipes/mothur/1.25.0/meta.yaml index 50ec7a4d5f8149..4b62261c9bee9f 100644 --- a/recipes/mothur/1.25.0/meta.yaml +++ b/recipes/mothur/1.25.0/meta.yaml @@ -16,12 +16,10 @@ build: requirements: build: - # - zlib - ncurses {{CONDA_NCURSES}}* - readline run: - # - zlib - ncurses {{CONDA_NCURSES}}* - readline diff --git a/recipes/mothur/1.36.1/meta.yaml b/recipes/mothur/1.36.1/meta.yaml index 2bba8856e5dac5..9c6d872434d049 100644 --- a/recipes/mothur/1.36.1/meta.yaml +++ b/recipes/mothur/1.36.1/meta.yaml @@ -11,7 +11,7 @@ source: - Build-Flags.patch build: - number: 3 + number: 4 string: boost1.60_{{PKG_BUILDNUM}} skip: True # [not linux64 or osx] @@ -19,14 +19,14 @@ requirements: build: - gcc # [linux] - llvm # [osx] - - zlib + - zlib {{CONDA_ZLIB}}* - ncurses - readline - boost >=1.55,1.60* # does not work with boost >1.60 - blast-legacy run: - libgcc # [linux] - - zlib + - zlib {{CONDA_ZLIB}}* - ncurses - readline - boost 1.60* diff --git a/recipes/mothur/meta.yaml b/recipes/mothur/meta.yaml index d27fd94db7f064..033e52a6b1386a 100644 --- a/recipes/mothur/meta.yaml +++ b/recipes/mothur/meta.yaml @@ -10,7 +10,7 @@ source: - Build-Flags.patch build: - number: 0 + number: 1 string: boost{{CONDA_BOOST}}_{{PKG_BUILDNUM}} skip: True # [not linux64 or osx] @@ -18,14 +18,14 @@ requirements: build: - gcc # [linux] - llvm # [osx] - - zlib + - zlib {{CONDA_ZLIB}}* - ncurses - readline - boost >=1.55,{{CONDA_BOOST}}* - blast-legacy run: - libgcc # [linux] - - zlib + - zlib {{CONDA_ZLIB}}* - ncurses - readline - boost {{CONDA_BOOST}}* @@ -39,4 +39,4 @@ about: home: http://www.mothur.org license: GPL license_file: LICENSE.md - summary: This project seeks to develop a single piece of open-source, expandable software to fill the bioinformatics needs of the microbial ecology community. \ No newline at end of file + summary: This project seeks to develop a single piece of open-source, expandable software to fill the bioinformatics needs of the microbial ecology community. diff --git a/recipes/msaboot/build.sh b/recipes/msaboot/build.sh new file mode 100644 index 00000000000000..5227f51eca79f9 --- /dev/null +++ b/recipes/msaboot/build.sh @@ -0,0 +1,3 @@ +#!/bin/bash + +$PYTHON setup.py install --single-version-externally-managed --record record.txt diff --git a/recipes/msaboot/meta.yaml b/recipes/msaboot/meta.yaml new file mode 100644 index 00000000000000..af0642770ff226 --- /dev/null +++ b/recipes/msaboot/meta.yaml @@ -0,0 +1,32 @@ +package: + name: msaboot + version: "0.1.1" + +source: + fn: msaboot-0.1.1.tar.gz + url: https://github.com/phac-nml/msaboot/archive/v0.1.1.tar.gz + sha256: 15c3aeeab425433026b5bfb8223e03c108c24d036abb79280ef83cdde262ee8c + +build: + number: 1 + entry_points: + - msaboot = msaboot.msaboot:main + +requirements: + build: + - python + - setuptools + run: + - python + - numpy + - biopython + +test: + commands: + - msaboot -h | grep "bootstraps FASTA input data" + +about: + home: https://github.com/phac-nml/msaboot + license: Apache 2.0 + license_file: LICENSE.txt + summary: "Generate bootstrapping replicates for multiple sequence alignment data." diff --git a/recipes/msprime/meta.yaml b/recipes/msprime/meta.yaml deleted file mode 100644 index a879d1ad9fce04..00000000000000 --- a/recipes/msprime/meta.yaml +++ /dev/null @@ -1,69 +0,0 @@ -package: - name: msprime - version: "0.4.0" - -source: - fn: msprime-0.4.0.tar.gz - url: https://pypi.python.org/packages/db/65/7010c12c8594b6a36b7b6bb7f108cce17003b45d676aafb3f275c7cd598a/msprime-0.4.0.tar.gz - md5: 83f78872174741d2de4db6689ae3d74f -# patches: - # List any patch files here - # - fix.patch - -build: - # noarch_python: True - # preserve_egg_dir: True - entry_points: - - mspms=msprime.cli:mspms_main - - msp=msprime.cli:msp_main - - # If this is a new build for the same version, increment the build - # number. If you do not include this key, it defaults to 0. - number: 2 - string: "py{{CONDA_PY}}_gsl{{CONDA_GSL}}_{{PKG_BUILDNUM}}" - -requirements: - build: - - gcc - - python - - setuptools - - setuptools_scm - - svgwrite - - hdf5 - - gsl {{CONDA_GSL}}* - - run: - - python - - svgwrite - - hdf5 - - numpy - - h5py - - gsl {{CONDA_GSL}}* - -test: - # Python imports - imports: - - msprime - - commands: - # You can put test commands to be run here. Use this to test that the - # entry points work. - - - msp --help > /dev/null - - mspms 2 1 -T > /dev/null - - # You can also put a file called run_test.py in the recipe that will be run - # at test time. - - # requires: - # Put any additional test requirements here. For example - # - nose - -about: - home: http://pypi.python.org/pypi/msprime - license: GNU Lesser General Public License v3 or later (LGPLv3+) - summary: 'A fast and accurate coalescent simulator.' - -# See -# http://docs.continuum.io/conda/build.html for -# more information about meta.yaml diff --git a/recipes/multiqc-bcbio/meta.yaml b/recipes/multiqc-bcbio/meta.yaml index 2826f06ad6df68..ffc3a3728e906f 100644 --- a/recipes/multiqc-bcbio/meta.yaml +++ b/recipes/multiqc-bcbio/meta.yaml @@ -1,16 +1,16 @@ -{% set tag="d6891b9" %} +{% set tag="a263e6b" %} package: name: multiqc-bcbio - version: "0.2.4" + version: "0.2.5" source: fn: multiqc-bcbio-{{ tag }}.tar.gz url: https://github.com/MultiQC/MultiQC_bcbio/archive/{{ tag }}.tar.gz - md5: fcbeb37db87b13fb480d035ece40aaa5 + md5: 67106c4d099ac39aede0af4b0a384fd8 build: - number: 1 + number: 0 preserve_egg_dir: True # multiqc does not support py3k because of click skip: true # [py3k] diff --git a/recipes/multiqc/meta.yaml b/recipes/multiqc/meta.yaml index 81bd083152230b..1002698f073c39 100644 --- a/recipes/multiqc/meta.yaml +++ b/recipes/multiqc/meta.yaml @@ -1,11 +1,11 @@ package: name: multiqc - version: "1.4" + version: "1.5a" source: - fn: v1.4.tar.gz - url: https://github.com/ewels/MultiQC/archive/v1.4.tar.gz - sha256: c4d0c43f1484c94371c0c70f444d6d181a55d0195b378247a56e672030bb4239 + fn: multiqc-ec54507.tar.gz + url: https://github.com/ewels/MultiQC/archive/ec54507.tar.gz + sha256: a44de98dca99b3ff6f6904f51baa1917a9646e9d3058962bc1afe6e17cf495bb build: number: 0 diff --git a/recipes/mummer4/meta.yaml b/recipes/mummer4/meta.yaml index 2d32fb5e9d86f7..eaf8c86da9899f 100644 --- a/recipes/mummer4/meta.yaml +++ b/recipes/mummer4/meta.yaml @@ -6,8 +6,7 @@ about: license: "The Artistic License 2.0" summary: "MUMmer is a system for rapidly aligning entire genomes" build: - number: 0 - skip: True #[osx] + number: 1 package: name: {{ name|lower }} version: {{ version }} diff --git a/recipes/muse/meta.yaml b/recipes/muse/meta.yaml index 7299f99c090b67..2c4d3e88a58e49 100644 --- a/recipes/muse/meta.yaml +++ b/recipes/muse/meta.yaml @@ -7,7 +7,7 @@ source: url: https://github.com/danielfan/MuSE/archive/v1.0-rc.tar.gz build: - number: 0 + number: 1 requirements: build: diff --git a/recipes/nanopolish/0.4.0/meta.yaml b/recipes/nanopolish/0.4.0/meta.yaml index 2a2f64908835ed..8943d1ea402e81 100644 --- a/recipes/nanopolish/0.4.0/meta.yaml +++ b/recipes/nanopolish/0.4.0/meta.yaml @@ -3,7 +3,7 @@ package: version: "0.4.0" build: - number: 0 + number: 1 skip: True # [osx] source: @@ -18,14 +18,14 @@ requirements: build: - gcc - fast5 - - htslib - - hdf5 + - htslib {{ CONDA_HTSLIB }}* + - hdf5 {{ CONDA_HDF5 }}* run: - libgcc - fast5 - - htslib - - hdf5 + - htslib {{ CONDA_HTSLIB }}* + - hdf5 {{ CONDA_HDF5 }}* - biopython test: @@ -37,4 +37,3 @@ about: license: MIT license_file: LICENSE summary: Signal-level algorithms for MinION data - diff --git a/recipes/nanopolish/meta.yaml b/recipes/nanopolish/meta.yaml index 4da2b281a562fb..0dada866c7639a 100644 --- a/recipes/nanopolish/meta.yaml +++ b/recipes/nanopolish/meta.yaml @@ -6,7 +6,7 @@ package: version: {{ version }} build: - number: 3 + number: 4 string: "ncurses{{CONDA_NCURSES}}_{{PKG_BUILDNUM}}" source: diff --git a/recipes/netcdf-metadata-info/build.sh b/recipes/netcdf-metadata-info/build.sh new file mode 100644 index 00000000000000..88c97aefcdadc3 --- /dev/null +++ b/recipes/netcdf-metadata-info/build.sh @@ -0,0 +1,5 @@ +#!/bin/bash +export LD_LIBRARY_PATH="$PREFIX/lib:$LD_LIBRARY_PATH" +make +mkdir -p "$PREFIX/bin" +cp netcdf-metadata-info "$PREFIX/bin" diff --git a/recipes/netcdf-metadata-info/meta.yaml b/recipes/netcdf-metadata-info/meta.yaml new file mode 100644 index 00000000000000..6dfc805cdcf7d6 --- /dev/null +++ b/recipes/netcdf-metadata-info/meta.yaml @@ -0,0 +1,32 @@ +{% set name = "Netcdf-Metadata-Info" %} +{% set version = "1.1.6" %} +{% set md5 = "5f4f947f90f7db319ba2d4b16c34708b" %} + +package: + name: {{name|lower}} + version: {{version}} + +source: + fn: {{ name }}-{{ version }}.tar.gz + url: https://github.com/Alanamosse/{{name}}/archive/v{{version}}.tar.gz + md5: {{md5}} + +build: + number: 0 + +requirements: + build: + - libnetcdf 4.4.* + - gcc + run: + - libgcc + - libnetcdf 4.4.* + +test: + commands: + - netcdf-metadata-info -h + +about: + home: https://github.com/Alanamosse/Netcdf-Metadata-Info/ + license: GNU GENERAL PUBLIC LICENSE Version 3, 29 June 2007 + summary: Metadata information from netcdf file for Galaxy use. diff --git a/recipes/netreg/meta.yaml b/recipes/netreg/meta.yaml index f971244b5dc5a6..f029e899c10705 100644 --- a/recipes/netreg/meta.yaml +++ b/recipes/netreg/meta.yaml @@ -10,7 +10,7 @@ about: doc_url: https://dirmeier.github.io/netReg/ build: - number: 0 + number: 1 package: name: {{ name }} diff --git a/recipes/nextflow/meta.yaml b/recipes/nextflow/meta.yaml index afbd7880c1f844..02a13b98d7a4c5 100644 --- a/recipes/nextflow/meta.yaml +++ b/recipes/nextflow/meta.yaml @@ -1,14 +1,14 @@ package: name: nextflow - version: "0.27.4" + version: "0.27.6" build: number: 0 source: fn: nextflow - url: https://www.nextflow.io/releases/v0.27.4/nextflow - md5: adec1a7d94a0136a508900e2b43250ea + url: https://www.nextflow.io/releases/v0.27.6/nextflow + md5: 1e87fe3620bf02003a0505f95b19e2e6 requirements: build: diff --git a/recipes/ngless/build.sh b/recipes/ngless/build.sh index 78362b82ab33ad..fae10436b768a8 100644 --- a/recipes/ngless/build.sh +++ b/recipes/ngless/build.sh @@ -6,6 +6,12 @@ export CPPFLAGS="-I${PREFIX}/include" export CFLAGS="-I$PREFIX/include" export CPATH=${PREFIX}/include +# internal download failes with: +# ERROR: cannot verify github.com's certificate, issued by ‘CN=DigiCert SHA2 Extended Validation Server CA,OU=www.digicert.com,O=DigiCert Inc,C=US’: +# Unable to locally verify the issuer's authority. +# +alias wget='wget --no-check-certificate' + stack setup stack update make install prefix=$PREFIX diff --git a/recipes/ngless/meta.yaml b/recipes/ngless/meta.yaml index 1c93f2065b1d1a..2c4bee2ae38ecd 100644 --- a/recipes/ngless/meta.yaml +++ b/recipes/ngless/meta.yaml @@ -12,7 +12,7 @@ source: md5: {{ md5 }} build: - number: 0 + number: 1 skip: True # [osx] requirements: @@ -23,7 +23,7 @@ requirements: - zlib {{CONDA_ZLIB}}* - perl - wget - - xz 5.2.* + - xz {{CONDA_XZ}}* - gcc # necessary for megahit run: - python @@ -31,7 +31,7 @@ requirements: - gmp {{CONDA_GMP}}* - zlib {{CONDA_ZLIB}}* - libgcc # for gomp (megahit) - - xz 5.2.* + - xz {{CONDA_XZ}}* test: diff --git a/recipes/ngmlr/0.2.2/build.sh b/recipes/ngmlr/0.2.2/build.sh deleted file mode 100644 index 7b1b11caa974ce..00000000000000 --- a/recipes/ngmlr/0.2.2/build.sh +++ /dev/null @@ -1,10 +0,0 @@ -#!/bin/bash - -mkdir -p build -cd build -cmake -DCMAKE_BUILD_TYPE=RELEASE -DCMAKE_INSTALL_PREFIX=${PREFIX} -DSTATIC=OFF -DCMAKE_EXE_LINKER_FLAGS=-L${PREFIX}/lib .. -make VERBOSE=1 - -mkdir -p $PREFIX/bin -cp ../bin/ngmlr-${PKG_VERSION}/ngmlr $PREFIX/bin/ - diff --git a/recipes/ngmlr/0.2.2/meta.yaml b/recipes/ngmlr/0.2.2/meta.yaml deleted file mode 100644 index 328807031dd3c7..00000000000000 --- a/recipes/ngmlr/0.2.2/meta.yaml +++ /dev/null @@ -1,30 +0,0 @@ -package: - name: ngmlr - version: '0.2.2' - -source: - fn: ngmlr-v0.2.2.tar.gz - url: "https://github.com/philres/ngmlr/archive/v0.2.2.tar.gz" - md5: "449f0d972c907c64c6ddee08c2308826" - -build: - number: 0 - -requirements: - build: - - gcc >=4.8.2 # [linux] - - llvm # [osx] - - cmake - - zlib - run: - - zlib - - libgcc # [linux] - -test: - commands: - - ngmlr --help - -about: - home: https://github.com/philres/ngmlr - license: GPL-3.0 - summary: ngmlr is a long-read mapper desigend to align PacBilo or Oxford Nanopore to a reference genome optimized for structural variation detection diff --git a/recipes/ngmlr/0.2.3/meta.yaml b/recipes/ngmlr/0.2.3/meta.yaml index 9643d7c5f8bbe7..8b0a39077b86cc 100644 --- a/recipes/ngmlr/0.2.3/meta.yaml +++ b/recipes/ngmlr/0.2.3/meta.yaml @@ -4,7 +4,7 @@ about: license: MIT summary: "ngmlr is a long-read mapper desigend to align PacBilo or Oxford Nanopore to a reference genome optimized for structural variation detection" build: - number: 0 + number: 1 package: name: ngmlr version: "0.2.3" @@ -13,9 +13,9 @@ requirements: - gcc >=4.8.2 # [linux] - llvm # [osx] - cmake - - zlib + - zlib {{CONDA_ZLIB}}* run: - - zlib + - zlib {{CONDA_ZLIB}}* - libgcc # [linux] source: fn: ngmlr-v0.2.3.tar.gz diff --git a/recipes/ngmlr/0.2.4/meta.yaml b/recipes/ngmlr/0.2.4/meta.yaml index acc8c227f74e66..c4b46366449d12 100644 --- a/recipes/ngmlr/0.2.4/meta.yaml +++ b/recipes/ngmlr/0.2.4/meta.yaml @@ -4,7 +4,7 @@ about: license: MIT summary: "ngmlr is a long-read mapper designed to align PacBio or Oxford Nanopore reads to a reference genome and optimized for structural variation detection" build: - number: 0 + number: 1 package: name: ngmlr version: "0.2.4" @@ -13,9 +13,9 @@ requirements: - gcc >=4.8.2 # [linux] - llvm # [osx] - cmake - - zlib + - zlib {{CONDA_ZLIB}}* run: - - zlib + - zlib {{CONDA_ZLIB}}* - libgcc # [linux] source: fn: ngmlr-v0.2.4.tar.gz diff --git a/recipes/ngmlr/meta.yaml b/recipes/ngmlr/meta.yaml index 2315c9a58ce9b6..8c97108c4a5b3b 100644 --- a/recipes/ngmlr/meta.yaml +++ b/recipes/ngmlr/meta.yaml @@ -1,6 +1,6 @@ {% set version = "0.2.6" %} -package: +package: name: ngmlr version: {{ version }} @@ -10,20 +10,20 @@ source: url: "https://github.com/philres/ngmlr/archive/v{{ version }}.tar.gz" build: - number: 0 + number: 1 -requirements: - build: +requirements: + build: - gcc >=4.8.2 # [linux] - llvm # [osx] - cmake - - zlib - run: - - zlib + - zlib {{CONDA_ZLIB}}* + run: + - zlib {{CONDA_ZLIB}}* - libgcc # [linux] -test: - commands: +test: + commands: - "ngmlr --help" about: diff --git a/recipes/ngs-disambiguate/meta.yaml b/recipes/ngs-disambiguate/meta.yaml index 846d798dab5f87..864ab8ef02c796 100644 --- a/recipes/ngs-disambiguate/meta.yaml +++ b/recipes/ngs-disambiguate/meta.yaml @@ -1,23 +1,27 @@ +{% set version = "1.0.0" %} + package: name: ngs-disambiguate - version: "2016.11.10" + version: {{ version }} source: - git_url: https://github.com/AstraZeneca-NGS/disambiguate - git_tag: 559452477737ea10d20c582aa9a3af880b197bd9 + fn: ngs-disambiguate-{{ version }}.tar.gz + url: https://github.com/AstraZeneca-NGS/disambiguate/archive/v{{ version }}.tar.gz + sha256: fae1385c57f249226eebd942e54aabbf92b8f8d575d228a874f64cdfdc45e21b build: number: 0 skip: true # [osx] + string: bamtools{{CONDA_BAMTOOLS}}_{{PKG_BUILDNUM}} requirements: build: - gcc - - bamtools + - bamtools {{ CONDA_BAMTOOLS }}* run: - libgcc - - bamtools + - bamtools {{ CONDA_BAMTOOLS }}* test: commands: diff --git a/recipes/novobreak/meta.yaml b/recipes/novobreak/meta.yaml index 7acf565df37f85..6e8596d4680f31 100644 --- a/recipes/novobreak/meta.yaml +++ b/recipes/novobreak/meta.yaml @@ -5,7 +5,7 @@ package: version: {{ version }} build: - number: 0 + number: 1 source: fn: novobreak-{{ version }}.zip diff --git a/recipes/nspdk/meta.yaml b/recipes/nspdk/meta.yaml index 3636eff37e84e3..c0c597ecd3e1c5 100644 --- a/recipes/nspdk/meta.yaml +++ b/recipes/nspdk/meta.yaml @@ -8,17 +8,17 @@ source: sha256: 90955549e7d3e268d194cb89a38018a323f050c1c524d35630733f4cd97664a6 build: - number: 0 + number: 1 skip: True # [not linux64 or osx] requirements: build: - gcc # [not osx] - - zlib + - zlib {{CONDA_ZLIB}}* run: - libgcc # [not osx] - - zlib + - zlib {{CONDA_ZLIB}}* test: commands: diff --git a/recipes/ntcard/meta.yaml b/recipes/ntcard/meta.yaml index c00244c7597d2d..60de79b0c0548f 100644 --- a/recipes/ntcard/meta.yaml +++ b/recipes/ntcard/meta.yaml @@ -6,7 +6,7 @@ package: version: {{ version }} build: - number: 0 + number: 1 source: fn: {{ name|lower }}_{{ version }}.tar.gz @@ -15,15 +15,15 @@ source: requirements: build: - - gcc - - automake - - autoconf - - perl - - zlib + - gcc + - automake + - autoconf + - perl + - zlib {{CONDA_ZLIB}}* run: - - libgcc - - zlib + - libgcc + - zlib {{CONDA_ZLIB}}* test: commands: diff --git a/recipes/nucleoatac/meta.yaml b/recipes/nucleoatac/meta.yaml index 047366bbc470cd..f368675516bcc1 100644 --- a/recipes/nucleoatac/meta.yaml +++ b/recipes/nucleoatac/meta.yaml @@ -17,7 +17,7 @@ source: md5: 668525f351241d71ce5263dba0464317 build: - number: 0 + number: 1 skip: True # [not py27] requirements: @@ -28,7 +28,7 @@ requirements: - scipy - matplotlib - pysam >=0.8.1 - - zlib + - zlib {{CONDA_ZLIB}}* run: - python - cython >=0.22 @@ -36,11 +36,11 @@ requirements: - scipy - matplotlib - pysam >=0.8.1 - - zlib + - zlib {{CONDA_ZLIB}}* test: commands: - nucleoatac run --help - pyatac --help import: - - pyatac.fragmentsizes \ No newline at end of file + - pyatac.fragmentsizes diff --git a/recipes/ococo/meta.yaml b/recipes/ococo/meta.yaml index edf369769115de..50bec78559a807 100644 --- a/recipes/ococo/meta.yaml +++ b/recipes/ococo/meta.yaml @@ -6,7 +6,7 @@ package: version: {{ version }} build: - number: 0 + number: 1 source: fn: ococo-{{ version }}.tar.gz diff --git a/recipes/octopus/build.sh b/recipes/octopus/build.sh old mode 100644 new mode 100755 index 8bbcd3da17cb9f..8ba816a6f8c44b --- a/recipes/octopus/build.sh +++ b/recipes/octopus/build.sh @@ -22,5 +22,5 @@ EOF install cd .. # octopus -cmake -DINSTALL_PREFIX=ON -DCMAKE_INSTALL_PREFIX=$PREFIX -DINSTALL_ROOT=ON .. +cmake -DINSTALL_PREFIX=ON -DCMAKE_INSTALL_PREFIX=$PREFIX -DINSTALL_ROOT=ON -DCMAKE_BUILD_TYPE=Release .. make install diff --git a/recipes/ont-tombo/meta.yaml b/recipes/ont-tombo/meta.yaml index 71342e40210b17..c7ed8c35064a29 100644 --- a/recipes/ont-tombo/meta.yaml +++ b/recipes/ont-tombo/meta.yaml @@ -1,6 +1,6 @@ {% set name = "ont-tombo" %} -{% set version = "1.1.1" %} -{% set hash = "e481e7ff88d2c752cb39ddf25e5b37871748e4178a285053b7dde19f2566c93b" %} +{% set version = "1.2" %} +{% set hash = "db3258d7f4e3d9b60d66d457aa8821ac8d0c2058a2eaa6a79e99dff54de8c18a" %} package: name: {{ name|lower }} @@ -15,39 +15,39 @@ build: entry_points: - tombo = tombo.__main__:main number: 0 - skip: True # [not py27] requirements: build: - python - - setuptools + - setuptools >=18.0 - h5py - - rpy2 >=2.4.2 + - rpy2 # [py3k] + - rpy2 <=2.8.6 # [not py3k] - numpy - scipy - cython - r-base - r-ggplot2 - - r-cowplot - - hdf5 - - graphmap - - bwa - - minimap2 + - r-gridextra + - mappy + - pyfaidx + - future run: - python + - setuptools >=18.0 - h5py - - rpy2 >=2.4.2 + - rpy2 # [py3k] + - rpy2 <=2.8.6 # [not py3k] - numpy - scipy - cython - r-base - r-ggplot2 - - r-cowplot - - hdf5 - - graphmap - - bwa - - minimap2 + - r-gridextra + - mappy + - pyfaidx + - future test: imports: @@ -57,7 +57,7 @@ test: - tombo --help about: - home: https://github.com/nanoporetech/tombo + home: https://nanoporetech.github.io/tombo/ license: mpl-2.0 license_file: LICENSE.md summary: 'Detection of modified bases from raw nanopore sequencing data.' diff --git a/recipes/openbabel/2.3.2/meta.yaml b/recipes/openbabel/2.3.2/meta.yaml index cb8faa40f48f82..de9aeaa306958a 100644 --- a/recipes/openbabel/2.3.2/meta.yaml +++ b/recipes/openbabel/2.3.2/meta.yaml @@ -8,25 +8,26 @@ about: build: skip: True # [not py27 or osx] - number: 1 + number: 2 package: name: openbabel version: 2.3.2 requirements: - build: - - python - - gcc # [linux] - - llvm # [osx] - - cmake - - eigen - - libxml2 - - zlib - - cairo - run: - - python - - libgcc # [linux] + build: + - python + - gcc # [linux] + - llvm # [osx] + - cmake + - eigen + - libxml2 + - zlib {{CONDA_ZLIB}}* + - cairo + run: + - python + - libgcc # [linux] + - zlib {{CONDA_ZLIB}}* source: fn: openbabel-2.3.2.tar.gz diff --git a/recipes/openbabel/2.4.1/meta.yaml b/recipes/openbabel/2.4.1/meta.yaml index e20a0f6051acde..1032dd1d91e2b4 100644 --- a/recipes/openbabel/2.4.1/meta.yaml +++ b/recipes/openbabel/2.4.1/meta.yaml @@ -18,7 +18,7 @@ source: build: # https://bugs.archlinux.org/task/52409 skip: true # [not py2k and not py35] - number: 1 + number: 2 detect_binary_files_with_prefix: true requirements: @@ -26,7 +26,7 @@ requirements: - gcc # [linux] - llvm # [osx] - cmake - - zlib + - zlib {{CONDA_ZLIB}}* - swig - eigen - bzip2 @@ -36,13 +36,14 @@ requirements: run: - python - libgcc # [linux] - - zlib + - zlib {{CONDA_ZLIB}}* - libxml2 - cairo # [linux] - xorg-libxau - xorg-libxdmcp - xorg-libxext - xorg-libxrender + - xorg-libsm test: imports: - openbabel diff --git a/recipes/openms/2.2.0/meta.yaml b/recipes/openms/2.2.0/meta.yaml index 4f544fa2dac260..db050b09967e55 100644 --- a/recipes/openms/2.2.0/meta.yaml +++ b/recipes/openms/2.2.0/meta.yaml @@ -11,7 +11,7 @@ source: sha256: 61e7d24890abb6f462e2f026efb0dc88b84639b228d96e919c8074d3b11d286e build: - number: 0 + number: 1 string: py{{CONDA_PY}}_boost{{ boost }}_{{PKG_BUILDNUM}} skip: True # [py3k] diff --git a/recipes/openms/2.3.0/activate.sh b/recipes/openms/2.3.0/activate.sh new file mode 100644 index 00000000000000..6e7d38fb4b70b5 --- /dev/null +++ b/recipes/openms/2.3.0/activate.sh @@ -0,0 +1,3 @@ +#!/bin/sh + +export OPENMS_DATA_PATH=${CONDA_PREFIX}/share/OpenMS/ diff --git a/recipes/openms/build.sh b/recipes/openms/2.3.0/build.sh similarity index 77% rename from recipes/openms/build.sh rename to recipes/openms/2.3.0/build.sh index 96f523c71f792e..0e94a475999afa 100644 --- a/recipes/openms/build.sh +++ b/recipes/openms/2.3.0/build.sh @@ -8,6 +8,11 @@ mkdir contrib-build cd contrib-build cmake -DBUILD_TYPE=WILDMAGIC ../contrib + +mkdir -p $PREFIX/etc/conda/activate.d/ $PREFIX/etc/conda/deactivate.d/ +cp $RECIPE_DIR/activate.sh $PREFIX/etc/conda/activate.d/openms.sh +cp $RECIPE_DIR/deactivate.sh $PREFIX/etc/conda/deactivate.d/openms.sh + cd .. mkdir build cd build diff --git a/recipes/openms/2.3.0/deactivate.sh b/recipes/openms/2.3.0/deactivate.sh new file mode 100644 index 00000000000000..fab50525e70125 --- /dev/null +++ b/recipes/openms/2.3.0/deactivate.sh @@ -0,0 +1,3 @@ +#!/bin/sh + +unset OPENMS_DATA_PATH diff --git a/recipes/openms/meta.yaml b/recipes/openms/2.3.0/meta.yaml similarity index 95% rename from recipes/openms/meta.yaml rename to recipes/openms/2.3.0/meta.yaml index 52bb4434012388..9583b952afb79b 100644 --- a/recipes/openms/meta.yaml +++ b/recipes/openms/2.3.0/meta.yaml @@ -9,9 +9,9 @@ source: fn: OpenMS-{{ version }}-src.tar.gz url: https://github.com/OpenMS/OpenMS/releases/download/Release{{ version }}/OpenMS-{{ version }}-src.tar.gz sha256: 574c3ea73ec3e57f87446a86563d2c954baa290b3cf72aff8fa149c2a086bba4 - + build: - number: 0 + number: 2 string: py{{CONDA_PY}}_boost{{ boost }}_{{PKG_BUILDNUM}} # osx times out on travis skip: True # [py3k or osx] @@ -53,7 +53,7 @@ requirements: - coinmp test: commands: - - OPENMS_DATA_PATH=$PREFIX/share/OpenMS/ FileMerger --help + - OPENMS_DATA_PATH=${PREFIX}/share/OpenMS/ FileMerger --help about: home: https://github.com/OpenMS/OpenMS diff --git a/recipes/openslide/meta.yaml b/recipes/openslide/meta.yaml index ed6ce0e48fe4e7..7963bf08832cf7 100644 --- a/recipes/openslide/meta.yaml +++ b/recipes/openslide/meta.yaml @@ -3,11 +3,11 @@ package: name: openslide version: {{OPENSLIDE_VERSION}} - + build: - number: 2 + number: 3 skip: True # [py3k] - + source: fn: v{{OPENSLIDE_VERSION}}.zip url: https://github.com/openslide/openslide/archive/v{{OPENSLIDE_VERSION}}.zip @@ -19,9 +19,8 @@ requirements: - pkg-config - automake - perl - - gcc >=4.7 # [linux] - - llvm # [osx] - - zlib + - gcc >=4.7 + - zlib {{CONDA_ZLIB}}* - jpeg - libtiff >=4 - openjpeg >=2.1 @@ -33,13 +32,13 @@ requirements: - gdk-pixbuf - libtool - xorg-libxrender - - xorg-libxext + - xorg-libxext - xorg-libxau - xorg-libxdmcp run: - - libgcc # [linux] - - zlib + - libgcc + - zlib {{CONDA_ZLIB}}* - jpeg - libpng - libtiff >=4 @@ -49,14 +48,13 @@ requirements: - cairo >=1.2 - glib >=2.48.0 - gdk-pixbuf - + test: commands: - test -f $PREFIX/lib/libopenslide.so # [linux] - test -f $PREFIX/lib/libopenslide.dylib # [osx] - + about: home: http://openslide.org/ license: GNU LGPL 2.1 summary: OpenSlide is a C library that provides a simple interface to read whole-slide images (also known as virtual slides). - diff --git a/recipes/osra/2.1.0/meta.yaml b/recipes/osra/2.1.0/meta.yaml index 3674ca2b20b1cf..ab7bd5efc59819 100644 --- a/recipes/osra/2.1.0/meta.yaml +++ b/recipes/osra/2.1.0/meta.yaml @@ -3,13 +3,13 @@ package: version: 2.1.0 build: - number: 0 + number: 1 skip: True # [not py27 or osx] source: fn: osra-2.1.0-1.tgz - url: https://sourceforge.net/projects/osra/files/osra/2.1.0/osra-2.1.0-1.tgz - sha256: 077c611654f0c2cd5896bffa2b0a7eeeeb1eaa411a20673cb423366499b5ecc0 + url: https://osdn.net/projects/sfnet_osra/downloads/osra/2.1.0/osra-2.1.0-1.tgz + md5: a0317e323f042a9fa648ece3a2d94eaf requirements: build: @@ -25,7 +25,7 @@ requirements: - cmake - eigen - libxml2 - - zlib + - zlib {{CONDA_ZLIB}}* - cairo - wget @@ -37,6 +37,7 @@ requirements: - graphicsmagick >=1.3.26 - tesseract - ocrad + - zlib {{CONDA_ZLIB}}* - poppler test: @@ -45,5 +46,5 @@ test: about: home: http://cactus.nci.nih.gov/osra/ - license: Simplified BSD Licence + license: Simplified BSD Licence summary: OSRA is a utility designed to convert graphical representations of chemical structures, as they appear in journal articles, patent documents, textbooks, trade magazines etc., into SMILES or SDF. diff --git a/recipes/pairix/meta.yaml b/recipes/pairix/meta.yaml index 5e15770840cc4e..03156913a1e3b0 100644 --- a/recipes/pairix/meta.yaml +++ b/recipes/pairix/meta.yaml @@ -16,7 +16,6 @@ requirements: build: - gcc # [linux] - llvm # [osx] - - zlib - python - setuptools diff --git a/recipes/paladin/meta.yaml b/recipes/paladin/meta.yaml index f68d0b40243c3d..905b3d37589f3f 100644 --- a/recipes/paladin/meta.yaml +++ b/recipes/paladin/meta.yaml @@ -14,18 +14,18 @@ source: md5: {{ md5 }} build: - number: 0 + number: 1 requirements: build: - gcc # [not osx] - llvm # [osx] - - zlib + - zlib {{CONDA_ZLIB}}* - curl run: - libgcc # [not osx] - - zlib + - zlib {{CONDA_ZLIB}}* - curl test: diff --git a/recipes/pandaseq/build.sh b/recipes/pandaseq/build.sh index f0863465e2af0c..24f74680fe4f94 100644 --- a/recipes/pandaseq/build.sh +++ b/recipes/pandaseq/build.sh @@ -1,8 +1,11 @@ #!/bin/bash +export CPPFLAGS="-I$PREFIX/include" +export LDFLAGS="-L$PREFIX/lib" + mkdir -p $PREFIX/bin -./autogen.sh +./autogen.sh ./configure --prefix=$PREFIX -make +make make install diff --git a/recipes/pandaseq/meta.yaml b/recipes/pandaseq/meta.yaml index eed57af0e72cd5..2c7cd250578490 100644 --- a/recipes/pandaseq/meta.yaml +++ b/recipes/pandaseq/meta.yaml @@ -1,37 +1,39 @@ package: - name: pandaseq - version: "2.11" + name: pandaseq + version: "2.11" build: - number: 1 - skip: False + number: 2 + skip: False source: - fn: pandaseq_v2.11.tar.gz - url: https://github.com/neufeld/pandaseq/archive/v2.11.tar.gz - md5: a8ae0e938bac592fc07dfa668147d80b + fn: pandaseq_v2.11.tar.gz + url: https://github.com/neufeld/pandaseq/archive/v2.11.tar.gz + md5: a8ae0e938bac592fc07dfa668147d80b requirements: - build: - - gcc [linux] - - llvm [osx] - - autoconf 2.69 pl5.* - - automake 1.15 pl5.* - - zlib - - pkg-config - - libtool - - bzip2 + build: + - gcc [linux] + - llvm [osx] + - autoconf 2.69 pl5.* + - automake 1.15 pl5.* + - zlib {{CONDA_ZLIB}}* + - pkg-config + - libtool + - bzip2 {{CONDA_BZIP2}}* - run: - - libtool [linux] - - libgcc [linux] + run: + - libtool [linux] + - libgcc [linux] + - zlib {{CONDA_ZLIB}}* + - bzip2 {{CONDA_BZIP2}}* test: - commands: - - pandaseq -v 2>&1 | grep "pandaseq" > /dev/null + commands: + - pandaseq -v 2>&1 | grep "pandaseq" > /dev/null about: - home: https://github.com/neufeld/pandaseq - license: GPL3 - license_file: COPYING - summary: PANDASEQ is a program to align Illumina reads, optionally with PCR primers embedded in the sequence, and reconstruct an overlapping sequence. + home: https://github.com/neufeld/pandaseq + license: GPL3 + license_file: COPYING + summary: PANDASEQ is a program to align Illumina reads, optionally with PCR primers embedded in the sequence, and reconstruct an overlapping sequence. diff --git a/recipes/parafly/meta.yaml b/recipes/parafly/meta.yaml index 542bf283caab12..379ef1a502d00f 100644 --- a/recipes/parafly/meta.yaml +++ b/recipes/parafly/meta.yaml @@ -8,15 +8,15 @@ source: sha256: 64cf7ac2d4af0801b78d58f4057a1489d76b2b8ae59c78997f434d1239fa4abe build: - number: 0 + number: 1 requirements: build: - gcc - - zlib + - zlib {{CONDA_ZLIB}}* run: - libgcc - - zlib + - zlib {{CONDA_ZLIB}}* test: commands: diff --git a/recipes/pbbam/meta.yaml b/recipes/pbbam/meta.yaml index 0d56ece30fa1a0..9e2419a5bb8f5e 100644 --- a/recipes/pbbam/meta.yaml +++ b/recipes/pbbam/meta.yaml @@ -6,26 +6,26 @@ package: version: {{ version }} build: - number: 1 - skip: False - string: boost{{CONDA_BOOST}}_{{PKG_BUILDNUM}} + number: 2 + skip: False + string: boost{{CONDA_BOOST}}_{{PKG_BUILDNUM}} source: - git_url: https://github.com/PacificBiosciences/{{ name }}.git - git_rev: 928605a86ac024aced821fe4a4bce0b43d5ee680 - + git_url: https://github.com/PacificBiosciences/{{ name }}.git + git_rev: 928605a86ac024aced821fe4a4bce0b43d5ee680 + requirements: - build: - - llvm # [osx] - - gcc # [linux] - - cmake - - boost {{CONDA_BOOST}}* - - zlib + build: + - llvm # [osx] + - gcc # [linux] + - cmake + - boost {{CONDA_BOOST}}* + - zlib {{CONDA_ZLIB}}* - run: - - libgcc # [linux] - - htslib - - zlib + run: + - libgcc # [linux] + - htslib + - zlib {{CONDA_ZLIB}}* test: commands: @@ -38,4 +38,3 @@ about: home: https://github.com/PacificBiosciences/{{ name }} license: BSD-3-Clause-Clear summary: PacBio BAM C++ library, with SWIG bindings - diff --git a/recipes/peakranger/meta.yaml b/recipes/peakranger/meta.yaml index 9844d2270f48ce..f82c179a6d5dc7 100644 --- a/recipes/peakranger/meta.yaml +++ b/recipes/peakranger/meta.yaml @@ -10,7 +10,7 @@ source: - makefile.patch build: - number: 1 + number: 2 skip: True # [osx] string: boost{{CONDA_BOOST}}_{{PKG_BUILDNUM}} diff --git a/recipes/pear/meta.yaml b/recipes/pear/meta.yaml index 781d76737906b7..0b7488dda04745 100644 --- a/recipes/pear/meta.yaml +++ b/recipes/pear/meta.yaml @@ -10,24 +10,24 @@ about: source: fn: pear-0.9.6-src.tar.gz md5: 5ed68d50c1620cd55c58681e38771799 - url: http://sco.h-its.org/exelixis/web/software/pear/files/pear-0.9.6-src.tar.gz + url: https://depot.galaxyproject.org/software/pear/pear_0.9.6_src_all.tar.gz build: - number: 2 + number: 3 requirements: build: - gcc # [not osx] - llvm # [osx] - pkgconfig - - zlib - - bzip2 + - zlib {{CONDA_ZLIB}}* + - bzip2 {{CONDA_BZIP2}}* run: - libgcc # [not osx] - - zlib - - bzip2 + - zlib {{CONDA_ZLIB}}* + - bzip2 {{CONDA_BZIP2}}* test: commands: - - pear 2>&1 | grep 'PEAR v0.9.6' - - pearRM 2>&1 | grep 'PEAR v0.9.6' + - pear 2>&1 | grep "PEAR v0.9.6" + - pearRM 2>&1 | grep "PEAR v0.9.6" diff --git a/recipes/percolator/meta.yaml b/recipes/percolator/meta.yaml index 957c9aeff631b6..78ab516b83f9a1 100644 --- a/recipes/percolator/meta.yaml +++ b/recipes/percolator/meta.yaml @@ -8,7 +8,7 @@ source: md5: fcb37bc5fcd0149cc775c3e72ff3dc24 build: - number: 3 + number: 4 string: boost_1.62{{PKG_BUILDNUM}} skip: True # [osx] diff --git a/recipes/perl-bio-db-hts/meta.yaml b/recipes/perl-bio-db-hts/meta.yaml index 18bbff80e468c3..f3fdc01aac5970 100644 --- a/recipes/perl-bio-db-hts/meta.yaml +++ b/recipes/perl-bio-db-hts/meta.yaml @@ -10,19 +10,19 @@ source: md5: a09468d02a7e58673b177e60915f28b0 build: - number: 0 + number: 1 skip: true # [osx] string: "htslib{{CONDA_HTSLIB}}_{{PKG_BUILDNUM}}" requirements: build: - - zlib + - zlib {{CONDA_ZLIB}}* - perl - perl-module-build - perl-bioperl - htslib {{CONDA_HTSLIB}}* run: - - zlib + - zlib {{CONDA_ZLIB}}* - perl - perl-bioperl - htslib {{CONDA_HTSLIB}}* diff --git a/recipes/perl-bio-samtools/meta.yaml b/recipes/perl-bio-samtools/meta.yaml index 99a8dbf3cbc717..18a1266b2b8818 100644 --- a/recipes/perl-bio-samtools/meta.yaml +++ b/recipes/perl-bio-samtools/meta.yaml @@ -18,12 +18,12 @@ requirements: - perl-bioperl-core - perl-module-build - samtools <=0.1.17 - - zlib + - zlib {{CONDA_ZLIB}}* run: - perl-threaded - perl-bioperl-core - - zlib + - zlib {{CONDA_ZLIB}}* test: imports: diff --git a/recipes/perl-pathtools/build.sh b/recipes/perl-bio-viennangs/0.18/build.sh similarity index 85% rename from recipes/perl-pathtools/build.sh rename to recipes/perl-bio-viennangs/0.18/build.sh index 360c94507e0e8f..23eb50af99c524 100644 --- a/recipes/perl-pathtools/build.sh +++ b/recipes/perl-bio-viennangs/0.18/build.sh @@ -3,10 +3,10 @@ # If it has Build.PL use that, otherwise use Makefile.PL if [ -f Build.PL ]; then perl Build.PL - ./Build - ./Build test + perl ./Build + perl ./Build test # Make sure this goes in site - ./Build install --installdirs site + perl ./Build install --installdirs site elif [ -f Makefile.PL ]; then # Make sure this goes in site perl Makefile.PL INSTALLDIRS=site @@ -22,4 +22,4 @@ fi # See # http://docs.continuum.io/conda/build.html -# for a list of environment variables that are set during the build process. \ No newline at end of file +# for a list of environment variables that are set during the build process. diff --git a/recipes/perl-bio-viennangs/0.18/meta.yaml b/recipes/perl-bio-viennangs/0.18/meta.yaml new file mode 100644 index 00000000000000..432555ca9542c2 --- /dev/null +++ b/recipes/perl-bio-viennangs/0.18/meta.yaml @@ -0,0 +1,123 @@ +{% set name = "perl-bio-viennangs" %} +{% set version = "v0.18" %} +{% set sha256 = "fb8d3c1f55a8d79f5712db5345a2cfb864ca6c4857e712fa9f06c6ff494385d1" %} + +package: + name: {{ name }} + version: {{ version }} + +source: + fn: Bio-ViennaNGS-v0.18.tar.gz + url: https://cpan.metacpan.org/authors/id/M/MT/MTW/Bio-ViennaNGS-v0.18.tar.gz + sha256: {{ sha256 }} + +build: + number: 1 + +requirements: + build: + - bedtools >=2.24 + - ucsc-fetchchromsizes + - ucsc-bedgraphtobigwig + - ucsc-fatotwobit + - ucsc-bedtobigbed + - perl >=5.22,<6.0 + - perl-getopt-long + - perl-constant + - perl-moosex-clone + - perl-exporter + - perl-file-path + - perl-test-deep + - perl-moose + - perl-extutils-makemaker + - perl-test-prereq + - perl-math-round + - perl-test-files + - perl-file-temp + - perl-data-dumper + - perl-lib + - perl-test-file-contents + - perl-namespace-autoclean + - perl-file-slurp + - perl-path-class + - perl-params-coerce + - perl-pod-usage + - perl-ipc-cmd + - perl-carp + - perl-io-gzip + - perl-file-share + - perl-tie-hash-indexed + - perl-list-util + - perl-bioperl + - perl-test-more + - perl-template-toolkit + - perl-findbin + - perl-file-find + #- perl-bio-sequtils + - perl-bio-samtools + + run: + - bedtools >=2.24 + - ucsc-fetchchromsizes + - ucsc-bedgraphtobigwig + - ucsc-fatotwobit + - ucsc-bedtobigbed + - perl >=5.22,<6.0 + - perl-getopt-long + - perl-constant + - perl-moosex-clone + - perl-file-path + - perl-moose + - perl-math-round + - perl-file-temp + - perl-data-dumper + - perl-lib + - perl-namespace-autoclean + - perl-file-slurp + - perl-pod-usage + - perl-carp + - perl-file-share + - perl-tie-hash-indexed + - perl-exporter + - perl-test-deep + - perl-test-files + - perl-path-class + - perl-params-coerce + - perl-ipc-cmd + - perl-perlio-gzip + - perl-test-file-contents + - perl-posix + - perl-list-util + - perl-bioperl + - perl-file-find + - perl-bio-samtools + - perl-template-toolkit + - perl-findbin + +test: + imports: + - Bio::ViennaNGS + - Bio::ViennaNGS::AnnoC + - Bio::ViennaNGS::Bam + - Bio::ViennaNGS::Bed + - Bio::ViennaNGS::BedGraphEntry + - Bio::ViennaNGS::Expression + - Bio::ViennaNGS::ExtFeature + - Bio::ViennaNGS::Fasta + - Bio::ViennaNGS::Feature + - Bio::ViennaNGS::FeatureChain + - Bio::ViennaNGS::FeatureInterval + - Bio::ViennaNGS::FeatureIO + - Bio::ViennaNGS::FeatureLine + - Bio::ViennaNGS::MinimalFeature + - Bio::ViennaNGS::Peak + - Bio::ViennaNGS::SpliceJunc + - Bio::ViennaNGS::Subtypes + - Bio::ViennaNGS::Tutorial + - Bio::ViennaNGS::UCSC + - Bio::ViennaNGS::Util + +about: + home: http://metacpan.org/pod/Bio::ViennaNGS + license: perl_5 + summary: 'A Perl distribution for Next-Generation Sequencing (NGS) data analysis' diff --git a/recipes/perl-class-xsaccessor/1.19/build.sh b/recipes/perl-class-xsaccessor/1.19/build.sh new file mode 100644 index 00000000000000..23eb50af99c524 --- /dev/null +++ b/recipes/perl-class-xsaccessor/1.19/build.sh @@ -0,0 +1,25 @@ +#!/bin/bash + +# If it has Build.PL use that, otherwise use Makefile.PL +if [ -f Build.PL ]; then + perl Build.PL + perl ./Build + perl ./Build test + # Make sure this goes in site + perl ./Build install --installdirs site +elif [ -f Makefile.PL ]; then + # Make sure this goes in site + perl Makefile.PL INSTALLDIRS=site + make + make test + make install +else + echo 'Unable to find Build.PL or Makefile.PL. You need to modify build.sh.' + exit 1 +fi + +# Add more build steps here, if they are necessary. + +# See +# http://docs.continuum.io/conda/build.html +# for a list of environment variables that are set during the build process. diff --git a/recipes/perl-class-xsaccessor/1.19/meta.yaml b/recipes/perl-class-xsaccessor/1.19/meta.yaml new file mode 100644 index 00000000000000..e65ea6dd66e1b3 --- /dev/null +++ b/recipes/perl-class-xsaccessor/1.19/meta.yaml @@ -0,0 +1,39 @@ +{% set name = "perl-class-xsaccessor" %} +{% set version = "1.19" %} +{% set sha256 = "99c56b395f1239af19901f2feeb125d9ecb4e351a0d80daa9529211a4700a6f2" %} + +package: + name: {{ name }} + version: {{ version }} + +source: + fn: Class-XSAccessor-1.19.tar.gz + url: https://cpan.metacpan.org/authors/id/S/SM/SMUELLER/Class-XSAccessor-1.19.tar.gz + sha256: {{ sha256 }} + +build: + number: 0 + +requirements: + build: + - perl >=5.22,<6.0 + - perl-extutils-makemaker + - perl-time-hires + - perl-xsloader + - perl-test-more + + run: + - perl >=5.22,<6.0 + - perl-time-hires + - perl-xsloader + +test: + # Perl 'use' tests + imports: + - Class::XSAccessor + - Class::XSAccessor::Array + +about: + home: http://metacpan.org/pod/Class::XSAccessor + license: perl_5 + summary: 'Generate fast XS accessors without runtime compilation' diff --git a/recipes/perl-compress-raw-zlib/meta.yaml b/recipes/perl-compress-raw-zlib/meta.yaml index 5d15b7c522eec1..146cc890c96e6b 100644 --- a/recipes/perl-compress-raw-zlib/meta.yaml +++ b/recipes/perl-compress-raw-zlib/meta.yaml @@ -7,17 +7,17 @@ source: url: https://cpan.metacpan.org/authors/id/P/PM/PMQS/Compress-Raw-Zlib-2.069.tar.gz build: - number: 3 + number: 4 requirements: build: - gcc - - perl-threaded + - perl - perl-app-cpanminus - perl-module-build run: - libgcc - - perl-threaded + - perl test: imports: diff --git a/recipes/perl-data-visitor/0.30/build.sh b/recipes/perl-data-visitor/0.30/build.sh new file mode 100644 index 00000000000000..67918fe672fe6b --- /dev/null +++ b/recipes/perl-data-visitor/0.30/build.sh @@ -0,0 +1,19 @@ +#!/bin/bash + +# If it has Build.PL use that, otherwise use Makefile.PL +if [ -f Build.PL ]; then + perl Build.PL + perl ./Build + perl ./Build test + # Make sure this goes in site + perl ./Build install --installdirs site +elif [ -f Makefile.PL ]; then + # Make sure this goes in site + perl Makefile.PL INSTALLDIRS=site + make + make test + make install +else + echo 'Unable to find Build.PL or Makefile.PL. You need to modify build.sh.' + exit 1 +fi diff --git a/recipes/perl-data-visitor/0.30/meta.yaml b/recipes/perl-data-visitor/0.30/meta.yaml new file mode 100644 index 00000000000000..7f876781c07311 --- /dev/null +++ b/recipes/perl-data-visitor/0.30/meta.yaml @@ -0,0 +1,44 @@ +{% set name = "perl-data-visitor" %} +{% set version = "0.30" %} +{% set sha256 = "8ea24abcc3659e760aa94aee2ba7dd54cacaf20302705524143f39554009ed54" %} + +package: + name: {{ name }} + version: {{ version }} + +source: + fn: Data-Visitor-0.30.tar.gz + url: https://cpan.metacpan.org/authors/id/D/DO/DOY/Data-Visitor-0.30.tar.gz + sha256: {{ sha256 }} + +build: + number: 0 + +requirements: + build: + - perl >=5.22,<6.0 + - perl-test-requires + - perl-namespace-clean + - perl-moose + - perl-tie-toobject + - perl-extutils-makemaker + - perl-task-weaken + - perl-class-load >=0.06 + + run: + - perl >=5.22,<6.0 + - perl-namespace-clean + - perl-task-weaken + - perl-moose + - perl-tie-toobject + - perl-class-load >=0.06 + +test: + imports: + - Data::Visitor + - Data::Visitor::Callback + +about: + home: http://metacpan.org/release/Data-Visitor + license: perl_5 + summary: 'Visitor style traversal of Perl data structures' diff --git a/recipes/perl-devel-symdump/2.18/meta.yaml b/recipes/perl-devel-symdump/2.18/meta.yaml index 49c602317f044d..6ec289908c4a0d 100644 --- a/recipes/perl-devel-symdump/2.18/meta.yaml +++ b/recipes/perl-devel-symdump/2.18/meta.yaml @@ -20,13 +20,8 @@ requirements: build: - perl - perl-extutils-makemaker - #- perl-compress-zlib - #- perl-test-more - run: - perl - #- perl-compress-zlib - #- perl-test-more test: # Perl 'use' tests diff --git a/recipes/perl-file-remove/1.57/build.sh b/recipes/perl-file-remove/1.57/build.sh new file mode 100644 index 00000000000000..23eb50af99c524 --- /dev/null +++ b/recipes/perl-file-remove/1.57/build.sh @@ -0,0 +1,25 @@ +#!/bin/bash + +# If it has Build.PL use that, otherwise use Makefile.PL +if [ -f Build.PL ]; then + perl Build.PL + perl ./Build + perl ./Build test + # Make sure this goes in site + perl ./Build install --installdirs site +elif [ -f Makefile.PL ]; then + # Make sure this goes in site + perl Makefile.PL INSTALLDIRS=site + make + make test + make install +else + echo 'Unable to find Build.PL or Makefile.PL. You need to modify build.sh.' + exit 1 +fi + +# Add more build steps here, if they are necessary. + +# See +# http://docs.continuum.io/conda/build.html +# for a list of environment variables that are set during the build process. diff --git a/recipes/perl-file-remove/1.57/meta.yaml b/recipes/perl-file-remove/1.57/meta.yaml new file mode 100644 index 00000000000000..53567802dee367 --- /dev/null +++ b/recipes/perl-file-remove/1.57/meta.yaml @@ -0,0 +1,39 @@ +{% set name = "perl-file-remove" %} +{% set version = "1.57" %} +{% set sha256 = "b3becd60165c38786d18285f770b8b06ebffe91797d8c00cc4730614382501ad" %} + +package: + name: {{ name }} + version: {{ version }} + +source: + fn: File-Remove-1.57.tar.gz + url: https://cpan.metacpan.org/authors/id/S/SH/SHLOMIF/File-Remove-1.57.tar.gz + sha256: {{ sha256 }} + +build: + number: 0 + +requirements: + build: + - perl >=5.22,<6.0 + - perl-extutils-makemaker + - perl-io-handle + - perl-file-spec + - perl-test-more + + run: + - perl >=5.22,<6.0 + - perl-io-handle + - perl-file-spec + - perl-test-more + +test: + # Perl 'use' tests + imports: + - File::Remove + +about: + home: http://metacpan.org/pod/File::Remove + license: perl_5 + summary: 'Remove files and directories' diff --git a/recipes/perl-file-share/0.25/build.sh b/recipes/perl-file-share/0.25/build.sh new file mode 100644 index 00000000000000..23eb50af99c524 --- /dev/null +++ b/recipes/perl-file-share/0.25/build.sh @@ -0,0 +1,25 @@ +#!/bin/bash + +# If it has Build.PL use that, otherwise use Makefile.PL +if [ -f Build.PL ]; then + perl Build.PL + perl ./Build + perl ./Build test + # Make sure this goes in site + perl ./Build install --installdirs site +elif [ -f Makefile.PL ]; then + # Make sure this goes in site + perl Makefile.PL INSTALLDIRS=site + make + make test + make install +else + echo 'Unable to find Build.PL or Makefile.PL. You need to modify build.sh.' + exit 1 +fi + +# Add more build steps here, if they are necessary. + +# See +# http://docs.continuum.io/conda/build.html +# for a list of environment variables that are set during the build process. diff --git a/recipes/perl-file-share/0.25/meta.yaml b/recipes/perl-file-share/0.25/meta.yaml new file mode 100644 index 00000000000000..1c266e26a48342 --- /dev/null +++ b/recipes/perl-file-share/0.25/meta.yaml @@ -0,0 +1,28 @@ +package: + name: perl-file-share + version: "0.25" + +source: + fn: File-Share-0.25.tar.gz + url: https://cpan.metacpan.org/authors/id/I/IN/INGY/File-Share-0.25.tar.gz + md5: 214cb8d14627cbff13e0a6de3ac18bb0 + +requirements: + build: + - perl + - perl-file-sharedir + - perl-extutils-makemaker + + run: + - perl + - perl-file-sharedir + +test: + # Perl 'use' tests + imports: + - File::Share + +about: + home: https://github.com/ingydotnet/file-share-pm + license: perl_5 + summary: 'Extend File::ShareDir to Local Libraries' diff --git a/recipes/perl-filedirutil/0.03/build.sh b/recipes/perl-filedirutil/0.03/build.sh new file mode 100644 index 00000000000000..23eb50af99c524 --- /dev/null +++ b/recipes/perl-filedirutil/0.03/build.sh @@ -0,0 +1,25 @@ +#!/bin/bash + +# If it has Build.PL use that, otherwise use Makefile.PL +if [ -f Build.PL ]; then + perl Build.PL + perl ./Build + perl ./Build test + # Make sure this goes in site + perl ./Build install --installdirs site +elif [ -f Makefile.PL ]; then + # Make sure this goes in site + perl Makefile.PL INSTALLDIRS=site + make + make test + make install +else + echo 'Unable to find Build.PL or Makefile.PL. You need to modify build.sh.' + exit 1 +fi + +# Add more build steps here, if they are necessary. + +# See +# http://docs.continuum.io/conda/build.html +# for a list of environment variables that are set during the build process. diff --git a/recipes/perl-filedirutil/0.03/meta.yaml b/recipes/perl-filedirutil/0.03/meta.yaml new file mode 100644 index 00000000000000..efc5fe58ee39b0 --- /dev/null +++ b/recipes/perl-filedirutil/0.03/meta.yaml @@ -0,0 +1,51 @@ +{% set name = "perl-filedirutil" %} +{% set version = "v0.03" %} +{% set sha256 = "2923383d588c3ff1b3e60267da2b05318a2493c1756d4c8a110ddabf14a33b9d" %} + +package: + name: {{ name }} + version: {{ version }} + +source: + fn: FileDirUtil-v0.03.tar.gz + url: https://cpan.metacpan.org/authors/id/M/MT/MTW/FileDirUtil-v0.03.tar.gz + sha256: {{ sha256 }} + +build: + number: 0 + +requirements: + build: + - perl >5.22,<6.0 + - perl-moose + - perl-namespace-autoclean + - perl-extutils-makemaker + - perl-params-coerce + - perl-path-class + #- perl-file-basename + #- perl-path-class-file + #- perl-path-class-dir + #- perl-test-more + #- perl-moose-role + #- perl-moose-util-typeconstraints + + run: + - perl >5.22,<6.0 + - perl-moose + - perl-namespace-autoclean + - perl-params-coerce + - perl-path-class + #- perl-path-class-file + #- perl-path-class-dir + #- perl-moose-util-typeconstraints + #- perl-file-basename + #- perl-moose-role + +test: + imports: + - FileDirUtil + +about: + home: http://metacpan.org/pod/FileDirUtil + license: agpl_3 + summary: 'A Moose Role for basic File IO' diff --git a/recipes/perl-hash-util-fieldhash-compat/0.11/build.sh b/recipes/perl-hash-util-fieldhash-compat/0.11/build.sh new file mode 100644 index 00000000000000..23eb50af99c524 --- /dev/null +++ b/recipes/perl-hash-util-fieldhash-compat/0.11/build.sh @@ -0,0 +1,25 @@ +#!/bin/bash + +# If it has Build.PL use that, otherwise use Makefile.PL +if [ -f Build.PL ]; then + perl Build.PL + perl ./Build + perl ./Build test + # Make sure this goes in site + perl ./Build install --installdirs site +elif [ -f Makefile.PL ]; then + # Make sure this goes in site + perl Makefile.PL INSTALLDIRS=site + make + make test + make install +else + echo 'Unable to find Build.PL or Makefile.PL. You need to modify build.sh.' + exit 1 +fi + +# Add more build steps here, if they are necessary. + +# See +# http://docs.continuum.io/conda/build.html +# for a list of environment variables that are set during the build process. diff --git a/recipes/perl-hash-util-fieldhash-compat/0.11/meta.yaml b/recipes/perl-hash-util-fieldhash-compat/0.11/meta.yaml new file mode 100644 index 00000000000000..655c38eec42b2d --- /dev/null +++ b/recipes/perl-hash-util-fieldhash-compat/0.11/meta.yaml @@ -0,0 +1,46 @@ +{% set name = "perl-hash-util-fieldhash-compat" %} +{% set version = "0.11" %} +{% set sha256 = "642e46a75b537ba11420b30f8b03403c90a06a15458cd8009f339fe9e5f3741b" %} + +package: + name: {{ name }} + version: {{ version }} + +source: + fn: Hash-Util-FieldHash-Compat-0.11.tar.gz + url: https://cpan.metacpan.org/authors/id/E/ET/ETHER/Hash-Util-FieldHash-Compat-0.11.tar.gz + sha256: {{ sha256 }} + +build: + number: 0 + +requirements: + build: + - perl >5.22,<6.0 + - perl-constant + - perl-extutils-makemaker + - perl-parent + - perl-exporter + - perl-test-more + - perl-file-spec + - perl-tie-refhash >=1.38 + - perl-tie-refhash-weak >=0.08 + + run: + - perl >5.22,<6.0 + - perl-constant + - perl-parent + - perl-exporter + - perl-tie-refhash >=1.38 + - perl-tie-refhash-weak >=0.08 + +test: + # Perl 'use' tests + imports: + - Hash::Util::FieldHash::Compat + - Hash::Util::FieldHash::Compat::Heavy + +about: + home: https://github.com/karenetheridge/Hash-Util-FieldHash-Compat + license: perl_5 + summary: 'Use Hash::Util::FieldHash or ties, depending on availability' diff --git a/recipes/perl-hook-lexwrap/0.26/build.sh b/recipes/perl-hook-lexwrap/0.26/build.sh new file mode 100644 index 00000000000000..23eb50af99c524 --- /dev/null +++ b/recipes/perl-hook-lexwrap/0.26/build.sh @@ -0,0 +1,25 @@ +#!/bin/bash + +# If it has Build.PL use that, otherwise use Makefile.PL +if [ -f Build.PL ]; then + perl Build.PL + perl ./Build + perl ./Build test + # Make sure this goes in site + perl ./Build install --installdirs site +elif [ -f Makefile.PL ]; then + # Make sure this goes in site + perl Makefile.PL INSTALLDIRS=site + make + make test + make install +else + echo 'Unable to find Build.PL or Makefile.PL. You need to modify build.sh.' + exit 1 +fi + +# Add more build steps here, if they are necessary. + +# See +# http://docs.continuum.io/conda/build.html +# for a list of environment variables that are set during the build process. diff --git a/recipes/perl-hook-lexwrap/0.26/meta.yaml b/recipes/perl-hook-lexwrap/0.26/meta.yaml new file mode 100644 index 00000000000000..e9d2ca1a48674d --- /dev/null +++ b/recipes/perl-hook-lexwrap/0.26/meta.yaml @@ -0,0 +1,37 @@ +{% set name = "perl-hook-lexwrap" %} +{% set version = "0.26" %} +{% set sha256 = "b60bdc5f98f94f9294b06adef82b1d996da192d5f183f9f434b610fd1137ec2d" %} + +package: + name: {{ name }} + version: {{ version }} + +source: + fn: Hook-LexWrap-0.26.tar.gz + url: https://cpan.metacpan.org/authors/id/E/ET/ETHER/Hook-LexWrap-0.26.tar.gz + sha256: {{ sha256 }} + +build: + number: 0 + +requirements: + build: + - perl >=5.22,<6.0 + - perl-extutils-makemaker + - perl-carp + - perl-test-more + - perl-file-spec + + run: + - perl >=5.22,<6.0 + - perl-carp + +test: + # Perl 'use' tests + imports: + - Hook::LexWrap + +about: + home: https://github.com/karenetheridge/Hook-LexWrap + license: perl_5 + summary: 'Lexically scoped subroutine wrappers' diff --git a/recipes/perl-io-compress/meta.yaml b/recipes/perl-io-compress/meta.yaml index 433ace5fdadd30..edb1c325e941d1 100644 --- a/recipes/perl-io-compress/meta.yaml +++ b/recipes/perl-io-compress/meta.yaml @@ -8,18 +8,18 @@ source: md5: b26925161e3f01919f60344d1bbb49c4 build: - number: 1 + number: 2 requirements: build: - - perl-threaded + - perl - perl-compress-raw-zlib - perl-compress-raw-bzip2 >=2.069 - perl-scalar-list-utils - perl-extutils-makemaker run: - - perl-threaded + - perl - perl-compress-raw-zlib - perl-compress-raw-bzip2 >=2.069 - perl-scalar-list-utils diff --git a/recipes/perl-io-gzip/meta.yaml b/recipes/perl-io-gzip/meta.yaml index f2202f1399fb5d..90b1aa8fa0516e 100644 --- a/recipes/perl-io-gzip/meta.yaml +++ b/recipes/perl-io-gzip/meta.yaml @@ -8,7 +8,7 @@ source: md5: 0393eae5d0b23df6cf40ed44af7d711c build: - number: 0 + number: 1 requirements: build: diff --git a/recipes/perl-ipc-cmd/1.00/build.sh b/recipes/perl-ipc-cmd/1.00/build.sh new file mode 100644 index 00000000000000..23eb50af99c524 --- /dev/null +++ b/recipes/perl-ipc-cmd/1.00/build.sh @@ -0,0 +1,25 @@ +#!/bin/bash + +# If it has Build.PL use that, otherwise use Makefile.PL +if [ -f Build.PL ]; then + perl Build.PL + perl ./Build + perl ./Build test + # Make sure this goes in site + perl ./Build install --installdirs site +elif [ -f Makefile.PL ]; then + # Make sure this goes in site + perl Makefile.PL INSTALLDIRS=site + make + make test + make install +else + echo 'Unable to find Build.PL or Makefile.PL. You need to modify build.sh.' + exit 1 +fi + +# Add more build steps here, if they are necessary. + +# See +# http://docs.continuum.io/conda/build.html +# for a list of environment variables that are set during the build process. diff --git a/recipes/perl-ipc-cmd/1.00/meta.yaml b/recipes/perl-ipc-cmd/1.00/meta.yaml new file mode 100644 index 00000000000000..1e52ba8e85b71f --- /dev/null +++ b/recipes/perl-ipc-cmd/1.00/meta.yaml @@ -0,0 +1,46 @@ +{% set name = "perl-ipc-cmd" %} +{% set version = "1.00" %} +{% set sha256 = "db3eaaf23517d71d4d2e97189bad3d86c338102cdf22ec5f974ace2ddb7df630" %} + +package: + name: {{ name }} + version: {{ version }} + +source: + fn: IPC-Cmd-1.00.tar.gz + url: https://cpan.metacpan.org/authors/id/B/BI/BINGOS/IPC-Cmd-1.00.tar.gz + sha256: {{ sha256 }} + +build: + number: 0 + +requirements: + build: + - perl >=5.22,<6.0 + - perl-extutils-makemaker + - perl-file-temp + - perl-module-load-conditional >=0.66 + - perl-params-check + - perl-locale-maketext-simple + - perl-file-spec + - perl-test-more + + run: + - perl >=5.22,<6.0 + - perl-extutils-makemaker + - perl-file-temp + - perl-params-check + - perl-locale-maketext-simple + - perl-module-load-conditional >=0.66 + - perl-file-spec + - perl-test-more + +test: + # Perl 'use' tests + imports: + - IPC::Cmd + +about: + home: http://metacpan.org/pod/IPC::Cmd + license: perl_5 + summary: 'A cross platform way of running (interactive) commandline programs.' diff --git a/recipes/perl-json-create/build.sh b/recipes/perl-json-create/build.sh new file mode 100644 index 00000000000000..64652ea2132d90 --- /dev/null +++ b/recipes/perl-json-create/build.sh @@ -0,0 +1,19 @@ +#!/bin/bash + +# If it has Build.PL use that, otherwise use Makefile.PL +if [ -f Build.PL ]; then + perl Build.PL + ./Build + ./Build test + # Make sure this goes in site + ./Build install --installdirs site +elif [ -f Makefile.PL ]; then + # Make sure this goes in site + perl Makefile.PL INSTALLDIRS=site + make + make test + make install +else + echo 'Unable to find Build.PL or Makefile.PL. You need to modify build.sh.' + exit 1 +fi diff --git a/recipes/perl-json-create/meta.yaml b/recipes/perl-json-create/meta.yaml new file mode 100644 index 00000000000000..2907733f7567ab --- /dev/null +++ b/recipes/perl-json-create/meta.yaml @@ -0,0 +1,28 @@ +package: + name: perl-json-create + version: "0.24" + +source: + url: http://search.cpan.org/CPAN/authors/id/B/BK/BKB/JSON-Create-0.24.tar.gz + md5: 388aa2fee4540ed7b862c3c06c51a5f1 + +build: + number: 0 + +requirements: + build: + - perl + - perl-json-parse + + run: + - perl + +test: + # Perl 'use' tests + imports: + - JSON::Create + +about: + home: https://metacpan.org/pod/distribution/JSON-Create/lib/JSON/Create.pod + license: Artistic License (Perl) 1.0 | GNU General Public License (GPL) + summary: 'Fast, minimal, UTF-8-only serialization of data to JSON.' diff --git a/recipes/perl-mime-base64/build.sh b/recipes/perl-mime-base64/build.sh new file mode 100644 index 00000000000000..6f4625802a6e91 --- /dev/null +++ b/recipes/perl-mime-base64/build.sh @@ -0,0 +1,20 @@ +#!/bin/bash + +# If it has Build.PL use that, otherwise use Makefile.PL +if [ -f Build.PL ]; then + perl Build.PL + perl ./Build + perl ./Build test + # Make sure this goes in site + perl ./Build install --installdirs site +elif [ -f Makefile.PL ]; then + # Make sure this goes in site + perl Makefile.PL INSTALLDIRS=site + make + make test + make install +else + echo 'Unable to find Build.PL or Makefile.PL. You need to modify build.sh.' + exit 1 +fi + diff --git a/recipes/perl-mime-base64/meta.yaml b/recipes/perl-mime-base64/meta.yaml new file mode 100644 index 00000000000000..b125bcb17882fb --- /dev/null +++ b/recipes/perl-mime-base64/meta.yaml @@ -0,0 +1,34 @@ +{% set name = "perl-mime-base64" %} +{% set version = "3.15" %} +{% set sha256 = "7f863566a6a9cb93eda93beadb77d9aa04b9304d769cea3bb921b9a91b3a1eb9" %} + +package: + name: {{ name }} + version: {{ version }} + +source: + fn: MIME-Base64-3.15.tar.gz + url: https://cpan.metacpan.org/authors/id/G/GA/GAAS/MIME-Base64-3.15.tar.gz + sha256: {{ sha256 }} + +build: + number: 0 + +requirements: + build: + - perl + - perl-extutils-makemaker + - perl-xsloader + + run: + - perl + - perl-xsloader + +test: + imports: + - MIME::Base64 + +about: + home: http://metacpan.org/pod/MIME::Base64 + license: perl_5 + summary: 'The RFC 2045 encodings; base64 and quoted-printable' diff --git a/recipes/perl-module-corelist/5.20180120/build.sh b/recipes/perl-module-corelist/5.20180120/build.sh new file mode 100644 index 00000000000000..23eb50af99c524 --- /dev/null +++ b/recipes/perl-module-corelist/5.20180120/build.sh @@ -0,0 +1,25 @@ +#!/bin/bash + +# If it has Build.PL use that, otherwise use Makefile.PL +if [ -f Build.PL ]; then + perl Build.PL + perl ./Build + perl ./Build test + # Make sure this goes in site + perl ./Build install --installdirs site +elif [ -f Makefile.PL ]; then + # Make sure this goes in site + perl Makefile.PL INSTALLDIRS=site + make + make test + make install +else + echo 'Unable to find Build.PL or Makefile.PL. You need to modify build.sh.' + exit 1 +fi + +# Add more build steps here, if they are necessary. + +# See +# http://docs.continuum.io/conda/build.html +# for a list of environment variables that are set during the build process. diff --git a/recipes/perl-module-corelist/5.20180120/meta.yaml b/recipes/perl-module-corelist/5.20180120/meta.yaml new file mode 100644 index 00000000000000..5ab907c8b34408 --- /dev/null +++ b/recipes/perl-module-corelist/5.20180120/meta.yaml @@ -0,0 +1,41 @@ +{% set name = "perl-module-corelist" %} +{% set version = "5.20180120" %} +{% set sha256 = "9ed9a9f07e262ac7ce982ae36a6277779411ddf5239b9d81cc2fcd5887fc25fc" %} + +package: + name: {{ name }} + version: {{ version }} + +source: + fn: Module-CoreList-5.20180120.tar.gz + url: https://cpan.metacpan.org/authors/id/B/BI/BINGOS/Module-CoreList-5.20180120.tar.gz + sha256: {{ sha256 }} + +build: + number: 0 + +requirements: + build: + - perl >=5.22,<6.0 + - perl-extutils-makemaker + #- perl-version + - perl-test-more + - perl-list-util + + run: + - perl >=5.22,<6.0 + #- perl-version + - perl-test-more + - perl-list-util + +test: + # Perl 'use' tests + imports: + - Module::CoreList + - Module::CoreList::TieHashDelta + - Module::CoreList::Utils + +about: + home: http://dev.perl.org/ + license: perl_5 + summary: 'what modules shipped with versions of perl' diff --git a/recipes/perl-module-extract-use/1.043/build.sh b/recipes/perl-module-extract-use/1.043/build.sh new file mode 100644 index 00000000000000..b6a89e493ff083 --- /dev/null +++ b/recipes/perl-module-extract-use/1.043/build.sh @@ -0,0 +1,18 @@ +#!/bin/bash + +if [ -f Build.PL ]; then + perl Build.PL + perl ./Build + perl ./Build test + # Make sure this goes in site + perl ./Build install --installdirs site +elif [ -f Makefile.PL ]; then + # Make sure this goes in site + perl Makefile.PL INSTALLDIRS=site + make + make test + make install +else + echo 'Unable to find Build.PL or Makefile.PL. You need to modify build.sh.' + exit 1 +fi diff --git a/recipes/perl-module-extract-use/1.043/meta.yaml b/recipes/perl-module-extract-use/1.043/meta.yaml new file mode 100644 index 00000000000000..e637e39f7fe5d8 --- /dev/null +++ b/recipes/perl-module-extract-use/1.043/meta.yaml @@ -0,0 +1,39 @@ +{% set name = "perl-module-extract-use" %} +{% set version = "1.043" %} +{% set sha256 = "44462c5c52c3fe64c89d2beea5942016e97828aed9535dc350ff0f1b65e29e59" %} + +package: + name: {{ name }} + version: {{ version }} + +source: + fn: Module-Extract-Use-1.043.tar.gz + url: https://cpan.metacpan.org/authors/id/B/BD/BDFOY/Module-Extract-Use-1.043.tar.gz + sha256: {{ sha256 }} + +build: + number: 0 + +requirements: + build: + - perl >=5.22,<6.0 + - perl-test-output + - perl-ppi + - perl-extutils-makemaker + - perl-test-more + - perl-pathtools + + run: + - perl >=5.22,<6.0 + - perl-ppi + - perl-pathtools + +test: + imports: + - Module::Extract::Use + #- Module::Extract::Use::Item + +about: + home: https://github.com/briandfoy/module-extract-use + license: artistic_2 + summary: 'Pull out the modules a module explicitly uses' diff --git a/recipes/perl-module-load-conditional/0.68/build.sh b/recipes/perl-module-load-conditional/0.68/build.sh new file mode 100644 index 00000000000000..23eb50af99c524 --- /dev/null +++ b/recipes/perl-module-load-conditional/0.68/build.sh @@ -0,0 +1,25 @@ +#!/bin/bash + +# If it has Build.PL use that, otherwise use Makefile.PL +if [ -f Build.PL ]; then + perl Build.PL + perl ./Build + perl ./Build test + # Make sure this goes in site + perl ./Build install --installdirs site +elif [ -f Makefile.PL ]; then + # Make sure this goes in site + perl Makefile.PL INSTALLDIRS=site + make + make test + make install +else + echo 'Unable to find Build.PL or Makefile.PL. You need to modify build.sh.' + exit 1 +fi + +# Add more build steps here, if they are necessary. + +# See +# http://docs.continuum.io/conda/build.html +# for a list of environment variables that are set during the build process. diff --git a/recipes/perl-module-load-conditional/0.68/meta.yaml b/recipes/perl-module-load-conditional/0.68/meta.yaml new file mode 100644 index 00000000000000..e4c870ce753521 --- /dev/null +++ b/recipes/perl-module-load-conditional/0.68/meta.yaml @@ -0,0 +1,46 @@ +{% set name = "perl-module-load-conditional" %} +{% set version = "0.68" %} +{% set sha256 = "7627b55cd94a2f1a4667f9203e2c990cad015bf34ec6b41b4f73af848f0698fd" %} + +package: + name: {{ name }} + version: {{ version }} + +source: + fn: Module-Load-Conditional-0.68.tar.gz + url: https://cpan.metacpan.org/authors/id/B/BI/BINGOS/Module-Load-Conditional-0.68.tar.gz + sha256: {{ sha256 }} + +build: + number: 0 + +requirements: + build: + - perl >=5.22,<6.0 + - perl-locale-maketext-simple + #- perl-version + - perl-module-corelist + - perl-module-metadata >=1.000005 + - perl-module-load + - perl-params-check + - perl-extutils-makemaker + - perl-test-more + + run: + - perl >=5.22,<6.0 + #- perl-version + - perl-module-corelist + - perl-module-metadata >=1.000005 + - perl-module-load + - perl-params-check + - perl-locale-maketext-simple + +test: + # Perl 'use' tests + imports: + - Module::Load::Conditional + +about: + home: http://metacpan.org/pod/Module::Load::Conditional + license: perl_5 + summary: 'Looking up module information / loading at runtime' diff --git a/recipes/perl-moosex-clone/0.06/build.sh b/recipes/perl-moosex-clone/0.06/build.sh new file mode 100644 index 00000000000000..67918fe672fe6b --- /dev/null +++ b/recipes/perl-moosex-clone/0.06/build.sh @@ -0,0 +1,19 @@ +#!/bin/bash + +# If it has Build.PL use that, otherwise use Makefile.PL +if [ -f Build.PL ]; then + perl Build.PL + perl ./Build + perl ./Build test + # Make sure this goes in site + perl ./Build install --installdirs site +elif [ -f Makefile.PL ]; then + # Make sure this goes in site + perl Makefile.PL INSTALLDIRS=site + make + make test + make install +else + echo 'Unable to find Build.PL or Makefile.PL. You need to modify build.sh.' + exit 1 +fi diff --git a/recipes/perl-moosex-clone/0.06/meta.yaml b/recipes/perl-moosex-clone/0.06/meta.yaml new file mode 100644 index 00000000000000..5a38fc04e0cf11 --- /dev/null +++ b/recipes/perl-moosex-clone/0.06/meta.yaml @@ -0,0 +1,48 @@ +{% set name = "perl-moosex-clone" %} +{% set version = "0.06" %} +{% set sha256 = "cbd7825db9e74b053f524544a014f066fdce290316ebb568f87679181b398da7" %} + +package: + name: {{ name }} + version: {{ version }} + +source: + fn: MooseX-Clone-0.06.tar.gz + url: https://cpan.metacpan.org/authors/id/E/ET/ETHER/MooseX-Clone-0.06.tar.gz + sha256: {{ sha256 }} + +build: + number: 0 + +requirements: + build: + - perl >=5.22,<6.0 + - perl-hash-util-fieldhash-compat + - perl-extutils-makemaker + - perl-module-build-tiny + - perl-data-visitor + - perl-moose + - perl-namespace-autoclean + - perl-carp + + run: + - perl >=5.22,<=6.0 + - perl-hash-util-fieldhash-compat + - perl-data-visitor + - perl-carp + - perl-namespace-autoclean + +test: + imports: + - MooseX::Clone + - MooseX::Clone::Meta::Attribute::Trait::Clone + - MooseX::Clone::Meta::Attribute::Trait::Clone::Base + - MooseX::Clone::Meta::Attribute::Trait::Clone::Std + - MooseX::Clone::Meta::Attribute::Trait::Copy + - MooseX::Clone::Meta::Attribute::Trait::NoClone + - MooseX::Clone::Meta::Attribute::Trait::StorableClone + +about: + home: https://github.com/moose/MooseX-Clone + license: perl_5 + summary: 'Fine-grained cloning support for Moose objects.' diff --git a/recipes/perl-net-ssleay/meta.yaml b/recipes/perl-net-ssleay/meta.yaml index dd04398a3ce4de..919f9a3b0158d0 100644 --- a/recipes/perl-net-ssleay/meta.yaml +++ b/recipes/perl-net-ssleay/meta.yaml @@ -1,36 +1,37 @@ +{% set version = "1.84" %} +{% set sha256 = "823ec3cbb428309d6a9e56f362a9300693ce3215b7fede109adb7be361fff177" %} + package: name: perl-net-ssleay - version: "1.74" + version: {{ version }} source: - fn: Net-SSLeay-1.74.tar.gz - url: https://cpan.metacpan.org/authors/id/M/MI/MIKEM/Net-SSLeay-1.74.tar.gz + fn: Net-SSLeay-{{ version }}.tar.gz + url: https://cpan.metacpan.org/authors/id/M/MI/MIKEM/Net-SSLeay-1.84.tar.gz + sha256: {{ sha256 }} build: number: 0 requirements: build: - - perl-threaded - - gcc + - perl + - perl-mime-base64 + - perl-extutils-makemaker - openssl - - zlib + - zlib {{CONDA_ZLIB}}* run: - - perl-threaded + - perl + - perl-mime-base64 - openssl - - zlib - - libgcc + - zlib {{CONDA_ZLIB}}* test: - # Perl 'use' tests: relying on "run_test.pl" due to version differences - # between the top-level and sub- packages. - - # Additional tests to ensure basic functionality - commands: - - perl -e 'use Net::SSLeay qw(get_https); get_https("www.google.com", 443, "/");' + imports: + - Net::SSLeay about: - home: http://metacpan.org/pod/Net-SSLeay + home: http://metacpan.org/pod/Net::SSLeay license: perl_5 summary: 'Perl extension for using OpenSSL' diff --git a/recipes/perl-params-coerce/0.14/build.sh b/recipes/perl-params-coerce/0.14/build.sh new file mode 100644 index 00000000000000..23eb50af99c524 --- /dev/null +++ b/recipes/perl-params-coerce/0.14/build.sh @@ -0,0 +1,25 @@ +#!/bin/bash + +# If it has Build.PL use that, otherwise use Makefile.PL +if [ -f Build.PL ]; then + perl Build.PL + perl ./Build + perl ./Build test + # Make sure this goes in site + perl ./Build install --installdirs site +elif [ -f Makefile.PL ]; then + # Make sure this goes in site + perl Makefile.PL INSTALLDIRS=site + make + make test + make install +else + echo 'Unable to find Build.PL or Makefile.PL. You need to modify build.sh.' + exit 1 +fi + +# Add more build steps here, if they are necessary. + +# See +# http://docs.continuum.io/conda/build.html +# for a list of environment variables that are set during the build process. diff --git a/recipes/perl-params-coerce/0.14/meta.yaml b/recipes/perl-params-coerce/0.14/meta.yaml new file mode 100644 index 00000000000000..ddc9201cd7f878 --- /dev/null +++ b/recipes/perl-params-coerce/0.14/meta.yaml @@ -0,0 +1,34 @@ +{% set name = "perl-params-coerce" %} +{% set version = "0.14" %} +{% set sha256 = "5c67b11b9859e8d0d048c1c529e16ff49458fe4a98a16ccbfec6cd66e49b7713" %} + +package: + name: {{ name }} + version: {{ version }} + +source: + fn: Params-Coerce-0.14.tar.gz + url: https://cpan.metacpan.org/authors/id/A/AD/ADAMK/Params-Coerce-0.14.tar.gz + sha256: {{ sha256 }} + +build: + number: 0 + +requirements: + build: + - perl >=5.22,<=6.0 + - perl-params-util + + run: + - perl >=5.22,<=6.0 + - perl-params-util + +test: + imports: + - Params::Coerce + +#test: +about: + home: http://metacpan.org/pod/Params::Coerce + license: perl_5 + summary: 'Allows your classes to do coercion of parameters' diff --git a/recipes/perl-pathtools/3.73/build.sh b/recipes/perl-pathtools/3.73/build.sh new file mode 100644 index 00000000000000..23eb50af99c524 --- /dev/null +++ b/recipes/perl-pathtools/3.73/build.sh @@ -0,0 +1,25 @@ +#!/bin/bash + +# If it has Build.PL use that, otherwise use Makefile.PL +if [ -f Build.PL ]; then + perl Build.PL + perl ./Build + perl ./Build test + # Make sure this goes in site + perl ./Build install --installdirs site +elif [ -f Makefile.PL ]; then + # Make sure this goes in site + perl Makefile.PL INSTALLDIRS=site + make + make test + make install +else + echo 'Unable to find Build.PL or Makefile.PL. You need to modify build.sh.' + exit 1 +fi + +# Add more build steps here, if they are necessary. + +# See +# http://docs.continuum.io/conda/build.html +# for a list of environment variables that are set during the build process. diff --git a/recipes/perl-pathtools/3.73/meta.yaml b/recipes/perl-pathtools/3.73/meta.yaml new file mode 100644 index 00000000000000..b22146263ed42c --- /dev/null +++ b/recipes/perl-pathtools/3.73/meta.yaml @@ -0,0 +1,41 @@ +{% set name = "perl-pathtools" %} +{% set version = "3.73" %} +{% set sha256 = "c1eadef2eab07ff7ceb5a5b6bc12a6db51e376093942d1960c07c280984161d3" %} + +package: + name: {{ name }} + version: {{ version }} + +source: + fn: PathTools-3.73.tar.gz + url: https://cpan.metacpan.org/authors/id/X/XS/XSAWYERX/PathTools-3.73.tar.gz + sha256: {{ sha256 }} + +build: + number: 0 + +requirements: + build: + - perl >=5.22,<6.0 + - perl-extutils-makemaker + - perl-carp + - perl-test-more + #- perl-scalar-util + #- perl-file-basename + + run: + - perl >=5.22,<6.0 + - perl-carp + - perl-test-more + #- perl-scalar-util + #- perl-file-basename + +test: + # Perl 'use' tests + imports: + - File::Spec::Functions + +about: + home: http://dev.perl.org/ + license: perl_5 + summary: 'Tools for working with directory and file names' diff --git a/recipes/perl-pathtools/meta.yaml b/recipes/perl-pathtools/meta.yaml deleted file mode 100644 index 7d3145b18d3988..00000000000000 --- a/recipes/perl-pathtools/meta.yaml +++ /dev/null @@ -1,41 +0,0 @@ -package: - name: perl-pathtools - version: 3.40 - -source: - fn: PathTools-3.40.tar.gz - url: http://cpan.metacpan.org/authors/id/S/SM/SMUELLER/PathTools-3.40.tar.gz - md5: 7da19c34dc2d1017cbb675a6ff4fe283 - -build: - number: 0 - -requirements: - build: - - perl-threaded - - perl-extutils-makemaker - - perl-scalar-list-utils - - run: - - perl-threaded - - perl-scalar-list-utils - -test: - # Perl 'use' tests - # imports: - - # You can also put a file called run_test.pl (or run_test.py) in the recipe - # that will be run at test time. - - # requires: - # Put any additional test requirements here. For example - # - nose - -about: - home: http://metacpan.org/pod/PathTools - license: unknown - summary: 'get pathname of current working directory' - -# See -# http://docs.continuum.io/conda/build.html for -# more information about meta.yaml diff --git a/recipes/perl-perlio-gzip/meta.yaml b/recipes/perl-perlio-gzip/meta.yaml index 70ce23f2db0c4b..9ddf4b047f39be 100644 --- a/recipes/perl-perlio-gzip/meta.yaml +++ b/recipes/perl-perlio-gzip/meta.yaml @@ -8,16 +8,16 @@ source: md5: "dbcfc1450f6b593b65048b8ced061c98" build: - number: 1 + number: 2 requirements: build: - perl - - zlib + - zlib {{CONDA_ZLIB}}* run: - perl - - zlib + - zlib {{CONDA_ZLIB}}* test: imports: diff --git a/recipes/perl-ppi/1.236/build.sh b/recipes/perl-ppi/1.236/build.sh new file mode 100644 index 00000000000000..67918fe672fe6b --- /dev/null +++ b/recipes/perl-ppi/1.236/build.sh @@ -0,0 +1,19 @@ +#!/bin/bash + +# If it has Build.PL use that, otherwise use Makefile.PL +if [ -f Build.PL ]; then + perl Build.PL + perl ./Build + perl ./Build test + # Make sure this goes in site + perl ./Build install --installdirs site +elif [ -f Makefile.PL ]; then + # Make sure this goes in site + perl Makefile.PL INSTALLDIRS=site + make + make test + make install +else + echo 'Unable to find Build.PL or Makefile.PL. You need to modify build.sh.' + exit 1 +fi diff --git a/recipes/perl-ppi/1.236/meta.yaml b/recipes/perl-ppi/1.236/meta.yaml new file mode 100644 index 00000000000000..cf7a554acb6d48 --- /dev/null +++ b/recipes/perl-ppi/1.236/meta.yaml @@ -0,0 +1,148 @@ +{% set name = "perl-ppi" %} +{% set version = "1.236" %} +{% set sha256 = "c6674b349c0b7d9a6d668e789a5e5215477d88ed4c8203aa69a2a50085308aec" %} + +package: + name: {{ name }} + version: {{ version }} + +source: + fn: PPI-1.236.tar.gz + url: https://cpan.metacpan.org/authors/id/M/MI/MITHALDU/PPI-1.236.tar.gz + sha256: {{ sha256 }} + +build: + number: 0 + +requirements: + build: + - perl >=5.22,<6.0 + - perl-class-inspector + - perl-clone + - perl-test-deep + - perl-test-object + - perl-extutils-makemaker + - perl-file-remove + - perl-params-util + - perl-test-subcalls + - perl-io-string + - perl-digest-md5 + - perl-list-moreutils + - perl-task-weaken + - perl-list-util + - perl-file-spec + - perl-test-more + - perl-hook-lexwrap + - perl-class-xsaccessor + + run: + - perl >=5.22,<6.0 + - perl-clone + - perl-params-util + - perl-io-string + - perl-digest-md5 + - perl-list-moreutils + - perl-task-weaken + - perl-list-util + - perl-file-spec + - perl-hook-lexwrap + - perl-class-xsaccessor + +test: + # Perl 'use' tests + imports: + - PPI + - PPI::Cache + - PPI::Document + - PPI::Document::File + - PPI::Document::Fragment + - PPI::Document::Normalized + - PPI::Dumper + - PPI::Element + - PPI::Exception + - PPI::Exception::ParserRejection + - PPI::Find + - PPI::Lexer + - PPI::Node + - PPI::Normal + - PPI::Normal::Standard + - PPI::Statement + - PPI::Statement::Break + - PPI::Statement::Compound + - PPI::Statement::Data + - PPI::Statement::End + - PPI::Statement::Expression + - PPI::Statement::Given + - PPI::Statement::Include + - PPI::Statement::Include::Perl6 + - PPI::Statement::Null + - PPI::Statement::Package + - PPI::Statement::Scheduled + - PPI::Statement::Sub + - PPI::Statement::Unknown + - PPI::Statement::UnmatchedBrace + - PPI::Statement::Variable + - PPI::Statement::When + - PPI::Structure + - PPI::Structure::Block + - PPI::Structure::Condition + - PPI::Structure::Constructor + - PPI::Structure::For + - PPI::Structure::Given + - PPI::Structure::List + - PPI::Structure::Subscript + - PPI::Structure::Unknown + - PPI::Structure::When + - PPI::Token + - PPI::Token::ArrayIndex + - PPI::Token::Attribute + - PPI::Token::BOM + - PPI::Token::Cast + - PPI::Token::Comment + - PPI::Token::DashedWord + - PPI::Token::Data + - PPI::Token::End + - PPI::Token::HereDoc + - PPI::Token::Label + - PPI::Token::Magic + - PPI::Token::Number + - PPI::Token::Number::Binary + - PPI::Token::Number::Exp + - PPI::Token::Number::Float + - PPI::Token::Number::Hex + - PPI::Token::Number::Octal + - PPI::Token::Number::Version + - PPI::Token::Operator + - PPI::Token::Pod + - PPI::Token::Prototype + - PPI::Token::Quote + - PPI::Token::Quote::Double + - PPI::Token::Quote::Interpolate + - PPI::Token::Quote::Literal + - PPI::Token::Quote::Single + - PPI::Token::QuoteLike + - PPI::Token::QuoteLike::Backtick + - PPI::Token::QuoteLike::Command + - PPI::Token::QuoteLike::Readline + - PPI::Token::QuoteLike::Regexp + - PPI::Token::QuoteLike::Words + - PPI::Token::Regexp + - PPI::Token::Regexp::Match + - PPI::Token::Regexp::Substitute + - PPI::Token::Regexp::Transliterate + - PPI::Token::Separator + - PPI::Token::Structure + - PPI::Token::Symbol + - PPI::Token::Unknown + - PPI::Token::Whitespace + - PPI::Token::Word + - PPI::Tokenizer + - PPI::Transform + - PPI::Transform::UpdateCopyright + - PPI::Util + - PPI::XSAccessor + +about: + home: https://github.com/adamkennedy/PPI + license: perl_5 + summary: 'Parse, Analyze and Manipulate Perl (without perl)' diff --git a/recipes/perl-test-file-contents/0.23/build.sh b/recipes/perl-test-file-contents/0.23/build.sh new file mode 100644 index 00000000000000..23eb50af99c524 --- /dev/null +++ b/recipes/perl-test-file-contents/0.23/build.sh @@ -0,0 +1,25 @@ +#!/bin/bash + +# If it has Build.PL use that, otherwise use Makefile.PL +if [ -f Build.PL ]; then + perl Build.PL + perl ./Build + perl ./Build test + # Make sure this goes in site + perl ./Build install --installdirs site +elif [ -f Makefile.PL ]; then + # Make sure this goes in site + perl Makefile.PL INSTALLDIRS=site + make + make test + make install +else + echo 'Unable to find Build.PL or Makefile.PL. You need to modify build.sh.' + exit 1 +fi + +# Add more build steps here, if they are necessary. + +# See +# http://docs.continuum.io/conda/build.html +# for a list of environment variables that are set during the build process. diff --git a/recipes/perl-test-file-contents/0.23/meta.yaml b/recipes/perl-test-file-contents/0.23/meta.yaml new file mode 100644 index 00000000000000..8572c2b18cdde9 --- /dev/null +++ b/recipes/perl-test-file-contents/0.23/meta.yaml @@ -0,0 +1,44 @@ +{% set name = "perl-test-file-contents" %} +{% set version = "0.23" %} +{% set sha256 = "cd6fadfb910b34b4b53991ff231dad99929ca8850abec3ad0e2810c4bd7b1f3d" %} + +package: + name: {{ name }} + version: {{ version }} + +source: + fn: Test-File-Contents-0.23.tar.gz + url: https://cpan.metacpan.org/authors/id/D/DW/DWHEELER/Test-File-Contents-0.23.tar.gz + sha256: {{ sha256 }} + +build: + number: 0 + +requirements: + build: + - perl >=5.22,<6.0 + - perl-text-diff + - perl-module-build + - perl-digest-md5 + - perl-file-spec + - perl-test-more + - perl-test-pod + - perl-test-pod-coverage + + run: + - perl >=5.22,<6.0 + - perl-text-diff + - perl-digest-md5 + - perl-file-spec + - perl-test-pod + - perl-test-pod-coverage + +test: + # Perl 'use' tests + imports: + - Test::File::Contents + +about: + home: http://search.cpan.org/dist/Test-File-Contents/ + license: perl_5 + summary: 'Test routines for examining the contents of files' diff --git a/recipes/perl-test-object/0.08/build.sh b/recipes/perl-test-object/0.08/build.sh new file mode 100644 index 00000000000000..23eb50af99c524 --- /dev/null +++ b/recipes/perl-test-object/0.08/build.sh @@ -0,0 +1,25 @@ +#!/bin/bash + +# If it has Build.PL use that, otherwise use Makefile.PL +if [ -f Build.PL ]; then + perl Build.PL + perl ./Build + perl ./Build test + # Make sure this goes in site + perl ./Build install --installdirs site +elif [ -f Makefile.PL ]; then + # Make sure this goes in site + perl Makefile.PL INSTALLDIRS=site + make + make test + make install +else + echo 'Unable to find Build.PL or Makefile.PL. You need to modify build.sh.' + exit 1 +fi + +# Add more build steps here, if they are necessary. + +# See +# http://docs.continuum.io/conda/build.html +# for a list of environment variables that are set during the build process. diff --git a/recipes/perl-test-object/0.08/meta.yaml b/recipes/perl-test-object/0.08/meta.yaml new file mode 100644 index 00000000000000..f94743402417e0 --- /dev/null +++ b/recipes/perl-test-object/0.08/meta.yaml @@ -0,0 +1,43 @@ +{% set name = "perl-test-object" %} +{% set version = "0.08" %} +{% set sha256 = "65278964147837313f4108e55b59676e8a364d6edf01b3dc198aee894ab1d0bb" %} + +package: + name: {{ name }} + version: {{ version }} + +source: + fn: Test-Object-0.08.tar.gz + url: https://cpan.metacpan.org/authors/id/E/ET/ETHER/Test-Object-0.08.tar.gz + sha256: {{ sha256 }} + +build: + number: 0 + +requirements: + build: + - perl >=5.22,<6.0 + - perl-carp + - perl-extutils-makemaker + - perl-test-builder-tester + #- perl-overload + #- perl-file-spec-functions + - perl-test-more + + run: + - perl >=5.22,<6.0 + - perl-exporter + - perl-carp + #- perl-overload + - perl-test-more + +test: + # Perl 'use' tests + imports: + - Test::Object + - Test::Object::Test + +about: + home: https://github.com/karenetheridge/Test-Object + license: perl_5 + summary: 'Thoroughly testing objects via registered handlers' diff --git a/recipes/perl-test-prereq/2.002/build.sh b/recipes/perl-test-prereq/2.002/build.sh new file mode 100644 index 00000000000000..23eb50af99c524 --- /dev/null +++ b/recipes/perl-test-prereq/2.002/build.sh @@ -0,0 +1,25 @@ +#!/bin/bash + +# If it has Build.PL use that, otherwise use Makefile.PL +if [ -f Build.PL ]; then + perl Build.PL + perl ./Build + perl ./Build test + # Make sure this goes in site + perl ./Build install --installdirs site +elif [ -f Makefile.PL ]; then + # Make sure this goes in site + perl Makefile.PL INSTALLDIRS=site + make + make test + make install +else + echo 'Unable to find Build.PL or Makefile.PL. You need to modify build.sh.' + exit 1 +fi + +# Add more build steps here, if they are necessary. + +# See +# http://docs.continuum.io/conda/build.html +# for a list of environment variables that are set during the build process. diff --git a/recipes/perl-test-prereq/2.002/meta.yaml b/recipes/perl-test-prereq/2.002/meta.yaml new file mode 100644 index 00000000000000..fdfb96abc1cfdb --- /dev/null +++ b/recipes/perl-test-prereq/2.002/meta.yaml @@ -0,0 +1,45 @@ +{% set name = "perl-test-prereq" %} +{% set version = "2.002" %} +{% set sha256 = "a1353cbb7691dd33d233f4f6f970c99b025e0fde10b52f47274b9dec8b1b47cf" %} + +package: + name: {{ name }} + version: {{ version }} + +source: + fn: Test-Prereq-2.002.tar.gz + url: https://cpan.metacpan.org/authors/id/B/BD/BDFOY/Test-Prereq-2.002.tar.gz + sha256: {{ sha256 }} + +build: + number: 0 + +requirements: + build: + - perl >=5.22,<6.0 + - perl-test-builder-tester + - perl-parent + - perl-module-build + - perl-module-extract-use + - perl-carp + - perl-extutils-makemaker + - perl-file-find + + run: + - perl >=5.22,<6.0 + - perl-module-extract-use + - perl-carp + - perl-parent + - perl-module-build + - perl-lib + - perl-file-find + +test: + imports: + - Test::Prereq + - Test::Prereq::Build + +about: + home: https://github.com/briandfoy/test-prereq + license: artistic_2 + summary: 'check if Makefile.PL has the right pre-requisites' diff --git a/recipes/perl-test-subcalls/1.10/build.sh b/recipes/perl-test-subcalls/1.10/build.sh new file mode 100644 index 00000000000000..23eb50af99c524 --- /dev/null +++ b/recipes/perl-test-subcalls/1.10/build.sh @@ -0,0 +1,25 @@ +#!/bin/bash + +# If it has Build.PL use that, otherwise use Makefile.PL +if [ -f Build.PL ]; then + perl Build.PL + perl ./Build + perl ./Build test + # Make sure this goes in site + perl ./Build install --installdirs site +elif [ -f Makefile.PL ]; then + # Make sure this goes in site + perl Makefile.PL INSTALLDIRS=site + make + make test + make install +else + echo 'Unable to find Build.PL or Makefile.PL. You need to modify build.sh.' + exit 1 +fi + +# Add more build steps here, if they are necessary. + +# See +# http://docs.continuum.io/conda/build.html +# for a list of environment variables that are set during the build process. diff --git a/recipes/perl-test-subcalls/1.10/meta.yaml b/recipes/perl-test-subcalls/1.10/meta.yaml new file mode 100644 index 00000000000000..f263445ac7a3fc --- /dev/null +++ b/recipes/perl-test-subcalls/1.10/meta.yaml @@ -0,0 +1,43 @@ +{% set name = "perl-test-subcalls" %} +{% set version = "1.10" %} +{% set sha256 = "cbc1e9b35a05e71febc13e5ef547a31c8249899bb6011dbdc9d9ff366ddab6c2" %} + +package: + name: {{ name }} + version: {{ version }} + +source: + fn: Test-SubCalls-1.10.tar.gz + url: https://cpan.metacpan.org/authors/id/E/ET/ETHER/Test-SubCalls-1.10.tar.gz + sha256: {{ sha256 }} + +build: + number: 0 + +requirements: + build: + - perl >=5.22,<6.0 + - perl-extutils-makemaker + - perl-file-spec >=0.80 + - perl-test-builder-tester + - perl-test-more >=0.42 + - perl-pathtools + - perl-hook-lexwrap + + run: + - perl >=5.22,<6.0 + - perl-pathtools + - perl-test-more >=0.42 + - perl-file-spec >=0.80 + - perl-test-builder-tester + - perl-hook-lexwrap + +test: + # Perl 'use' tests + imports: + - Test::SubCalls + +about: + home: http://dev.perl.org/ + license: perl_5 + summary: 'Track the number of times subs are called' diff --git a/recipes/perl-tie-refhash-weak/0.09/build.sh b/recipes/perl-tie-refhash-weak/0.09/build.sh new file mode 100644 index 00000000000000..23eb50af99c524 --- /dev/null +++ b/recipes/perl-tie-refhash-weak/0.09/build.sh @@ -0,0 +1,25 @@ +#!/bin/bash + +# If it has Build.PL use that, otherwise use Makefile.PL +if [ -f Build.PL ]; then + perl Build.PL + perl ./Build + perl ./Build test + # Make sure this goes in site + perl ./Build install --installdirs site +elif [ -f Makefile.PL ]; then + # Make sure this goes in site + perl Makefile.PL INSTALLDIRS=site + make + make test + make install +else + echo 'Unable to find Build.PL or Makefile.PL. You need to modify build.sh.' + exit 1 +fi + +# Add more build steps here, if they are necessary. + +# See +# http://docs.continuum.io/conda/build.html +# for a list of environment variables that are set during the build process. diff --git a/recipes/perl-tie-refhash-weak/0.09/meta.yaml b/recipes/perl-tie-refhash-weak/0.09/meta.yaml new file mode 100644 index 00000000000000..ed4e45b1bb3f46 --- /dev/null +++ b/recipes/perl-tie-refhash-weak/0.09/meta.yaml @@ -0,0 +1,49 @@ +{% set name = "perl-tie-refhash-weak" %} +{% set version = "0.09" %} +{% set sha256 = "bcb4fb2b7575e4caec320577e21e500b0f3ad29fede380d5b54bb84543e76988" %} + +package: + name: {{ name }} + version: {{ version }} + +source: + fn: Tie-RefHash-Weak-0.09.tar.gz + url: https://cpan.metacpan.org/authors/id/N/NU/NUFFIN/Tie-RefHash-Weak-0.09.tar.gz + sha256: {{ sha256 }} + +# If this is a new build for the same version, increment the build +# number. If you do not include this key, it defaults to 0. +build: + number: 0 + +requirements: + build: + - perl >5.22,<6.0 + - perl-tie-refhash + - perl-variable-magic + - perl-task-weaken + #- perl-scalar-util + + run: + - perl >5.22,<6.0 + - perl-tie-refhash + - perl-variable-magic + - perl-task-weaken + #- perl-scalar-util + +test: + #perl -MTie::RefHash::Weak -e 'print "hello world\n"' + imports: + - Tie::RefHash::Weak + + # You can also put a file called run_test.pl (or run_test.py) in the recipe + # that will be run at test time. + +about: + home: http://metacpan.org/pod/Tie::RefHash::Weak + license: unknown + summary: 'A Tie::RefHash subclass with weakened references in the keys.' + +# See +# http://docs.continuum.io/conda/build.html for +# more information about meta.yaml diff --git a/recipes/perl-tie-refhash/1.39/build.sh b/recipes/perl-tie-refhash/1.39/build.sh new file mode 100644 index 00000000000000..23eb50af99c524 --- /dev/null +++ b/recipes/perl-tie-refhash/1.39/build.sh @@ -0,0 +1,25 @@ +#!/bin/bash + +# If it has Build.PL use that, otherwise use Makefile.PL +if [ -f Build.PL ]; then + perl Build.PL + perl ./Build + perl ./Build test + # Make sure this goes in site + perl ./Build install --installdirs site +elif [ -f Makefile.PL ]; then + # Make sure this goes in site + perl Makefile.PL INSTALLDIRS=site + make + make test + make install +else + echo 'Unable to find Build.PL or Makefile.PL. You need to modify build.sh.' + exit 1 +fi + +# Add more build steps here, if they are necessary. + +# See +# http://docs.continuum.io/conda/build.html +# for a list of environment variables that are set during the build process. diff --git a/recipes/perl-tie-refhash/1.39/meta.yaml b/recipes/perl-tie-refhash/1.39/meta.yaml new file mode 100644 index 00000000000000..c3c8debeb52dc9 --- /dev/null +++ b/recipes/perl-tie-refhash/1.39/meta.yaml @@ -0,0 +1,33 @@ +{% set name = "perl-tie-refhash" %} +{% set version = "1.39" %} +{% set sha256 = "b0b80ef571e7dadb726b8214f7352a932a8fa82af29072895aa1aadc89f48bec" %} + +package: + name: {{ name }} + version: {{ version }} + +source: + fn: Tie-RefHash-1.39.tar.gz + url: https://cpan.metacpan.org/authors/id/F/FL/FLORA/Tie-RefHash-1.39.tar.gz + sha256: {{ sha256 }} + +build: + number: 0 + +requirements: + build: + - perl >5.22,<6.0 + - perl-extutils-makemaker + + run: + - perl >5.22,<6.0 + +test: + imports: + - Tie::RefHash + #- Tie::RefHash::Nestable + +about: + home: http://metacpan.org/pod/Tie::RefHash + license: perl_5 + summary: 'use references as hash keys' diff --git a/recipes/perl-tie-toobject/0.03/build.sh b/recipes/perl-tie-toobject/0.03/build.sh new file mode 100644 index 00000000000000..23eb50af99c524 --- /dev/null +++ b/recipes/perl-tie-toobject/0.03/build.sh @@ -0,0 +1,25 @@ +#!/bin/bash + +# If it has Build.PL use that, otherwise use Makefile.PL +if [ -f Build.PL ]; then + perl Build.PL + perl ./Build + perl ./Build test + # Make sure this goes in site + perl ./Build install --installdirs site +elif [ -f Makefile.PL ]; then + # Make sure this goes in site + perl Makefile.PL INSTALLDIRS=site + make + make test + make install +else + echo 'Unable to find Build.PL or Makefile.PL. You need to modify build.sh.' + exit 1 +fi + +# Add more build steps here, if they are necessary. + +# See +# http://docs.continuum.io/conda/build.html +# for a list of environment variables that are set during the build process. diff --git a/recipes/perl-tie-toobject/0.03/meta.yaml b/recipes/perl-tie-toobject/0.03/meta.yaml new file mode 100644 index 00000000000000..c4bb6a84574456 --- /dev/null +++ b/recipes/perl-tie-toobject/0.03/meta.yaml @@ -0,0 +1,35 @@ +{% set name = "perl-tie-toobject" %} +{% set version = "0.03" %} +{% set sha256 = "a31a0d4430fe14f59622f31db7f25b2275dad2ec52f1040beb030d3e83ad3af4" %} + +package: + name: {{ name }} + version: {{ version }} + +source: + fn: Tie-ToObject-0.03.tar.gz + url: https://cpan.metacpan.org/authors/id/N/NU/NUFFIN/Tie-ToObject-0.03.tar.gz + sha256: {{ sha256 }} + +build: + number: 0 + +requirements: + build: + - perl >5.22,<6.0 + - perl-tie-refhash + - perl-test-more + + run: + - perl >5.22,<6.0 + - perl-tie-refhash + - perl-test-more + +test: + imports: + - Tie::ToObject + +about: + home: http://metacpan.org/pod/Tie::ToObject + license: perl_5 + summary: 'Tie to an existing object.' diff --git a/recipes/perl-yaml/1.24/build.sh b/recipes/perl-yaml/1.24/build.sh new file mode 100644 index 00000000000000..23eb50af99c524 --- /dev/null +++ b/recipes/perl-yaml/1.24/build.sh @@ -0,0 +1,25 @@ +#!/bin/bash + +# If it has Build.PL use that, otherwise use Makefile.PL +if [ -f Build.PL ]; then + perl Build.PL + perl ./Build + perl ./Build test + # Make sure this goes in site + perl ./Build install --installdirs site +elif [ -f Makefile.PL ]; then + # Make sure this goes in site + perl Makefile.PL INSTALLDIRS=site + make + make test + make install +else + echo 'Unable to find Build.PL or Makefile.PL. You need to modify build.sh.' + exit 1 +fi + +# Add more build steps here, if they are necessary. + +# See +# http://docs.continuum.io/conda/build.html +# for a list of environment variables that are set during the build process. diff --git a/recipes/perl-yaml/1.24/meta.yaml b/recipes/perl-yaml/1.24/meta.yaml new file mode 100644 index 00000000000000..f0cdbd75b4d39e --- /dev/null +++ b/recipes/perl-yaml/1.24/meta.yaml @@ -0,0 +1,34 @@ +{% set name = "perl-yaml" %} +{% set version = "1.24" %} +{% set sha256 = "b58d045a72a5e1ce714f1d42b64ccddbb055a4afac10b74972dba3b6a47dffb6" %} + +package: + name: {{ name }} + version: {{ version }} + +source: + fn: YAML-1.24.tar.gz + url: https://cpan.metacpan.org/authors/id/T/TI/TINITA/YAML-1.24.tar.gz + sha256: {{ sha256 }} + +build: + number: 0 + +requirements: + build: + - perl >=5.22,<6.0 + - perl-extutils-makemaker + - perl-test-yaml + - perl-test-more + + run: + - perl >=5.22,<6.0 + +test: + impprts: + - YAML + +about: + home: https://github.com/ingydotnet/yaml-pm + license: perl_5 + summary: "YAML Ain't Markup Language™" diff --git a/recipes/perl-yaml/meta.yaml b/recipes/perl-yaml/meta.yaml index 5c8de0662ff3b0..c0ba8b7018b934 100644 --- a/recipes/perl-yaml/meta.yaml +++ b/recipes/perl-yaml/meta.yaml @@ -8,19 +8,19 @@ source: md5: 79b6cc821fe157790a6448d1f791f6de build: - number: 0 + number: 1 requirements: build: - - perl-threaded + - perl >=5.22,<6.0 - perl-test-yaml run: - - perl-threaded + - perl >=5.22,<6.0 test: - # Perl 'use' tests: relying on "run_test.pl" due to version differences - # between the top-level and sub- packages. + includes: + - YAML about: home: https://github.com/ingydotnet/yaml-pm diff --git a/recipes/picard/meta.yaml b/recipes/picard/meta.yaml index 84e7c1837a39f7..0e9a1580b05462 100644 --- a/recipes/picard/meta.yaml +++ b/recipes/picard/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "2.17.8" %} +{% set version = "2.17.10" %} package: name: picard @@ -7,7 +7,7 @@ package: source: fn: picard.jar url: https://github.com/broadinstitute/picard/releases/download/{{ version }}/picard.jar - sha256: 9f7c8a8d29ac3b34e33ad2223906e0068786d2dfc7806050158586f3b6bff07a + sha256: 0f122bbba593099f72fe9cf74689ba130d0c7b02daaf9f63edd518cdee55c951 build: number: 0 diff --git a/recipes/pileometh/meta.yaml b/recipes/pileometh/meta.yaml index 0021d6890931fd..3721a1b33185e5 100644 --- a/recipes/pileometh/meta.yaml +++ b/recipes/pileometh/meta.yaml @@ -3,20 +3,20 @@ package: version: "0.1.13" build: - number: 0 + number: 1 skip: False source: fn: PileOMeth-0.1.13.tar.gz - sha256: 9f70f847223ebf3bd074553928a4097fa9a6db5cdc5e7632b2062c96edb3c6a8 + sha256: 82230a54632bb62bc52791ff868ed7e1fd413982e97a7f1f245b3770224c5503 url: https://github.com/dpryan79/PileOMeth/archive/0.1.13.tar.gz requirements: build: - - zlib + - zlib {{CONDA_ZLIB}}* - gcc run: - - zlib + - zlib {{CONDA_ZLIB}}* test: commands: diff --git a/recipes/pindel/meta.yaml b/recipes/pindel/meta.yaml index 818f264cea5828..31d452734b0a04 100644 --- a/recipes/pindel/meta.yaml +++ b/recipes/pindel/meta.yaml @@ -6,7 +6,7 @@ package: version: {{ version }} build: - number: 0 + number: 1 skip: True # [osx] string: "htslib{{CONDA_HTSLIB}}_{{PKG_BUILDNUM}}" diff --git a/recipes/piranha/meta.yaml b/recipes/piranha/meta.yaml index 586a1a0a453593..397502e1261d70 100644 --- a/recipes/piranha/meta.yaml +++ b/recipes/piranha/meta.yaml @@ -2,9 +2,11 @@ about: home: 'http://smithlabresearch.org/software/piranha/' license: 'GNU General Public License v3 (GPLv3)' summary: 'Piranha is a peak-caller for CLIP- and RIP-Seq data.' + package: name: "piranha" version: '1.2.1' + source: fn: piranha-1.2.1.tar.gz url: http://smithlabresearch.org/downloads/piranha-1.2.1.tar.gz @@ -12,9 +14,10 @@ source: patches: - 0001-compile-with-conda-gsl-patch.patch build: - number: 2 + number: 3 skip: True # [not py27 or osx] - string: gsl{{CONDA_GSL}}_{{PKG_BUILDNUM}} + string: gsl{{CONDA_GSL}}_bamtools{{CONDA_BAMTOOLS}}_{{PKG_BUILDNUM}} + requirements: build: - autoconf @@ -22,12 +25,13 @@ requirements: - llvm # [osx] - gawk - python - - bamtools + - bamtools {{ CONDA_BAMTOOLS }}* - gsl {{CONDA_GSL}}* run: - libgcc # [linux] - - bamtools + - bamtools {{ CONDA_BAMTOOLS }}* - gsl {{CONDA_GSL}}* + test: commands: - 'Piranha 2>&1 | grep "^Usage"' diff --git a/recipes/plastid/meta.yaml b/recipes/plastid/meta.yaml index be61e8779a702c..206fb3b8388b6e 100644 --- a/recipes/plastid/meta.yaml +++ b/recipes/plastid/meta.yaml @@ -7,7 +7,7 @@ source: md5: 1a1c750b9081d46fa688cf8fcbaa2ad3 build: - number: 0 + number: 1 requirements: build: @@ -23,7 +23,7 @@ requirements: - matplotlib >=1.4.0 - biopython >=1.64 - twobitreader >=3.0.0 - - zlib + - zlib {{CONDA_ZLIB}}* - gcc # [not osx] - llvm # [osx] @@ -40,7 +40,7 @@ requirements: - matplotlib >=1.4.0 - biopython >=1.64 - twobitreader >=3.0.0 - - zlib + - zlib {{CONDA_ZLIB}}* - bowtie - ucsc-bedtobigbed - fastx_toolkit diff --git a/recipes/platypus-variant/meta.yaml b/recipes/platypus-variant/meta.yaml index 1e713d48698af5..329c3b003b01dd 100644 --- a/recipes/platypus-variant/meta.yaml +++ b/recipes/platypus-variant/meta.yaml @@ -7,7 +7,7 @@ package: name: platypus-variant version: {{ version }} build: - number: 0 + number: 1 skip: True # [not py27] string: "htslib{{CONDA_HTSLIB}}_{{PKG_BUILDNUM}}" source: diff --git a/recipes/plink/meta.yaml b/recipes/plink/meta.yaml index 2c91f7926c9a94..78faff418f9cdb 100644 --- a/recipes/plink/meta.yaml +++ b/recipes/plink/meta.yaml @@ -9,16 +9,19 @@ source: sha1: 9f41c77daa84c365aa659adf0619197fde1337bf sha256: af7bfa27bb303f9bf19b15d4a99e5e8f85de76013b54c05f3479385830598b4d +build: + number: 1 + requirements: build: - gcc # [not osx] - llvm # [osx] - openblas # [not osx] - - zlib + - zlib {{CONDA_ZLIB}}* run: - libgcc # [not osx] - openblas # [not osx] - - zlib + - zlib {{CONDA_ZLIB}}* test: commands: diff --git a/recipes/preseq/meta.yaml b/recipes/preseq/meta.yaml index 6e661caf68d2b3..c57b78d6bea5e7 100644 --- a/recipes/preseq/meta.yaml +++ b/recipes/preseq/meta.yaml @@ -10,19 +10,18 @@ source: - makefile.patch build: - number: 0 + number: 1 string: "gsl{{CONDA_GSL}}_{{PKG_BUILDNUM}}" requirements: build: - - gcc # [not osx] - - llvm # [osx] - - zlib + - gcc + - zlib {{CONDA_ZLIB}}* - gsl {{CONDA_GSL}}* run: - - libgcc # [not osx] - - zlib + - libgcc + - zlib {{CONDA_ZLIB}}* - gsl {{CONDA_GSL}}* test: diff --git a/recipes/prophyle/0.1.0/meta.yaml b/recipes/prophyle/0.1.0/meta.yaml index f3a820cee3297f..d0ca2667b233fd 100644 --- a/recipes/prophyle/0.1.0/meta.yaml +++ b/recipes/prophyle/0.1.0/meta.yaml @@ -11,7 +11,7 @@ source: sha256: {{ sha256 }} build: - number: 0 + number: 1 skip: True # [py27] script: python setup.py install diff --git a/recipes/prophyle/0.2.0/meta.yaml b/recipes/prophyle/0.2.0/meta.yaml index ae255c8ea73947..4f4eb7be2b1e2a 100644 --- a/recipes/prophyle/0.2.0/meta.yaml +++ b/recipes/prophyle/0.2.0/meta.yaml @@ -11,7 +11,7 @@ source: sha256: {{ sha256 }} build: - number: 0 + number: 1 skip: True # [py27] script: $PYTHON setup.py install --single-version-externally-managed --record=record.txt diff --git a/recipes/prophyle/0.2.1/meta.yaml b/recipes/prophyle/0.2.1/meta.yaml index daa7a94e26a61e..49af1b09cffe2a 100644 --- a/recipes/prophyle/0.2.1/meta.yaml +++ b/recipes/prophyle/0.2.1/meta.yaml @@ -11,7 +11,7 @@ source: sha256: {{ sha256 }} build: - number: 0 + number: 1 skip: True # [py27] script: entry_points: diff --git a/recipes/prophyle/0.3.0/meta.yaml b/recipes/prophyle/0.3.0/meta.yaml index 97991afb2e95d2..88aabc178c9cc3 100644 --- a/recipes/prophyle/0.3.0/meta.yaml +++ b/recipes/prophyle/0.3.0/meta.yaml @@ -11,7 +11,7 @@ source: sha256: {{ sha256 }} build: - number: 1 + number: 2 skip: True # [py27] script: entry_points: diff --git a/recipes/prophyle/meta.yaml b/recipes/prophyle/meta.yaml index d1edb23199992b..786258db12e8c8 100644 --- a/recipes/prophyle/meta.yaml +++ b/recipes/prophyle/meta.yaml @@ -11,7 +11,7 @@ source: sha256: {{ sha256 }} build: - number: 1 + number: 2 skip: True # [py27] script: entry_points: diff --git a/recipes/prosic/meta.yaml b/recipes/prosic/meta.yaml index 754d5c403d401f..5e747aa88dad4e 100644 --- a/recipes/prosic/meta.yaml +++ b/recipes/prosic/meta.yaml @@ -5,7 +5,7 @@ package: version: {{ version }} build: - number: 0 + number: 1 string: "gsl{{CONDA_GSL}}_{{PKG_BUILDNUM}}" source: @@ -19,11 +19,11 @@ requirements: - gcc 4.8.2* # work around broken 4.8.5 - rust >=1.12 - gsl {{CONDA_GSL}}* - - zlib + - zlib {{CONDA_ZLIB}}* run: - gsl {{CONDA_GSL}}* - libgcc - - zlib + - zlib {{CONDA_ZLIB}}* test: commands: diff --git a/recipes/prosolo/build.sh b/recipes/prosolo/build.sh index b104052355566c..7dfbd2f05df46d 100644 --- a/recipes/prosolo/build.sh +++ b/recipes/prosolo/build.sh @@ -1,4 +1,10 @@ #!/bin/bash -euo +# circumvent a bug in conda-build >=2.1.18,<3.0.10 +# https://github.com/conda/conda-build/issues/2255 +# TODO: remove once CI uses conda-build >=3.0.10 +[[ -z $REQUESTS_CA_BUNDLE && ${REQUESTS_CA_BUNDLE+x} ]] && unset REQUESTS_CA_BUNDLE +[[ -z $SSL_CERT_FILE && ${SSL_CERT_FILE+x} ]] && unset SSL_CERT_FILE + # build statically linked binary with Rust C_INCLUDE_PATH=$PREFIX/include LIBRARY_PATH=$PREFIX/lib:/usr/lib64 cargo install --root $PREFIX --verbose --debug diff --git a/recipes/prosolo/meta.yaml b/recipes/prosolo/meta.yaml index 5d432d1076eef8..4e315fc333b53b 100644 --- a/recipes/prosolo/meta.yaml +++ b/recipes/prosolo/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "0.3.1" %} +{% set version = "0.4.0" %} package: name: prosolo @@ -8,13 +8,13 @@ build: # only on OSX, `cargo install` fails with: `thread 'main' panicked at 'assertion failed: src_path.is_absolute()', src/tools/cargo/src/cargo/core/manifest.rs:311` # looks like a `cargo` bug, that may go away with newer `rust` versions; check osx with rust>1.21 when available skip: True # [not linux64] - number: 0 + number: 1 string: "gsl{{CONDA_GSL}}_{{PKG_BUILDNUM}}" source: url: https://github.com/PROSIC/prosolo/archive/v{{ version }}.tar.gz fn: prosolo-{{ version }}.tar.gz - md5: 57c767cda5c796fc689928cf21e88cdf + md5: 6b91b9a3dfb915891fb9df702249ff99 requirements: build: @@ -25,7 +25,7 @@ requirements: - zlib {{ CONDA_ZLIB }}* # new cram dependencies for rust-htslib 0.16.0 - bzip2 {{ CONDA_BZIP2 }}* # [linux] - - xz + - xz {{CONDA_XZ}}* - clangdev run: - gsl {{CONDA_GSL}}* @@ -33,7 +33,7 @@ requirements: - zlib {{ CONDA_ZLIB }}* # new cram dependencies for rust-htslib 0.16.0 - bzip2 {{ CONDA_BZIP2 }}* # [linux] - - xz + - xz {{CONDA_XZ}}* - clangdev test: diff --git a/recipes/pullseq/meta.yaml b/recipes/pullseq/meta.yaml index 177eb06469768e..4b30b83b8f6ba0 100644 --- a/recipes/pullseq/meta.yaml +++ b/recipes/pullseq/meta.yaml @@ -8,7 +8,7 @@ source: md5: a4ef6e5b4b5c77be2ef5d444c44fb6c0 build: - number: 1 + number: 2 requirements: build: @@ -18,12 +18,12 @@ requirements: - autoconf 2.69 pl5.* - automake 1.15 pl5.* - libtool - - zlib + - zlib {{CONDA_ZLIB}}* run: - libgcc # [linux] - pcre - - zlib + - zlib {{CONDA_ZLIB}}* test: commands: diff --git a/recipes/py2bit/meta.yaml b/recipes/py2bit/meta.yaml index 75f665e21f0766..bc79e4ece401aa 100644 --- a/recipes/py2bit/meta.yaml +++ b/recipes/py2bit/meta.yaml @@ -1,11 +1,11 @@ package: name: py2bit - version: "0.2.2" + version: "0.3.0" source: - fn: py2bit-0.2.2.tar.gz - url: https://files.pythonhosted.org/packages/24/9d/7ea7a90078148392d591845147a07bb8d2f60c6e0a2b186a7c28c29365e6/py2bit-0.2.2.tar.gz - md5: 4df56f5fcee32b84fb94e4621d1cffe5 + fn: py2bit-0.3.0.tar.gz + url: https://files.pythonhosted.org/packages/53/bb/547a927bed736ead3dc909e1e552d57c9034bb9493eff80544c0cf6e4828/py2bit-0.3.0.tar.gz + md5: 544a4bb602985d4026da0e01d96d2e3d requirements: build: @@ -20,6 +20,6 @@ test: - py2bitTest about: - home: https://github.com/dpryan79/py2bit + home: https://github.com/deeptools/py2bit license: 'MIT' summary: 'A package for accessing 2bit files using lib2bit' diff --git a/recipes/pybedtools/0.6.9/meta.yaml b/recipes/pybedtools/0.6.9/meta.yaml index d8bac6708afbe6..c0c2c03de76795 100644 --- a/recipes/pybedtools/0.6.9/meta.yaml +++ b/recipes/pybedtools/0.6.9/meta.yaml @@ -8,7 +8,7 @@ source: md5: a24e4bcd0c89beb9535295db964f6a4a build: - number: 0 + number: 1 skip: True # [py3k] requirements: diff --git a/recipes/pybedtools/meta.yaml b/recipes/pybedtools/meta.yaml index 16c5242264701f..51d6af7bd17470 100644 --- a/recipes/pybedtools/meta.yaml +++ b/recipes/pybedtools/meta.yaml @@ -8,7 +8,7 @@ source: md5: f003c67e22c48b77f070538368ece70c build: - number: 1 + number: 2 requirements: build: @@ -20,7 +20,7 @@ requirements: - cython - gcc # [linux] - llvm # [osx] - - zlib + - zlib {{CONDA_ZLIB}}* run: - python @@ -29,6 +29,7 @@ requirements: - pysam >=0.8.1 - pandas - libgcc # [linux] + - zlib {{CONDA_ZLIB}}* test: imports: diff --git a/recipes/pymvpa/2.6.0/meta.yaml b/recipes/pymvpa/2.6.0/meta.yaml index 4984d70ce011dc..75fc75c17e1ce6 100644 --- a/recipes/pymvpa/2.6.0/meta.yaml +++ b/recipes/pymvpa/2.6.0/meta.yaml @@ -14,7 +14,7 @@ source: # If this is a new build for the same version, increment the build # number. If you do not include this key, it defaults to 0. build: - number: 0 + number: 1 requirements: build: @@ -25,11 +25,11 @@ requirements: - scipy - numpy - swig - - zlib + - zlib {{CONDA_ZLIB}}* run: - python - - zlib + - zlib {{CONDA_ZLIB}}* - libsvm ==3.21 - matplotlib - scipy diff --git a/recipes/pysam/0.10.0/meta.yaml b/recipes/pysam/0.10.0/meta.yaml index 1137b85b24e4fe..088c9a8decd9d8 100644 --- a/recipes/pysam/0.10.0/meta.yaml +++ b/recipes/pysam/0.10.0/meta.yaml @@ -10,7 +10,7 @@ source: - osx_rpath.patch [osx] build: - number: 3 + number: 4 skip: False binary_relocation: False # [linux] @@ -24,7 +24,7 @@ requirements: - cython - python - setuptools - - zlib + - zlib {{CONDA_ZLIB}}* - curl run: @@ -33,7 +33,7 @@ requirements: - samtools >=1.3,<1.4 - bcftools >=1.3,<1.4 - python - - zlib + - zlib {{CONDA_ZLIB}}* - curl test: diff --git a/recipes/pysam/0.7.7/meta.yaml b/recipes/pysam/0.7.7/meta.yaml index c045904a3669cd..ac18cd47455c61 100644 --- a/recipes/pysam/0.7.7/meta.yaml +++ b/recipes/pysam/0.7.7/meta.yaml @@ -1,13 +1,16 @@ package: name: pysam version: "0.7.7" + source: fn: pysam-0.7.7.tar.gz url: https://pypi.python.org/packages/source/p/pysam/pysam-0.7.7.tar.gz sha256: c9f3018482eec99ee199dda3fdef2aa7424dde6574672a4c0d209a10985755cc + build: - number: 0 + number: 1 skip: True # [not py27] + requirements: build: - python @@ -15,14 +18,16 @@ requirements: - cython - gcc # [linux] - llvm # [osx] - - zlib + - zlib {{CONDA_ZLIB}}* run: - python <3.0.0 - libgcc # [linux] - - zlib + - zlib {{CONDA_ZLIB}}* + test: imports: - pysam + about: home: https://github.com/pysam-developers/pysam license: MIT diff --git a/recipes/pysam/0.8.3/meta.yaml b/recipes/pysam/0.8.3/meta.yaml index 3443685381849a..e097ac5e20969f 100644 --- a/recipes/pysam/0.8.3/meta.yaml +++ b/recipes/pysam/0.8.3/meta.yaml @@ -1,12 +1,15 @@ package: name: pysam version: "0.8.3" + source: fn: pysam-0.8.3.tar.gz url: https://pypi.python.org/packages/source/p/pysam/pysam-0.8.3.tar.gz md5: b1ae2a8ec3c6d20be30b2bc1aa995bbf + build: - number: 2 + number: 3 + requirements: build: - python @@ -14,11 +17,12 @@ requirements: - cython - gcc # [linux] - llvm # [osx] - - zlib + - zlib {{CONDA_ZLIB}}* run: - python - libgcc # [linux] - - zlib + - zlib {{CONDA_ZLIB}}* + test: # Python imports imports: @@ -28,6 +32,7 @@ test: # - pysam.include.htslib.htslib # - pysam.include.samtools # - pysam.include.samtools.win32 + about: home: https://github.com/pysam-developers/pysam license: MIT diff --git a/recipes/pysam/0.9.1/meta.yaml b/recipes/pysam/0.9.1/meta.yaml index 1736c57da5ec81..dedc17c6710e81 100644 --- a/recipes/pysam/0.9.1/meta.yaml +++ b/recipes/pysam/0.9.1/meta.yaml @@ -8,7 +8,7 @@ source: md5: d87765ad1e0afe534255c20cce5478e4 build: - number: 2 + number: 3 skip: False requirements: @@ -21,7 +21,7 @@ requirements: - cython - python - setuptools - - zlib + - zlib {{CONDA_ZLIB}}* - curl run: @@ -30,7 +30,7 @@ requirements: - samtools ==1.3.1 - bcftools ==1.3.1 - python - - zlib + - zlib {{CONDA_ZLIB}}* - curl test: diff --git a/recipes/pysam/meta.yaml b/recipes/pysam/meta.yaml index ea5fa09e73c694..60da2f1bf15989 100644 --- a/recipes/pysam/meta.yaml +++ b/recipes/pysam/meta.yaml @@ -8,7 +8,7 @@ source: md5: 9e4546ef1657690e486288d3251b7186 build: - number: 0 + number: 1 skip: False binary_relocation: False # [linux] string: "py{{CONDA_PY}}_htslib1.7_{{PKG_BUILDNUM}}" diff --git a/recipes/pysamstats/meta.yaml b/recipes/pysamstats/meta.yaml index 3e105e7633a441..84d3f1b4d31067 100644 --- a/recipes/pysamstats/meta.yaml +++ b/recipes/pysamstats/meta.yaml @@ -8,7 +8,7 @@ source: md5: db8a5ad0db0027f55fd954a5510a797a build: - number: 0 + number: 1 # skip: True # [osx or not py35 or not py27] requirements: @@ -16,7 +16,7 @@ requirements: - python - cython - pysam >=0.11 - - zlib + - zlib {{CONDA_ZLIB}}* - gcc - numpy - pytables @@ -25,7 +25,7 @@ requirements: run: - python - pysam >=0.11 - - zlib + - zlib {{CONDA_ZLIB}}* - libgcc - numpy - pytables diff --git a/recipes/pytabix/meta.yaml b/recipes/pytabix/meta.yaml index eb9b1b2a6d85de..dca0bbef11a5dc 100644 --- a/recipes/pytabix/meta.yaml +++ b/recipes/pytabix/meta.yaml @@ -3,7 +3,7 @@ package: version: 0.0.2 build: - number: 2 + number: 3 skip: True # [osx] source: @@ -15,11 +15,11 @@ requirements: build: - python - setuptools - - zlib + - zlib {{CONDA_ZLIB}}* run: - python - - zlib + - zlib {{CONDA_ZLIB}}* test: imports: diff --git a/recipes/python-edlib/build.sh b/recipes/python-edlib/build.sh new file mode 100644 index 00000000000000..3786386a73c834 --- /dev/null +++ b/recipes/python-edlib/build.sh @@ -0,0 +1,3 @@ +#!/bin/bash + +$PYTHON setup.py install --single-version-externally-managed --record=record.txt diff --git a/recipes/python-edlib/meta.yaml b/recipes/python-edlib/meta.yaml new file mode 100644 index 00000000000000..75f97daed09bb8 --- /dev/null +++ b/recipes/python-edlib/meta.yaml @@ -0,0 +1,35 @@ +{% set version = "1.2.3" %} + +package: + name: python-edlib + version: {{ version }} + +source: + fn: edlib-{{ version }}.tar.gz + url: https://pypi.io/packages/source/e/edlib/edlib-{{ version }}.tar.gz + sha256: 5f32e02653402f9f649c1e256c39f6fc7361d16fecb2aae6d425c40d4d936be9 + +build: + number: 0 + +requirements: + build: + - python + - setuptools + - gcc # [not osx] + - llvm # [osx] + - libgcc # [not osx] + + run: + - python + - libgcc # [not osx] + +test: + imports: + - edlib + +about: + home: https://github.com/Martinsos/edlib + license: MIT License + summary: 'Lightweight, super fast C/C++ (& Python) library for sequence alignment using edit (Levenshtein) distance.' + license_family: MIT diff --git a/recipes/pythonnet/meta.yaml b/recipes/pythonnet/meta.yaml index 1141656de4d1d5..a71485c9f25904 100644 --- a/recipes/pythonnet/meta.yaml +++ b/recipes/pythonnet/meta.yaml @@ -18,7 +18,7 @@ requirements: - ca-certificates - mono - clangdev - - zlib 1.2.11 + - zlib {{CONDA_ZLIB}}* - setuptools - sqlite 3.20.* - readline diff --git a/recipes/r-asics/build.sh b/recipes/r-asics/build.sh new file mode 100644 index 00000000000000..6864ae6daf6145 --- /dev/null +++ b/recipes/r-asics/build.sh @@ -0,0 +1,8 @@ +#!/bin/bash + +# R refuses to build packages that mark themselves as Priority: Recommended +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION + +$R CMD INSTALL --build . + diff --git a/recipes/r-asics/meta.yaml b/recipes/r-asics/meta.yaml new file mode 100644 index 00000000000000..92192552337e60 --- /dev/null +++ b/recipes/r-asics/meta.yaml @@ -0,0 +1,54 @@ +{% set name = 'ASICS' %} +{% set version = '1.0.1' %} + +package: + name: r-{{ name|lower }} + version: {{ version|replace("-", "_") }} + +source: + fn: {{ name }}_{{ version }}.tar.gz + url: + - https://cran.r-project.org/src/contrib/{{ name }}_{{ version }}.tar.gz + - https://cran.r-project.org/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz + sha1: f0b6d0c44e26ee0350c9ec10e27d115c30307e63 + +build: + number: 0 + + # This is required to make R link correctly on Linux. + rpaths: + - lib/R/lib/ + - lib/ + +# Suggests: knitr, rmarkdown +requirements: + build: + - r-base + - r-doparallel + - r-foreach + - r-ggplot2 + - r-plyr + - r-quadprog + - r-zoo + + run: + - r-base + - r-doparallel + - r-foreach + - r-ggplot2 + - r-plyr + - r-quadprog + - r-zoo + +test: + commands: + - $R -e "library('ASICS')" + +about: + home: https://CRAN.R-project.org/package=ASICS + license: GPL (>= 2) + summary: 'With a set of pure metabolite spectra, ASICS quantifies metabolites concentration + in a complex spectrum. The identification of metabolites is performed by fitting + a mixture model to the spectra of the library with a sparse penalty. The method + and its statistical properties are described in Tardivel et al. (2017) . ' + diff --git a/recipes/r-basejump/build.sh b/recipes/r-basejump/build.sh new file mode 100644 index 00000000000000..81250b8ff4aaaa --- /dev/null +++ b/recipes/r-basejump/build.sh @@ -0,0 +1,7 @@ +#!/bin/bash + +# R refuses to build packages that mark themselves as Priority: Recommended +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION + +$R CMD INSTALL --build . diff --git a/recipes/r-basejump/meta.yaml b/recipes/r-basejump/meta.yaml new file mode 100644 index 00000000000000..f16654761901f9 --- /dev/null +++ b/recipes/r-basejump/meta.yaml @@ -0,0 +1,89 @@ +package: + name: r-basejump + # Note that conda versions cannot contain -, so any -'s in the version have + # been replaced with _'s. + version: "0.1.1" + +source: + #fn: v0.1.1.tar.gz + #url: https://github.com/steinbaugh/basejump/archive/v0.1.1.tar.gz + fn: 93d0b61.tar.gz + url: https://github.com/roryk/basejump/archive/93d0b61.tar.gz + sha256: e95cbac095d7b3755ca7c37c90ea8b6d55120cae27c403e71f25ee6958e9d9d3 + +build: + number: 0 + # This is required to make R link correctly on Linux. + rpaths: + - lib/R/lib/ + - lib/ + +requirements: + build: + - 'r-base >=3.4.0' + - bioconductor-annotationhub + - bioconductor-biobase + - bioconductor-biocgenerics + - r-cowplot + - r-dendsort + - r-matrix.utils + - r-dplyr + - r-devtools + - bioconductor-ensembldb + - r-ggplot2 + - r-knitr + - r-magrittr + - r-matrix + - r-pheatmap + - r-rcolorbrewer + - r-rcurl + - r-readr + - r-readxl + - r-rlang + - r-r.utils + - r-scales + - r-stringr + - bioconductor-s4vectors + - r-tibble + - r-tidyr + - r-viridis + - r-yaml + + run: + - 'r-base >=3.4.0' + - bioconductor-annotationhub + - bioconductor-biobase + - bioconductor-biocgenerics + - r-cowplot + - r-dendsort + - r-matrix.utils + - r-dplyr + - r-devtools + - bioconductor-ensembldb + - r-ggplot2 + - r-knitr + - r-magrittr + - r-matrix + - r-pheatmap + - r-rcolorbrewer + - r-rcurl + - r-readr + - r-readxl + - r-rlang + - r-r.utils + - r-scales + - r-stringr + - bioconductor-s4vectors + - r-tibble + - r-tidyr + - r-viridis + - r-yaml + +test: + commands: + - $R -e "library('basejump')" + +about: + home: https://github.com/steinbaugh/basejump + license: MIT + summary: Base functions for bioinformatics and R package development. diff --git a/recipes/r-factominer/build.sh b/recipes/r-bcbiobase/build.sh similarity index 100% rename from recipes/r-factominer/build.sh rename to recipes/r-bcbiobase/build.sh diff --git a/recipes/r-bcbiobase/meta.yaml b/recipes/r-bcbiobase/meta.yaml new file mode 100644 index 00000000000000..e87f4f43f84c71 --- /dev/null +++ b/recipes/r-bcbiobase/meta.yaml @@ -0,0 +1,57 @@ +{% set version = '0.0.3' %} + +package: + name: r-bcbiobase + version: {{ version|replace("-", "_") }} + +source: +# fn: v{{ version }}.tar.gz + fn: 7f905e0.tar.gz + url: https://github.com/hbc/bcbioBase/archive/7f905e0.tar.gz + sha256: 199a991cb8d6fc9c1f5cbcb9d15ecac48a0d4af592b2e95db1da2eba6bcb8a06 + +build: + number: 0 + + rpaths: + - lib/R/lib/ + - lib/ + +requirements: + build: + - 'r-base >=3.4.0' + - r-basejump + - bioconductor-biocgenerics + - bioconductor-biostrings + - r-dplyr + - r-magrittr + - r-readr + - r-rlang + - r-scales + - r-stringr + - r-tidyr + - r-rmysql + + run: + - 'r-base >=3.4.0' + - r-basejump + - bioconductor-biocgenerics + - bioconductor-biostrings + - r-dplyr + - r-magrittr + - r-readr + - r-rlang + - r-scales + - r-stringr + - r-tidyr + - r-rmysql + +test: + commands: + - $R -e "library('bcbioBase')" + +about: + home: http://bioinformatics.sph.harvard.edu/bcbioBase/ + license: MIT + summary: Base functions and generics for bcbio R packages. + license_family: MIT diff --git a/recipes/r-bcbiornaseq/build.sh b/recipes/r-bcbiornaseq/build.sh new file mode 100644 index 00000000000000..81250b8ff4aaaa --- /dev/null +++ b/recipes/r-bcbiornaseq/build.sh @@ -0,0 +1,7 @@ +#!/bin/bash + +# R refuses to build packages that mark themselves as Priority: Recommended +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION + +$R CMD INSTALL --build . diff --git a/recipes/r-bcbiornaseq/meta.yaml b/recipes/r-bcbiornaseq/meta.yaml new file mode 100644 index 00000000000000..cbda6aa4b2f651 --- /dev/null +++ b/recipes/r-bcbiornaseq/meta.yaml @@ -0,0 +1,52 @@ +package: + name: r-bcbiornaseq + # Note that conda versions cannot contain -, so any -'s in the version have + # been replaced with _'s. + version: "0.1.2" + +source: + fn: deac1c0.tar.gz + url: https://github.com/hbc/bcbioRNASeq/archive/deac1c0.tar.gz + sha256: 65a7b0e5d1e1a49589c5c8f97783d686b161fadae7f32d2c54076ca3f6964e56 + +build: + number: 0 + # This is required to make R link correctly on Linux. + rpaths: + - lib/R/lib/ + - lib/ + +requirements: + build: + - 'r-base >=3.4.0' + - bioconductor-summarizedexperiment + - r-bcbiobase + - bioconductor-deseq2 + - bioconductor-degreport + - bioconductor-edger + - r-ggrepel + - r-pbapply + - bioconductor-tximport + - bioconductor-vsn + + run: + - 'r-base >=3.4.0' + - bioconductor-summarizedexperiment + - r-bcbiobase + - bioconductor-deseq2 + - bioconductor-degreport + - bioconductor-edger + - r-ggrepel + - r-pbapply + - bioconductor-tximport + - bioconductor-vsn + + +test: + commands: + - $R -e "library('bcbioRNASeq')" + +about: + home: https://github.com/hbc/bcbioRNASeq + license: MIT + summary: Quality control and differential expression for bcbio RNA-seq experiments. diff --git a/recipes/msprime/build.sh b/recipes/r-deconstructsigs/build.sh similarity index 51% rename from recipes/msprime/build.sh rename to recipes/r-deconstructsigs/build.sh index cb2310e1717c48..0c37df6e8efec5 100644 --- a/recipes/msprime/build.sh +++ b/recipes/r-deconstructsigs/build.sh @@ -1,9 +1,10 @@ #!/bin/bash -export CFLAGS="-I${PREFIX}/include" -export LDFLAGS="-L${PREFIX}/lib" +# R refuses to build packages that mark themselves as Priority: Recommended +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION -$PYTHON setup.py install +$R CMD INSTALL --build . # Add more build steps here, if they are necessary. diff --git a/recipes/r-deconstructsigs/meta.yaml b/recipes/r-deconstructsigs/meta.yaml new file mode 100644 index 00000000000000..434888b8b93b9e --- /dev/null +++ b/recipes/r-deconstructsigs/meta.yaml @@ -0,0 +1,45 @@ +{% set version = '1.8.0' %} + +package: + name: r-deconstructsigs + version: {{ version|replace("-", "_") }} + +source: + fn: deconstructSigs_{{ version }}.tar.gz + url: + - https://cran.r-project.org/src/contrib/deconstructSigs_{{ version }}.tar.gz + - https://cran.r-project.org/src/contrib/Archive/deconstructSigs/deconstructSigs_{{ version }}.tar.gz + sha256: 2ab8f6c0fd674bd270035ba2112f1a79d63de1155ba9698c4169c92196059d04 + +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + +requirements: + build: + - bioconductor-bsgenome + - bioconductor-bsgenome.hsapiens.ucsc.hg19 + - bioconductor-genomeinfodb + - r-base + - r-reshape2 + + run: + - bioconductor-bsgenome + - bioconductor-bsgenome.hsapiens.ucsc.hg19 + - bioconductor-genomeinfodb + - r-base + - r-reshape2 + +test: + commands: + - $R -e "library('deconstructSigs')" + +about: + home: https + license: GPL (>= 2) + summary: Takes sample information in the form of the fraction of mutations in each of 96 trinucleotide + contexts and identifies the weighted combination of published signatures that, when + summed, most closely reconstructs the mutational profile. + license_family: GPL3 diff --git a/recipes/r-factominer/meta.yaml b/recipes/r-factominer/meta.yaml deleted file mode 100644 index 8bb66bc7d278b6..00000000000000 --- a/recipes/r-factominer/meta.yaml +++ /dev/null @@ -1,65 +0,0 @@ -{% set version = '1.38' %} - -package: - name: r-factominer - version: {{ version|replace("-", "_") }} - -source: - fn: FactoMineR_{{ version }}.tar.gz - url: - - https://cran.r-project.org/src/contrib/FactoMineR_{{ version }}.tar.gz - - https://cran.r-project.org/src/contrib/Archive/FactoMineR/FactoMineR_{{ version }}.tar.gz - sha256: f13059c84c53f8761bd5a61e980f8609e2119e36c5d35233fc2baac93268086f - -build: - number: 0 - - rpaths: - - lib/R/lib/ - - lib/ - -requirements: - build: - - r-base - - r-mass - - r-car - - r-cluster - - r-ellipse - - r-flashclust - - # prev version: - # - r-knitr - - - r-lattice - - r-leaps - - r-scatterplot3d - - run: - - r-base - - r-mass - - r-car - - r-cluster - - r-ellipse - - r-flashclust - - # prev version: - # - r-knitr - - r-lattice - - r-leaps - - r-scatterplot3d - -test: - commands: - - $R -e "library('FactoMineR')" - -about: - home: http://factominer.free.fr - license: GPL (>= 2) - summary: 'Exploratory data analysis methods to summarize, visualize and describe datasets. - The main principal component methods are available, those with the largest potential - in terms of applications: principal component analysis (PCA) when variables are - quantitative, correspondence analysis (CA) and multiple correspondence analysis - (MCA) when variables are categorical, Multiple Factor Analysis when variables are - structured in groups, etc. and hierarchical cluster analysis.' - - license_family: GPL3 diff --git a/recipes/r-fnn/meta.yaml b/recipes/r-fnn/meta.yaml deleted file mode 100644 index 954548d7cee3ff..00000000000000 --- a/recipes/r-fnn/meta.yaml +++ /dev/null @@ -1,40 +0,0 @@ -{% set version = '1.1' %} - -package: - name: r-fnn - version: {{ version|replace("-", "_") }} - -source: - fn: FNN_{{ version }}.tar.gz - url: - - https://cran.r-project.org/src/contrib/FNN_{{ version }}.tar.gz - - https://cran.r-project.org/src/contrib/Archive/FNN/FNN_{{ version }}.tar.gz - sha256: b2a2e97af14aa50ef4dce15a170e1d7329aebb7643bab4a6cf35609555acccce - -build: - number: 0 - - rpaths: - - lib/R/lib/ - - lib/ - -requirements: - build: - - r-base - - gcc # [linux] - - llvm # [osx] - - run: - - r-base - - libgcc # [linux] - -test: - commands: - - $R -e "library('FNN')" - -about: - home: https://CRAN.R-project.org/package=FNN - license: GPL (>= 2.1) - summary: Cover-tree and kd-tree fast k-nearest neighbor search algorithms and related applications - including KNN classification, regression and information measures are implemented. - license_family: GPL3 diff --git a/recipes/r-ggsignif/meta.yaml b/recipes/r-ggsignif/meta.yaml deleted file mode 100644 index 2af51469a89b1e..00000000000000 --- a/recipes/r-ggsignif/meta.yaml +++ /dev/null @@ -1,49 +0,0 @@ -{% set version = '0.4.0' %} - -{% set posix = 'm2-' if win else '' %} -{% set native = 'm2w64-' if win else '' %} - -package: - name: r-ggsignif - version: {{ version|replace("-", "_") }} - -source: - fn: ggsignif_{{ version }}.tar.gz - url: - - https://cran.r-project.org/src/contrib/ggsignif_{{ version }}.tar.gz - - https://cran.r-project.org/src/contrib/Archive/ggsignif/ggsignif_{{ version }}.tar.gz - - - sha256: c7a1d3155cd848d008762a7aa15453e6f09fa7f719c60899995d8d754f43c5e6 - -build: - number: 0 - - rpaths: - - lib/R/lib/ - - lib/ - -requirements: - build: - - r-base - - r-ggplot2 >=2.0.0 - - run: - - r-base - - r-ggplot2 >=2.0.0 - -test: - commands: - - $R -e "library('ggsignif')" # [not win] - - "\"%R%\" -e \"library('ggsignif')\"" # [win] - -about: - home: https://github.com/const-ae/ggsignif - license: GPL-3 - summary: Enrich your 'ggplots' with group-wise comparisons. This package provides an easy way - to indicate if two groups are significantly different. Commonly this is shown by - a bracket on top connecting the groups of interest which itself is annotated with - the level of significance (NS, *, **, ***). The package provides a single layer - (geom_signif()) that takes the groups for comparison and the test (t.test(), wilcox.text() - etc.) as arguments and adds the annotation to the plot. - license_family: GPL3 diff --git a/recipes/r-ggthemes/build.sh b/recipes/r-ggthemes/build.sh deleted file mode 100644 index af6547bf3c22ee..00000000000000 --- a/recipes/r-ggthemes/build.sh +++ /dev/null @@ -1,2 +0,0 @@ -#!/bin/bash -$R CMD INSTALL --build . diff --git a/recipes/r-ggthemes/meta.yaml b/recipes/r-ggthemes/meta.yaml deleted file mode 100644 index 66d8a220698e25..00000000000000 --- a/recipes/r-ggthemes/meta.yaml +++ /dev/null @@ -1,47 +0,0 @@ -{% set version = '3.4.0' %} - -package: - name: r-ggthemes - version: {{ version|replace("-", "_") }} - -source: - fn: ggthemes_{{ version }}.tar.gz - url: - - https://cran.r-project.org/src/contrib/ggthemes_{{ version }}.tar.gz - - https://cran.r-project.org/src/contrib/Archive/ggthemes/ggthemes_{{ version }}.tar.gz - sha256: 1a1aeb7fe5a60fab0d0b82e959dd7c01d80b6f5984af77674264cc25cfa548ca - -build: - number: 0 - - rpaths: - - lib/R/lib/ - - lib/ - -requirements: - build: - - r-base - - r-assertthat - - r-colorspace - - r-ggplot2 >=2.2.0 - - r-scales - - run: - - r-base - - r-assertthat - - r-colorspace - - r-ggplot2 >=2.2.0 - - r-scales - -test: - commands: - - $R -e "library('ggthemes')" - -about: - home: http://github.com/jrnold/ggthemes - license: GPL-2 - summary: Some extra themes, geoms, and scales for 'ggplot2'. Provides 'ggplot2' themes and - scales that replicate the look of plots by Edward Tufte, Stephen Few, 'Fivethirtyeight', - 'The Economist', 'Stata', 'Excel', and 'The Wall Street Journal', among others. - Provides 'geoms' for Tufte's box plot and range frame. - license_family: GPL2 diff --git a/recipes/r-idpmisc/build.sh b/recipes/r-idpmisc/build.sh deleted file mode 100644 index af6547bf3c22ee..00000000000000 --- a/recipes/r-idpmisc/build.sh +++ /dev/null @@ -1,2 +0,0 @@ -#!/bin/bash -$R CMD INSTALL --build . diff --git a/recipes/r-idpmisc/meta.yaml b/recipes/r-idpmisc/meta.yaml deleted file mode 100644 index c7015fc7dafa3b..00000000000000 --- a/recipes/r-idpmisc/meta.yaml +++ /dev/null @@ -1,49 +0,0 @@ -{% set version = '1.1.17' %} - -package: - name: r-idpmisc - version: {{ version|replace("-", "_") }} - -source: - fn: IDPmisc_{{ version }}.tar.gz - url: - - https://cran.r-project.org/src/contrib/IDPmisc_{{ version }}.tar.gz - - https://cran.r-project.org/src/contrib/Archive/IDPmisc/IDPmisc_{{ version }}.tar.gz - sha256: 18ec9db0aab1de526b8e57ac1f0223811806a814777149b793722b999e6f7c59 - -build: - number: 0 - - rpaths: - - lib/R/lib/ - - lib/ - -requirements: - build: - - r-base - - r-lattice >=0.19_26 - - gcc # [linux] - - llvm # [osx] - - run: - - r-base - - r-lattice >=0.19_26 - - libgcc # [linux] - -test: - commands: - - $R -e "library('IDPmisc')" - -about: - home: https://CRAN.R-project.org/package=IDPmisc - license: GPL (>= 3) - summary: 'The IDPmisc package contains different high-level graphics functions for displaying - large datasets, displaying circular data in a very flexible way, finding local maxima, - brewing color ramps, drawing nice arrows, zooming 2D-plots, creating figures with - differently colored margin and plot region. In addition, the package contains auxiliary - functions for data manipulation like omitting observations with irregular values - or selecting data by logical vectors, which include NAs. Other functions are especially - useful in spectroscopy and analyses of environmental data: robust baseline fitting, - finding peaks in spectra.' - - license_family: GPL3 diff --git a/recipes/r-spp/Makevars.patch b/recipes/r-spp/Makevars.patch index d4a75c52e00e72..a11f353d10d365 100644 --- a/recipes/r-spp/Makevars.patch +++ b/recipes/r-spp/Makevars.patch @@ -1,9 +1,9 @@ --- src/Makevars.in +++ src/Makevars.in @@ -1,4 +1,4 @@ - PKG_LIBS=@LIBS@ -lz --PKG_CFLAGS=-I./ -D_FASTMAP -DMAQ_LONGREADS @HAVE_LIBBZ2@ --PKG_CXXFLAGS=-I./ -D_FASTMAP -DMAQ_LONGREADS @HAVE_LIBBZ2@ @BOOST_CPPFLAGS@ + PKG_LIBS=@LIBS@ -lz +-PKG_CFLAGS=-I./ -D_FASTMAP -DMAQ_LONGREADS @HAVE_LIBBZ2@ +-PKG_CXXFLAGS=-I./ -D_FASTMAP -DMAQ_LONGREADS @HAVE_LIBBZ2@ @BOOST_CPPFLAGS@ +PKG_CFLAGS=-I./ -D_FASTMAP -DMAQ_LONGREADS @HAVE_LIBBZ2@ -ferror-limit=0 -stdlib=libstdc++ -+PKG_CXXFLAGS=-I./ -D_FASTMAP -DMAQ_LONGREADS @HAVE_LIBBZ2@ @BOOST_CPPFLAGS@ -ferror-limit=0 -stdlib=libstdc++ - ++PKG_CXXFLAGS=-I./ -D_FASTMAP -DMAQ_LONGREADS @HAVE_LIBBZ2@ @BOOST_CPPFLAGS@ -ferror-limit=0 -stdlib=libstdc++ + CXX_STD=CXX11 diff --git a/recipes/r-spp/meta.yaml b/recipes/r-spp/meta.yaml index 4a08089c65ec56..b9c758e0ac56de 100644 --- a/recipes/r-spp/meta.yaml +++ b/recipes/r-spp/meta.yaml @@ -1,19 +1,17 @@ package: name: r-spp - version: "1.14post" + version: "1.15.2" source: - fn: "1.14post.zip" - url: https://github.com/hms-dbmi/spp/archive/c6526d2bc8eeaaa889970cd2f8d30c998f3ea320.zip - sha256: 61f0d21f2c5127e570bf619445c89968009cfbd32b995984cf20788f986e666b + url: https://github.com/hms-dbmi/spp/archive/1.15.2.tar.gz + sha256: bf0d6f42d9461aeb7a20b1ddb12b57bc42d11732ca6f69ec3eb2157364cefd5b patches: # [osx] - Makevars.patch # [osx] build: number: 0 string: r_{{CONDA_R}}_boost{{CONDA_BOOST}}_{{PKG_BUILDNUM}} - - # This is required to make R link correctly on Linux. + skip: True # [osx] rpaths: - lib/R/lib/ - lib/ @@ -21,22 +19,23 @@ build: requirements: build: - r-base + - r-rcpp - boost {{CONDA_BOOST}}* - r-catools - bioconductor-rsamtools - - gcc # [linux] - - llvm # [osx] - - zlib - - bzip2 + - gcc + - zlib {{CONDA_ZLIB}}* + - bzip2 {{CONDA_BZIP2}}* run: - r-base + - r-rcpp - boost {{CONDA_BOOST}}* - r-catools - bioconductor-rsamtools - - libgcc # [linux] - - zlib - - bzip2 + - libgcc + - zlib {{CONDA_ZLIB}}* + - bzip2 {{CONDA_BZIP2}}* test: commands: diff --git a/recipes/r-fnn/build.sh b/recipes/r-tidygenomics/build.sh similarity index 100% rename from recipes/r-fnn/build.sh rename to recipes/r-tidygenomics/build.sh diff --git a/recipes/r-tidygenomics/meta.yaml b/recipes/r-tidygenomics/meta.yaml new file mode 100644 index 00000000000000..c9eb24021f95ed --- /dev/null +++ b/recipes/r-tidygenomics/meta.yaml @@ -0,0 +1,52 @@ +{% set version = '0.1.0' %} + +package: + name: r-tidygenomics + version: {{ version|replace("-", "_") }} + +source: + fn: tidygenomics_{{ version }}.tar.gz + url: + - https://cran.r-project.org/src/contrib/tidygenomics_{{ version }}.tar.gz + - https://cran.r-project.org/src/contrib/Archive/tidygenomics/tidygenomics_{{ version }}.tar.gz + sha256: 966095c07f7f9e9e9a33585c6fa81e3e35038acd55fd6c2c536fd506bfa8d358 + +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + +requirements: + build: + - r-base + - r-rcpp + - r-dplyr + - r-fuzzyjoin >=0.1.3 + - r-purrr + - r-tidyr + - bioconductor-iranges + - gcc + + run: + - r-base + - r-rcpp + - r-dplyr + - r-fuzzyjoin >=0.1.3 + - r-purrr + - r-tidyr + - bioconductor-iranges + - libgcc + +test: + commands: + - $R -e "library('tidygenomics')" + +about: + home: https://github.com/const-ae/tidygenomics + license: GPL-3 + summary: Handle genomic data within data frames just as you would with 'GRanges'. This package + provides methods to deal with genomic intervals the "tidy-way" which makes it simpler + to integrate in the the general data munging process. The API is inspired by the + popular 'bedtools' and the genome_join() method from the 'fuzzyjoin' package. + license_family: GPL3 diff --git a/recipes/racon/build.sh b/recipes/racon/build.sh index 87e16ae8d9c79b..02d7aff58fd2ce 100644 --- a/recipes/racon/build.sh +++ b/recipes/racon/build.sh @@ -1,8 +1,9 @@ #!/bin/bash mkdir -p $PREFIX/bin - -make -j - -mv bin/racon $PREFIX/bin +mkdir build +cd build +cmake -DCMAKE_BUILD_TYPE=Release -D CMAKE_INSTALL_PREFIX=${PREFIX} .. +make +make install diff --git a/recipes/racon/meta.yaml b/recipes/racon/meta.yaml index 4e36c7350c9610..ff87eb8628e2e8 100644 --- a/recipes/racon/meta.yaml +++ b/recipes/racon/meta.yaml @@ -1,21 +1,22 @@ {% set name = "Racon" %} -{% set version = "0.5.0" %} +{% set version = "1.0.1" %} package: name: {{ name|lower }} version: {{ version }} build: - number: 1 + number: 0 source: fn: {{ name|lower }}_{{ version }}.tar.gz - url: https://github.com/isovic/racon/files/741519/racon-v0.5.0.tar.gz - md5: 4de02dc66849b067aa90b26c5610e524 + url: https://github.com/isovic/racon/releases/download/{{ version }}/racon-v{{ version }}.tar.gz + sha256: 6da26c3fbc4a3257edc547025613c32ca4daa0b51e2a263aa4e86e72907ea577 requirements: build: - gcc + - cmake - zlib {{ CONDA_ZLIB }}* run: @@ -24,7 +25,7 @@ requirements: test: commands: - - racon 2>&1 | grep 'options' + - racon --version about: home: https://github.com/isovic/racon diff --git a/recipes/rascaf/meta.yaml b/recipes/rascaf/meta.yaml index 93e3cfacaa9dc2..5b890ec952d1b2 100644 --- a/recipes/rascaf/meta.yaml +++ b/recipes/rascaf/meta.yaml @@ -6,7 +6,7 @@ package: version: {{ version }} build: - number: 0 + number: 1 script: "mkdir -p $PREFIX/bin; make; mv *.pl $PREFIX/bin; mv rascaf $PREFIX/bin; mv rascaf-join $PREFIX/bin" source: @@ -16,13 +16,13 @@ source: requirements: build: - - gcc # [not osx] - - llvm # [osx] - - zlib + - gcc # [not osx] + - llvm # [osx] + - zlib {{CONDA_ZLIB}}* run: - - libgcc # [not osx] - - zlib + - libgcc # [not osx] + - zlib {{CONDA_ZLIB}}* test: commands: diff --git a/recipes/razers3/meta.yaml b/recipes/razers3/meta.yaml index dcb9b305da0e72..36296077d811d3 100644 --- a/recipes/razers3/meta.yaml +++ b/recipes/razers3/meta.yaml @@ -8,7 +8,7 @@ source: sha256: df083d5939d7e73fd00bbc6bb291ac7ea7b8d446cf89a9758fdffdc0eca9ec1c build: - number: 0 + number: 1 skip: True # [osx] requirements: diff --git a/recipes/reaper/meta.yaml b/recipes/reaper/meta.yaml index 52d0ead6f76b12..5f0fb19f394766 100644 --- a/recipes/reaper/meta.yaml +++ b/recipes/reaper/meta.yaml @@ -5,7 +5,7 @@ package: version: {{ version|replace("-", ".") }} build: - number: 0 + number: 1 source: fn: reaper-{{ version }}.tgz diff --git a/recipes/rgi/3.1.1/meta.yaml b/recipes/rgi/3.1.1/meta.yaml index 8f0229ba90c37b..a83c1adcefbf9d 100644 --- a/recipes/rgi/3.1.1/meta.yaml +++ b/recipes/rgi/3.1.1/meta.yaml @@ -13,7 +13,7 @@ source: build: skip: True # [py3k] - number: 1 + number: 2 requirements: build: @@ -22,14 +22,14 @@ requirements: - six >=1.7.0 - gcc # [not osx] - llvm # [osx] - - zlib + - zlib {{CONDA_ZLIB}}* run: - python - blast - biopython - six >=1.7.0 - libgcc # [not osx] - - zlib + - zlib {{CONDA_ZLIB}}* - prodigal test: diff --git a/recipes/rgi/3.1.2/meta.yaml b/recipes/rgi/3.1.2/meta.yaml index 82221bf06d85cf..aeeb663e7bee6a 100644 --- a/recipes/rgi/3.1.2/meta.yaml +++ b/recipes/rgi/3.1.2/meta.yaml @@ -13,7 +13,7 @@ source: build: skip: True # [py3k] - number: 1 + number: 2 # We pin on gcc version to avoid gcc-5 dual ABI issues depending on boost. requirements: @@ -23,14 +23,14 @@ requirements: - six >=1.7.0 - gcc # [not osx] - llvm # [osx] - - zlib + - zlib {{CONDA_ZLIB}}* run: - python - blast - biopython - six >=1.7.0 - libgcc # [not osx] - - zlib + - zlib {{CONDA_ZLIB}}* - prodigal - diamond >=0.8.24.86 diff --git a/recipes/rgi/3.2.0/meta.yaml b/recipes/rgi/3.2.0/meta.yaml index 3e2700ef3cb4ce..e4b30607c121b8 100644 --- a/recipes/rgi/3.2.0/meta.yaml +++ b/recipes/rgi/3.2.0/meta.yaml @@ -13,7 +13,7 @@ source: build: skip: True # [py3k] - number: 1 + number: 2 # We pin on gcc version to avoid gcc-5 dual ABI issues depending on boost. requirements: @@ -23,14 +23,14 @@ requirements: - six >=1.7.0 - gcc # [not osx] - llvm # [osx] - - zlib + - zlib {{CONDA_ZLIB}}* run: - python - blast - biopython - six >=1.7.0 - libgcc # [not osx] - - zlib + - zlib {{CONDA_ZLIB}}* - prodigal - diamond >=0.8.24.86 diff --git a/recipes/rgi/3.2.1/meta.yaml b/recipes/rgi/3.2.1/meta.yaml index 80f0a098e88d3d..99502911fe5fb4 100644 --- a/recipes/rgi/3.2.1/meta.yaml +++ b/recipes/rgi/3.2.1/meta.yaml @@ -13,7 +13,7 @@ source: build: skip: True # [py3k] - number: 2 + number: 3 requirements: build: @@ -22,14 +22,14 @@ requirements: - six >=1.7.0 - gcc # [not osx] - llvm # [osx] - - zlib + - zlib {{CONDA_ZLIB}}* run: - python - blast - biopython - six >=1.7.0 - libgcc # [not osx] - - zlib + - zlib {{CONDA_ZLIB}}* - prodigal - diamond >=0.8.24.86 diff --git a/recipes/rmblast/meta.yaml b/recipes/rmblast/meta.yaml index 96929bb4733739..641823ef877d02 100644 --- a/recipes/rmblast/meta.yaml +++ b/recipes/rmblast/meta.yaml @@ -10,7 +10,7 @@ source: md5: 421c5ddf2c425800d934562c965e8706 # [osx] build: - number: 2 + number: 3 requirements: build: diff --git a/recipes/rnalien/meta.yaml b/recipes/rnalien/meta.yaml index 0a8497598f3cf7..fd77199f5791eb 100644 --- a/recipes/rnalien/meta.yaml +++ b/recipes/rnalien/meta.yaml @@ -12,14 +12,14 @@ source: md5: {{ md5 }} build: - number: 3 + number: 4 skip: True # [osx] requirements: build: - stack >=1.3.2 - gmp - - zlib + - zlib {{CONDA_ZLIB}}* - perl run: @@ -31,7 +31,7 @@ requirements: - gmp - perl - libgcc - - zlib + - zlib {{CONDA_ZLIB}}* - openssl test: diff --git a/recipes/rnftools/0.3.0.2/meta.yaml b/recipes/rnftools/0.3.0.2/meta.yaml index f4b24a1cf6025f..bea766da3ff597 100644 --- a/recipes/rnftools/0.3.0.2/meta.yaml +++ b/recipes/rnftools/0.3.0.2/meta.yaml @@ -25,7 +25,6 @@ requirements: - python - samtools - pysam - - zlib - wgsim - dwgsim - art @@ -33,6 +32,7 @@ requirements: - curesim - snakemake - argparse + test: commands: - rnftools -h diff --git a/recipes/rnftools/0.3.1.0/meta.yaml b/recipes/rnftools/0.3.1.0/meta.yaml index 0f07edf6cede7b..1cb0bfc189915a 100644 --- a/recipes/rnftools/0.3.1.0/meta.yaml +++ b/recipes/rnftools/0.3.1.0/meta.yaml @@ -26,7 +26,6 @@ requirements: - python - samtools - pysam - - zlib - wgsim - dwgsim - art diff --git a/recipes/rnftools/0.3.1.1/meta.yaml b/recipes/rnftools/0.3.1.1/meta.yaml index 509cfc2df217d2..e89d855bc07952 100644 --- a/recipes/rnftools/0.3.1.1/meta.yaml +++ b/recipes/rnftools/0.3.1.1/meta.yaml @@ -25,7 +25,6 @@ requirements: - python - samtools - pysam - - zlib - wgsim - dwgsim - art diff --git a/recipes/rnftools/meta.yaml b/recipes/rnftools/meta.yaml index 9a3fd10e26d31c..b5848cd25276f1 100644 --- a/recipes/rnftools/meta.yaml +++ b/recipes/rnftools/meta.yaml @@ -25,7 +25,6 @@ requirements: - python - samtools - pysam - - zlib - wgsim - dwgsim - art diff --git a/recipes/ropebwt2/meta.yaml b/recipes/ropebwt2/meta.yaml index 1194efd691581c..87c558681be6c0 100644 --- a/recipes/ropebwt2/meta.yaml +++ b/recipes/ropebwt2/meta.yaml @@ -3,7 +3,7 @@ package: version: "r187" build: - number: 1 + number: 2 source: fn: ropebwt2_r187.tar.gz @@ -14,12 +14,12 @@ requirements: build: - gcc # [not osx] - llvm # [osx] - - zlib + - zlib {{CONDA_ZLIB}}* run: - libgcc # [not osx] - llvm - - zlib + - zlib {{CONDA_ZLIB}}* test: commands: diff --git a/recipes/rseg/meta.yaml b/recipes/rseg/meta.yaml index 1eb08f92ee8aeb..053ee9964f7402 100644 --- a/recipes/rseg/meta.yaml +++ b/recipes/rseg/meta.yaml @@ -15,12 +15,12 @@ build: requirements: build: - - zlib - - gcc + - zlib {{CONDA_ZLIB}}* + - gcc run: - - zlib - - libgcc + - zlib {{CONDA_ZLIB}}* + - libgcc test: commands: diff --git a/recipes/rsem/meta.yaml b/recipes/rsem/meta.yaml index 7e79614b2d4f66..fd10002b0d3e52 100644 --- a/recipes/rsem/meta.yaml +++ b/recipes/rsem/meta.yaml @@ -15,7 +15,7 @@ build: rpaths: - lib/R/lib/ - lib/ - number: 2 + number: 3 skip: False string: boost{{CONDA_BOOST}}_{{PKG_BUILDNUM}} diff --git a/recipes/ruby/1.9/build.sh b/recipes/ruby/1.9/build.sh deleted file mode 100644 index f6fdd777a24610..00000000000000 --- a/recipes/ruby/1.9/build.sh +++ /dev/null @@ -1,4 +0,0 @@ -#!/bin/bash -./configure --prefix=$PREFIX --disable-install-doc --enable-load-relative -make -make install diff --git a/recipes/ruby/1.9/meta.yaml b/recipes/ruby/1.9/meta.yaml deleted file mode 100644 index 0209b317ac3438..00000000000000 --- a/recipes/ruby/1.9/meta.yaml +++ /dev/null @@ -1,35 +0,0 @@ -build: - number: 0 - skip: True # [osx] - -# Based on channel tswicegood -package: - name: ruby - version: 1.9.3 - -source: - fn: ruby-1.9.3-p484.tar.gz - url: http://cache.ruby-lang.org/pub/ruby/1.9/ruby-1.9.3-p484.tar.gz - sha256: d684bc3a5ba72cda9ef30039f783c0f8cdc325bae5c8738c7bf05577cbe8f31d - -test: - commands: - - ruby --version - - ruby -e 'puts "Hi, from Ruby!"' - - ruby -e 'require "rubygems"' - - gem --version - -requirements: - build: - - ncurses ==5.9 - - libxml2 ==2.9.2 - - readline ==6.2 - - yaml - - openssl 1.0.1g - - zlib - run: - - zlib - -about: - home: https://www.ruby-lang.org/ - license: BSD diff --git a/recipes/ruby/2.0/build.sh b/recipes/ruby/2.0/build.sh deleted file mode 100644 index f6fdd777a24610..00000000000000 --- a/recipes/ruby/2.0/build.sh +++ /dev/null @@ -1,4 +0,0 @@ -#!/bin/bash -./configure --prefix=$PREFIX --disable-install-doc --enable-load-relative -make -make install diff --git a/recipes/ruby/2.0/meta.yaml b/recipes/ruby/2.0/meta.yaml deleted file mode 100644 index e1e81b4f4d26cf..00000000000000 --- a/recipes/ruby/2.0/meta.yaml +++ /dev/null @@ -1,35 +0,0 @@ -build: - number: 0 - skip: True # [osx] - -# Based on channel tswicegood -package: - name: ruby - version: 2.0.0 - -source: - fn: ruby-2.0.0-p647.tar.gz - url: http://cache.ruby-lang.org/pub/ruby/2.0/ruby-2.0.0-p647.tar.gz - sha256: c88aaf5b4ec72e2cb7d290ff854f04d135939f6134f517002a9d65d5fc5e5bec - -test: - commands: - - ruby --version - - ruby -e 'puts "Hi, from Ruby!"' - - ruby -e 'require "rubygems"' - - gem --version - -requirements: - build: - - ncurses ==5.9 - - libxml2 ==2.9.2 - - readline ==6.2 - - yaml - - openssl 1.0.1g - - zlib - run: - - zlib - -about: - home: https://www.ruby-lang.org/ - license: BSD diff --git a/recipes/ruby/2.1.7/build.sh b/recipes/ruby/2.1.7/build.sh deleted file mode 100644 index f6fdd777a24610..00000000000000 --- a/recipes/ruby/2.1.7/build.sh +++ /dev/null @@ -1,4 +0,0 @@ -#!/bin/bash -./configure --prefix=$PREFIX --disable-install-doc --enable-load-relative -make -make install diff --git a/recipes/ruby/2.1.7/meta.yaml b/recipes/ruby/2.1.7/meta.yaml deleted file mode 100644 index cc57ae00ba6617..00000000000000 --- a/recipes/ruby/2.1.7/meta.yaml +++ /dev/null @@ -1,35 +0,0 @@ -build: - number: 0 - skip: True # [osx] - -# Based on channel tswicegood -package: - name: ruby - version: 2.1.7 - -source: - fn: ruby-2.1.7.tar.gz - url: https://cache.ruby-lang.org/pub/ruby/2.1/ruby-2.1.7.tar.gz - sha256: f59c1596ac39cc7e60126e7d3698c19f482f04060674fdfe0124e1752ba6dd81 - -test: - commands: - - ruby --version - - ruby -e 'puts "Hi, from Ruby!"' - - ruby -e 'require "rubygems"' - - gem --version - -requirements: - build: - - ncurses ==5.9 - - libxml2 ==2.9.2 - - readline ==6.2 - - yaml - - openssl 1.0.1g - - zlib - run: - - zlib - -about: - home: https://www.ruby-lang.org/ - license: BSD diff --git a/recipes/ruby/build.sh b/recipes/ruby/build.sh deleted file mode 100644 index 68a6a4eca8e5f3..00000000000000 --- a/recipes/ruby/build.sh +++ /dev/null @@ -1,19 +0,0 @@ -#!/bin/bash - -./configure \ - --prefix=$PREFIX \ - --enable-load-relative \ - --disable-install-doc \ - --enable-shared \ - --enable-rpath \ - --with-jemalloc \ - --with-opt-dir=$PREFIX \ - --with-libyaml-dir=$PREFIX \ - --with-openssl-dir=$PREFIX \ - --with-readline-dir=$PREFIX \ - --with-zlib-dir=$PREFIX - # --with-static-linked-ext \ - -make -make install - diff --git a/recipes/ruby/meta.yaml b/recipes/ruby/meta.yaml deleted file mode 100644 index b352c8958c7606..00000000000000 --- a/recipes/ruby/meta.yaml +++ /dev/null @@ -1,44 +0,0 @@ -package: - name: ruby - version: 2.2.3 - -build: - number: 1 - -source: - fn: ruby-2.2.3.tar.gz - url: https://cache.ruby-lang.org/pub/ruby/2.2/ruby-2.2.3.tar.gz - sha256: df795f2f99860745a416092a4004b016ccf77e8b82dec956b120f18bdc71edce - -requirements: - build: - - jemalloc 4.4.* - - openssl 1.0.* - - readline 6.2* - - yaml - - zlib 1.2.* - - gmp >=5.0.1,<7 - - gcc # [linux] - - llvm # [osx] - run: - - libgcc # [linux] - - jemalloc 4.4.* - - openssl 1.0.* - - readline 6.2* - - yaml - - gmp >=5.0.1,<7 - - zlib 1.2.* - -test: - commands: - - ruby --version - #- ruby -e "puts 'Hi, from Ruby!'" - #- ruby -e "require 'rubygems'" - # Tests failes on osx due to local installed gem versions - - gem --version # [linux] - - ruby -ropenssl -e "puts :OK" - -about: - home: https://www.ruby-lang.org - summary: Ruby is a dynamic, reflective, object-oriented, general-purpose programming language. - license: BSD diff --git a/recipes/rust-bio-tools/meta.yaml b/recipes/rust-bio-tools/meta.yaml index af7caa917ef06f..a960a7ac5d1489 100644 --- a/recipes/rust-bio-tools/meta.yaml +++ b/recipes/rust-bio-tools/meta.yaml @@ -1,17 +1,17 @@ -{% set version = "0.1.3" %} +{% set version = "0.2.0" %} package: name: rust-bio-tools version: {{version}} build: - number: 0 + number: 1 skip: true # [osx] source: fn: rust-bio-tools-{{version}}.tar.gz - url: https://github.com/rust-bio/rust-bio-tools/archive/v{{version}}.tar.gz - sha256: 8038ccfb26c1ae0e10f84bd09a8ec0313e8da1a8b1b097f2519b0c19cf00c0f4 + url: https://github.com/rust-bio/rust-bio-tools/archive/{{version}}.tar.gz + sha256: ae26b2687225dfcd229b2c8286daca62445eb34300d08030243e66eeade9bb15 requirements: build: diff --git a/recipes/rust-overlaps/meta.yaml b/recipes/rust-overlaps/meta.yaml index de0e16a1eab18b..16d8e31507a12e 100644 --- a/recipes/rust-overlaps/meta.yaml +++ b/recipes/rust-overlaps/meta.yaml @@ -5,7 +5,7 @@ package: version: {{version}} build: - number: 0 + number: 1 skip: True # [osx] source: @@ -17,9 +17,9 @@ requirements: build: - rust >=1.18.0 - gcc 4.8.2 - - zlib + - zlib {{CONDA_ZLIB}}* run: - - zlib + - zlib {{CONDA_ZLIB}}* - libgcc test: diff --git a/recipes/rust/build.sh b/recipes/rust/build.sh deleted file mode 100644 index 47b2f8710c4803..00000000000000 --- a/recipes/rust/build.sh +++ /dev/null @@ -1,3 +0,0 @@ -#!/bin/bash -e - -./install.sh --prefix=$PREFIX diff --git a/recipes/rust/meta.yaml b/recipes/rust/meta.yaml deleted file mode 100644 index 8f8afabb8299d5..00000000000000 --- a/recipes/rust/meta.yaml +++ /dev/null @@ -1,24 +0,0 @@ -{% set version = "1.14.0" %} - -package: - name: rust - version: {{ version }} - -build: - number: 0 - -source: - fn: rust-{{ version }}-x86_64-unknown-linux-gnu.tar.gz # [linux64] - url: https://static.rust-lang.org/dist/rust-{{ version }}-x86_64-unknown-linux-gnu.tar.gz # [linux64] - fn: rust-{{ version }}-x86_64-apple-darwin.tar.gz # [osx] - url: http://static.rust-lang.org/dist/rust-{{ version }}-x86_64-apple-darwin.tar.gz # [osx] - -test: - commands: - - rustc --help - - cargo --help - -about: - home: https://www.rust-lang.org - license: MIT - summary: Rust is a systems programming language that runs blazingly fast, prevents segfaults, and guarantees thread safety. diff --git a/recipes/salmon/meta.yaml b/recipes/salmon/meta.yaml index 2bf5581c82a379..eaf02f98ef3658 100644 --- a/recipes/salmon/meta.yaml +++ b/recipes/salmon/meta.yaml @@ -2,7 +2,7 @@ {% set llvm_version = "4.0.0" %} build: - number: 0 + number: 1 # OSX failing due to libary issues even though shipping with Salmon binary # dyld: Library not loaded: /usr/local/opt/tbb/lib/libtbbmalloc_proxy.dylib # https://travis-ci.org/bioconda/bioconda-recipes/jobs/211785820#L295 diff --git a/recipes/samsift/0.2.3/meta.yaml b/recipes/samsift/0.2.3/meta.yaml new file mode 100644 index 00000000000000..ecd6a98716ebd7 --- /dev/null +++ b/recipes/samsift/0.2.3/meta.yaml @@ -0,0 +1,42 @@ +{% set version = "0.2.3" %} +{% set sha256 = "893617fda0d4be2c2339848f2f7e9d93c4f45e98ace5729a796eb9e29c1d3d31" %} + +package: + name: samsift + version: {{ version }} + +source: + fn: samsift-{{ version }}.tar.gz + url: https://pypi.io/packages/source/s/samsift/samsift-{{version }}.tar.gz + sha256: {{ sha256 }} + +build: + number: 0 + skip: True # [py27] + entry_points: + - samsift = samsift.samsift:main + - samsift-norm-sam = samsift.samsift_norm_sam:main + + script: $PYTHON setup.py install --single-version-externally-managed --record=record.txt + +requirements: + build: + - python + - pysam + - wheel + - setuptools + run: + - python + - pysam + +test: + commands: + - samsift -v + - samsift -h + - samsift-norm-sam --help + - BAM=https://github.com/karel-brinda/samsift/raw/master/tests/tests/test.bam; curl -L ${BAM} | samsift + +about: + home: https://github.com/karel-brinda/samsift + license: MIT + summary: 'Advanced filtering and tagging of SAM/BAM alignments using Python expressions.' diff --git a/recipes/samsift/meta.yaml b/recipes/samsift/meta.yaml index ecd6a98716ebd7..bd8384394847d3 100644 --- a/recipes/samsift/meta.yaml +++ b/recipes/samsift/meta.yaml @@ -1,5 +1,5 @@ -{% set version = "0.2.3" %} -{% set sha256 = "893617fda0d4be2c2339848f2f7e9d93c4f45e98ace5729a796eb9e29c1d3d31" %} +{% set version = "0.2.5" %} +{% set sha256 = "1b02ec272201c0faf349ffbcc422fc1250f23f4f6a5563c1104cd37755044064" %} package: name: samsift diff --git a/recipes/samtools/0.1.12/meta.yaml b/recipes/samtools/0.1.12/meta.yaml index fb87eb20dbb349..11736fc757bd7e 100644 --- a/recipes/samtools/0.1.12/meta.yaml +++ b/recipes/samtools/0.1.12/meta.yaml @@ -3,7 +3,7 @@ about: license: MIT summary: Tools for dealing with SAM and BAM files build: - number: 1 + number: 2 package: name: samtools version: 0.1.12 diff --git a/recipes/samtools/0.1.13/meta.yaml b/recipes/samtools/0.1.13/meta.yaml index 8083dd777427ff..c14f192e70f9a2 100644 --- a/recipes/samtools/0.1.13/meta.yaml +++ b/recipes/samtools/0.1.13/meta.yaml @@ -3,7 +3,7 @@ about: license: MIT summary: Tools for dealing with SAM and BAM files build: - number: 0 + number: 1 package: name: samtools version: 0.1.13 diff --git a/recipes/samtools/0.1.14/meta.yaml b/recipes/samtools/0.1.14/meta.yaml index cc831572982bb0..cd291f7d488317 100644 --- a/recipes/samtools/0.1.14/meta.yaml +++ b/recipes/samtools/0.1.14/meta.yaml @@ -3,7 +3,7 @@ about: license: MIT summary: Tools for dealing with SAM and BAM files build: - number: 0 + number: 1 package: name: samtools version: 0.1.14 diff --git a/recipes/samtools/0.1.17/build.sh b/recipes/samtools/0.1.17/build.sh deleted file mode 100644 index 13ca6bd285f655..00000000000000 --- a/recipes/samtools/0.1.17/build.sh +++ /dev/null @@ -1,13 +0,0 @@ -#!/bin/bash - -CFLAGS="-fPIC ${CFLAGS}" - -env CFLAGS="${CFLAGS} $(pkg-config --cflags zlib)" \ - LDFLAGS="${LDFLAGS} $(pkg-config --libs zlib)" \ - make - -install -d "${PREFIX}/include/${PKG_NAME}" -install -d "${PREFIX}/lib" -install bam.h sam.h bgzf.h khash.h faidx.h \ - "${PREFIX}/include/${PKG_NAME}" -install libbam.a "${PREFIX}/lib" diff --git a/recipes/samtools/0.1.17/makefiles.patch b/recipes/samtools/0.1.17/makefiles.patch deleted file mode 100644 index 44cddcb6da7157..00000000000000 --- a/recipes/samtools/0.1.17/makefiles.patch +++ /dev/null @@ -1,102 +0,0 @@ ---- Makefile -+++ Makefile -@@ -1,6 +1,6 @@ - CC= gcc --CFLAGS= -g -Wall -O2 #-m64 #-arch ppc --DFLAGS= -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -+CFLAGS+= -Wall -+DFLAGS= -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=0 - KNETFILE_O= knetfile.o - LOBJS= bgzf.o kstring.o bam_aux.o bam.o bam_import.o sam.o bam_index.o \ - bam_pileup.o bam_lpileup.o bam_md.o razf.o faidx.o bedidx.o \ -@@ -13,7 +13,6 @@ - INCLUDES= -I. - SUBDIRS= . bcftools misc - LIBPATH= --LIBCURSES= -lcurses # -lXCurses - - .SUFFIXES:.c .o - -@@ -41,13 +40,13 @@ - $(AR) -csru $@ $(LOBJS) - - samtools:lib-recur $(AOBJS) -- $(CC) $(CFLAGS) -o $@ $(AOBJS) -Lbcftools $(LIBPATH) libbam.a -lbcf $(LIBCURSES) -lm -lz -+ $(CC) $(CFLAGS) -o $@ $(AOBJS) -Lbcftools $(LIBPATH) libbam.a -lbcf $(LIBCURSES) $(LDFLAGS) -lm -lz - - razip:razip.o razf.o $(KNETFILE_O) -- $(CC) $(CFLAGS) -o $@ razf.o razip.o $(KNETFILE_O) -lz -+ $(CC) $(CFLAGS) -o $@ razf.o razip.o $(KNETFILE_O) $(LDFLAGS) -lz - - bgzip:bgzip.o bgzf.o $(KNETFILE_O) -- $(CC) $(CFLAGS) -o $@ bgzf.o bgzip.o $(KNETFILE_O) -lz -+ $(CC) $(CFLAGS) -o $@ bgzf.o bgzip.o $(KNETFILE_O) $(LDFLAGS) -lz - - razip.o:razf.h - bam.o:bam.h razf.h bam_endian.h kstring.h sam_header.h -@@ -73,10 +72,10 @@ - - - libbam.1.dylib-local:$(LOBJS) -- libtool -dynamic $(LOBJS) -o libbam.1.dylib -lc -lz -+ libtool -dynamic $(LOBJS) -o libbam.1.dylib $(LDFLAGS) -lc -lz - - libbam.so.1-local:$(LOBJS) -- $(CC) -shared -Wl,-soname,libbam.so -o libbam.so.1 $(LOBJS) -lc -lz -+ $(CC) -shared -Wl,-soname,libbam.so -o libbam.so.1 $(LOBJS) $(LDFLAGS) -lc -lz - - dylib: - @$(MAKE) cleanlocal; \ ---- bcftools/Makefile -+++ bcftools/Makefile -@@ -31,7 +31,7 @@ - $(AR) -csru $@ $(LOBJS) - - bcftools:lib $(AOBJS) -- $(CC) $(CFLAGS) -o $@ $(AOBJS) -L. $(LIBPATH) -lbcf -lm -lz -+ $(CC) $(CFLAGS) -o $@ $(AOBJS) -L. $(LIBPATH) -lbcf $(LDFLAGS) -lm -lz - - bcf.o:bcf.h - vcf.o:bcf.h ---- examples/Makefile -+++ examples/Makefile -@@ -40,7 +40,7 @@ - (cd ..; make libbam.a) - - calDepth:../libbam.a calDepth.c -- gcc -g -Wall -O2 -I.. calDepth.c -o $@ -L.. -lbam -lm -lz -+ gcc -g -Wall -O2 -I.. calDepth.c -o $@ -L.. -lbam $(LDFLAGS) -lm -lz - - clean: - rm -fr *.bam *.bai *.glf* *.fai *.pileup* *~ calDepth *.dSYM ex1*.rg ex1.bcf ---- misc/Makefile -+++ misc/Makefile -@@ -28,13 +28,13 @@ - lib: - - afs2:afs2.o -- $(CC) $(CFLAGS) -o $@ afs2.o -lm -lz -L.. -lbam -+ $(CC) $(CFLAGS) -o $@ afs2.o $(LDFLAGS) -lm -lz -L.. -lbam - - wgsim:wgsim.o - $(CC) $(CFLAGS) -o $@ wgsim.o -lm - - md5fa:md5.o md5fa.o md5.h ../kseq.h -- $(CC) $(CFLAGS) -o $@ md5.o md5fa.o -lz -+ $(CC) $(CFLAGS) -o $@ md5.o md5fa.o $(LDFLAGS) -lz - - md5sum-lite:md5sum-lite.o - $(CC) $(CFLAGS) -o $@ md5sum-lite.o -@@ -43,10 +43,10 @@ - $(CC) -c $(CFLAGS) -DMD5SUM_MAIN -o $@ md5.c - - maq2sam-short:maq2sam.c -- $(CC) $(CFLAGS) -o $@ maq2sam.c -lz -+ $(CC) $(CFLAGS) -o $@ maq2sam.c $(LDFLAGS) -lz - - maq2sam-long:maq2sam.c -- $(CC) $(CFLAGS) -DMAQ_LONGREADS -o $@ maq2sam.c -lz -+ $(CC) $(CFLAGS) -DMAQ_LONGREADS -o $@ maq2sam.c $(LDFLAGS) -lz - - md5fa.o:md5.h md5fa.c - $(CC) $(CFLAGS) -c -I.. -o $@ md5fa.c diff --git a/recipes/samtools/0.1.17/meta.yaml b/recipes/samtools/0.1.17/meta.yaml deleted file mode 100644 index d858639397806c..00000000000000 --- a/recipes/samtools/0.1.17/meta.yaml +++ /dev/null @@ -1,36 +0,0 @@ -package: - name: samtools - version: 0.1.17 - -requirements: - build: - - gcc - - pkg-config - - zlib - run: - - pkg-config - - zlib - -source: - fn: samtools-0.1.17.tar.bz2 - url: - - http://downloads.sourceforge.net/project/samtools/samtools/0.1.17/samtools-0.1.17.tar.bz2 - - http://download.lab7.io/sources/samtools-0.1.17.tar.bz2 - md5: 9549f7a6bba894766df9c3dd18d61f0b - patches: - - makefiles.patch - - sources.patch - -build: - number: 0 - -about: - home: http://samtools.sourceforge.net/ - license: MIT - license_file: COPYING - summary: "Library for manipulating alignments in the SAM/BAM format" - -test: - commands: - - samtools --help - diff --git a/recipes/samtools/0.1.17/sources.patch b/recipes/samtools/0.1.17/sources.patch deleted file mode 100644 index 8e40146567ebaf..00000000000000 --- a/recipes/samtools/0.1.17/sources.patch +++ /dev/null @@ -1,28 +0,0 @@ ---- bgzf.c -+++ bgzf.c -@@ -73,7 +73,7 @@ - static const int Z_DEFAULT_MEM_LEVEL = 8; - - --inline -+static inline - void - packInt16(uint8_t* buffer, uint16_t value) - { -@@ -81,14 +81,14 @@ - buffer[1] = value >> 8; - } - --inline -+static inline - int - unpackInt16(const uint8_t* buffer) - { - return (buffer[0] | (buffer[1] << 8)); - } - --inline -+static inline - void - packInt32(uint8_t* buffer, uint32_t value) - { diff --git a/recipes/samtools/0.1.19/build.sh b/recipes/samtools/0.1.19/build.sh index 5bb6c0cf0cdcb6..b7fd9188b14c5f 100644 --- a/recipes/samtools/0.1.19/build.sh +++ b/recipes/samtools/0.1.19/build.sh @@ -1,5 +1,5 @@ #!/bin/sh -make INCLUDES="-I. -I$PREFIX/include -I$PREFIX/include/ncurses" LIBCURSES="-L$PREFIX/lib -lncurses" +make INCLUDES="-I. -I$PREFIX/include -I$PREFIX/include/ncurses" LIBCURSES="-L$PREFIX/lib -lncurses -ltinfo" mkdir -p $PREFIX/bin mv samtools $PREFIX/bin mv bcftools/bcftools $PREFIX/bin diff --git a/recipes/samtools/0.1.19/meta.yaml b/recipes/samtools/0.1.19/meta.yaml index e548d13bbbba8c..eb5b4402f534a6 100644 --- a/recipes/samtools/0.1.19/meta.yaml +++ b/recipes/samtools/0.1.19/meta.yaml @@ -3,20 +3,19 @@ about: license: MIT summary: Tools for dealing with SAM and BAM files build: - number: 2 + number: 3 package: name: samtools version: 0.1.19 requirements: build: - - gcc # [not osx] - - llvm # [osx] - - ncurses - - zlib + - gcc + - ncurses {{CONDA_NCURSES}}* + - zlib {{CONDA_ZLIB}}* run: - - libgcc # [not osx] - - ncurses - - zlib + - libgcc + - ncurses {{CONDA_NCURSES}}* + - zlib {{CONDA_ZLIB}}* source: fn: samtools-0.1.19.tar.bz2 sha256: d080c9d356e5f0ad334007e4461cbcee3c4ca97b8a7a5a48c44883cf9dee63d4 diff --git a/recipes/samtools/1.0/build.sh b/recipes/samtools/1.0/build.sh index 4b92f88afa221c..10203265a25651 100644 --- a/recipes/samtools/1.0/build.sh +++ b/recipes/samtools/1.0/build.sh @@ -1,2 +1,13 @@ #!/bin/sh +set -e + +# remove hard-coded *flags +sed -i.bak 's/^CPPFLAGS\s*=/CPPFLAGS +=/g' Makefile +sed -i.bak 's/^LDFLAGS\s*=/LDFLAGS +=/g' Makefile +sed -i.bak 's/^CPPFLAGS\s*=/CPPFLAGS +=/g' htslib-$PKG_VERSION/Makefile +sed -i.bak 's/^LDFLAGS\s*=/LDFLAGs +=/g' htslib-$PKG_VERSION/Makefile +sed -i.bak -e 's/-lcurses/-lncurses -ltinfo/' Makefile + +export CPPFLAGS="-I$PREFIX/include" +export LDFLAGS="-L$PREFIX/lib" make install prefix=$PREFIX diff --git a/recipes/samtools/1.0/meta.yaml b/recipes/samtools/1.0/meta.yaml index 4c5f5712722703..0d9d798ac54b55 100644 --- a/recipes/samtools/1.0/meta.yaml +++ b/recipes/samtools/1.0/meta.yaml @@ -2,22 +2,27 @@ about: home: https://github.com/samtools/samtools license: MIT summary: Tools for dealing with SAM, BAM and CRAM files + build: - number: 0 + number: 1 + package: name: samtools version: '1.0' + requirements: build: - - ncurses ==5.9 - - zlib ==1.2.8 + - ncurses {{CONDA_NCURSES}}* + - zlib {{CONDA_ZLIB}}* run: - - ncurses ==5.9 - - zlib ==1.2.8 + - ncurses {{CONDA_NCURSES}}* + - zlib {{CONDA_ZLIB}}* + source: fn: samtools-1.0.tar.bz2 sha256: 7340b843663c3f54a902a06f2f73c68198f3a62d29a2ed20671139957f7fd7c0 url: http://downloads.sourceforge.net/project/samtools/samtools/1.0/samtools-1.0.tar.bz2 + test: commands: - "samtools view --help 2>&1 | grep Notes > /dev/null" diff --git a/recipes/samtools/1.1/meta.yaml b/recipes/samtools/1.1/meta.yaml index fb2d10ed74c60c..33834190010ed1 100644 --- a/recipes/samtools/1.1/meta.yaml +++ b/recipes/samtools/1.1/meta.yaml @@ -3,17 +3,17 @@ about: license: MIT summary: Tools for dealing with SAM, BAM and CRAM files build: - number: 0 + number: 1 package: name: samtools version: '1.1' requirements: build: - - ncurses ==5.9 - - zlib ==1.2.8 + - ncurses {{CONDA_NCURSES}}* + - zlib {{CONDA_ZLIB}}* run: - - ncurses ==5.9 - - zlib ==1.2.8 + - ncurses {{CONDA_NCURSES}}* + - zlib {{CONDA_ZLIB}}* source: fn: samtools-1.1.tar.bz2 sha256: c24d26c303153d72b5bf3cc11f72c6c375a4ca1140cc485648c8c5473414b7f8 diff --git a/recipes/samtools/meta.yaml b/recipes/samtools/meta.yaml index 9f40d9385858b5..87e298055c36e5 100644 --- a/recipes/samtools/meta.yaml +++ b/recipes/samtools/meta.yaml @@ -5,7 +5,7 @@ package: version: {{ version }} build: - number: 0 + number: 1 source: fn: samtools-{{ version }}.tar.bz2 diff --git a/recipes/scalpel/meta.yaml b/recipes/scalpel/meta.yaml index bc20aa1a1167e6..bebac2895728d1 100644 --- a/recipes/scalpel/meta.yaml +++ b/recipes/scalpel/meta.yaml @@ -8,15 +8,16 @@ source: md5: 682c9f1cd6ab2cb11c6866f303c673f0 build: - number: 0 + number: 1 skip: True # [osx] + string: bamtools{{CONDA_BAMTOOLS}}_{{PKG_BUILDNUM}} requirements: build: - cmake - - bamtools + - bamtools {{ CONDA_BAMTOOLS }}* run: - - bamtools + - bamtools {{ CONDA_BAMTOOLS }}* - samtools - bcftools - perl diff --git a/recipes/schema-salad/meta.yaml b/recipes/schema-salad/meta.yaml index 6faa2f00521ae4..1453e49433ef7b 100644 --- a/recipes/schema-salad/meta.yaml +++ b/recipes/schema-salad/meta.yaml @@ -1,4 +1,4 @@ -{% set version="2.6.20171116190026" %} +{% set version="2.6.20171201034858" %} package: name: schema-salad @@ -7,7 +7,7 @@ package: source: fn: schema-salad-{{ version }}.tar.gz url: https://pypi.io/packages/source/s/schema-salad/schema-salad-{{ version }}.tar.gz - md5: a8909652bf4f764880e7a3275a2596e4 + md5: 937ce8e3702101e6c0f3711297e6163a build: entry_points: @@ -23,7 +23,7 @@ requirements: - rdflib >=4.2.0 - rdflib-jsonld >=0.3.0 - mistune >=0.7.3,<0.8 - - typing >=3.5.2,<3.6 + - typing >=3.5.3,<3.6 - ruamel.yaml >=0.12.4,<0.15 - cachecontrol >=0.11.7,<0.12 - lockfile @@ -35,8 +35,8 @@ requirements: - requests - rdflib >=4.2.0 - rdflib-jsonld >=0.3.0 - - mistune - - typing >=3.5.2,<3.6 + - mistune >=0.7.3,<0.8 + - typing >=3.5.3,<3.6 - ruamel.yaml >=0.12.4,<0.15 - cachecontrol >=0.11.7,<0.12 - lockfile diff --git a/recipes/segemehl/meta.yaml b/recipes/segemehl/meta.yaml index 46f858d770d88a..34f63217f5a13d 100644 --- a/recipes/segemehl/meta.yaml +++ b/recipes/segemehl/meta.yaml @@ -7,7 +7,7 @@ about: summary: Short read mapping with gaps build: - number: 2 + number: 3 source: fn: segemehl_0_2_0.tar.gz @@ -18,11 +18,11 @@ requirements: build: - llvm # [osx] - gcc # [linux] - - zlib + - zlib {{CONDA_ZLIB}}* - ncurses {{CONDA_NCURSES}}* run: - libgcc # [linux] - - zlib + - zlib {{CONDA_ZLIB}}* - ncurses {{CONDA_NCURSES}}* test: diff --git a/recipes/selectsequencesfrommsa/meta.yaml b/recipes/selectsequencesfrommsa/meta.yaml index 43551078756087..ed8646794a0ddb 100644 --- a/recipes/selectsequencesfrommsa/meta.yaml +++ b/recipes/selectsequencesfrommsa/meta.yaml @@ -12,21 +12,21 @@ source: md5: {{ md5 }} build: - number: 0 + number: 1 skip: True # [osx] requirements: build: - stack >=1.3.2 - gmp - - zlib + - zlib {{CONDA_ZLIB}}* - perl run: - gmp - perl - libgcc - - zlib + - zlib {{CONDA_ZLIB}}* test: commands: diff --git a/recipes/selscan/meta.yaml b/recipes/selscan/meta.yaml index b6013d0ea45282..746f8505a09f49 100644 --- a/recipes/selscan/meta.yaml +++ b/recipes/selscan/meta.yaml @@ -2,7 +2,7 @@ package: name: selscan version: "1.1.0b" build: - number: 0 + number: 1 skip: False source: fn: 1.1.0b.zip @@ -16,12 +16,12 @@ requirements: - gcc #- openblas #- gsl - - zlib + - zlib {{CONDA_ZLIB}}* run: - libgcc #- openblas #- gsl - - zlib + - zlib {{CONDA_ZLIB}}* #- perl-threaded test: commands: diff --git a/recipes/sentieon/meta.yaml b/recipes/sentieon/meta.yaml index 2975acf6947bff..002a96ca0be196 100644 --- a/recipes/sentieon/meta.yaml +++ b/recipes/sentieon/meta.yaml @@ -17,7 +17,7 @@ source: - bwa_symlinks.patch build: - number: 1 + number: 2 # Currently failing on OSX when copying and fixing shared libraries # included with sentieon package. I don't understand problem: # https://travis-ci.org/bioconda/bioconda-recipes/jobs/141822657 diff --git a/recipes/seqan_tcoffee/meta.yaml b/recipes/seqan_tcoffee/meta.yaml index 9f07323bd1c3c9..ee6ff19b119735 100755 --- a/recipes/seqan_tcoffee/meta.yaml +++ b/recipes/seqan_tcoffee/meta.yaml @@ -8,7 +8,7 @@ source: sha256: df083d5939d7e73fd00bbc6bb291ac7ea7b8d446cf89a9758fdffdc0eca9ec1c build: - number: 0 + number: 1 skip: True # [osx] requirements: diff --git a/recipes/seqprep/1.1/meta.yaml b/recipes/seqprep/1.1/meta.yaml index f4088bfe2d66b5..f7e8ccac74efb3 100644 --- a/recipes/seqprep/1.1/meta.yaml +++ b/recipes/seqprep/1.1/meta.yaml @@ -1,5 +1,5 @@ build: - number: 0 + number: 1 skip: True # [osx] package: @@ -16,9 +16,9 @@ source: requirements: build: - - zlib + - zlib {{CONDA_ZLIB}}* run: - - zlib + - zlib {{CONDA_ZLIB}}* test: commands: diff --git a/recipes/seqprep/meta.yaml b/recipes/seqprep/meta.yaml index 48cc394e09c469..c7ee37bfbf6e2b 100644 --- a/recipes/seqprep/meta.yaml +++ b/recipes/seqprep/meta.yaml @@ -7,7 +7,7 @@ package: version: {{ version }} build: - number: 0 + number: 1 skip: True # [osx] source: @@ -20,9 +20,9 @@ source: requirements: build: - - zlib + - zlib {{CONDA_ZLIB}}* run: - - zlib + - zlib {{CONDA_ZLIB}}* test: commands: diff --git a/recipes/seqtk/meta.yaml b/recipes/seqtk/meta.yaml index b0243201d64646..1e617b5e68cc1d 100644 --- a/recipes/seqtk/meta.yaml +++ b/recipes/seqtk/meta.yaml @@ -8,15 +8,15 @@ source: md5: 255ffe05bf2f073dc57abcff97f11a37 build: - number: 0 + number: 1 requirements: build: - gcc # [not osx] - llvm # [osx] - - zlib + - zlib {{CONDA_ZLIB}}* run: - - zlib + - zlib {{CONDA_ZLIB}}* about: diff --git a/recipes/seqtk/r82/meta.yaml b/recipes/seqtk/r82/meta.yaml index 698ff6722eb924..6bc15852e4bfe1 100644 --- a/recipes/seqtk/r82/meta.yaml +++ b/recipes/seqtk/r82/meta.yaml @@ -8,17 +8,17 @@ source: sha256: dd4b54a3ba57279659153204aa59aa1d5efe4d307549ac7b8e93b67eb9d3248f build: - number: 0 + number: 1 skip: False requirements: build: - gcc # [not osx] - llvm # [osx] - - zlib + - zlib {{CONDA_ZLIB}}* run: - libgcc - - zlib + - zlib {{CONDA_ZLIB}}* about: home: https://github.com/lh3/seqtk diff --git a/recipes/sga/meta.yaml b/recipes/sga/meta.yaml index cbefde0e2ce041..48dd3578559f96 100644 --- a/recipes/sga/meta.yaml +++ b/recipes/sga/meta.yaml @@ -10,7 +10,8 @@ source: sha256: 1b18996e6ec47985bc4889a8cbc3cd4dd3a8c7d385ae9f450bd474e36342558b build: - number: 1 + number: 2 + string: bamtools{{CONDA_BAMTOOLS}}_{{PKG_BUILDNUM}} requirements: build: @@ -20,13 +21,13 @@ requirements: - automake - m4 - sparsehash - - bamtools + - bamtools {{ CONDA_BAMTOOLS }}* - zlib {{ CONDA_ZLIB }}* run: - libgcc # [not osx] - libcxx # [osx] - sparsehash - - bamtools + - bamtools {{ CONDA_BAMTOOLS }}* - zlib {{ CONDA_ZLIB }}* test: diff --git a/recipes/shorah/1.0.0/meta.yaml b/recipes/shorah/1.0.0/meta.yaml index ecc59977468a53..32e0e8b7802672 100644 --- a/recipes/shorah/1.0.0/meta.yaml +++ b/recipes/shorah/1.0.0/meta.yaml @@ -4,7 +4,7 @@ package: build: skip: True # [py3k] - number: 0 + number: 1 source: fn: shorah-1.0.0.tar.bz2 @@ -13,17 +13,17 @@ source: requirements: build: - - gcc # [linux] - - llvm # [osx] - - python - - gsl - - zlib + - gcc # [linux] + - llvm # [osx] + - python + - gsl {{CONDA_GSL}}* + - zlib {{CONDA_ZLIB}}* run: - - python - - samtools - - biopython - - gsl - - zlib + - python + - samtools + - biopython + - gsl {{CONDA_GSL}}* + - zlib {{CONDA_ZLIB}}* about: home: https://github.com/cbg-ethz/shorah diff --git a/recipes/shorah/1.1.0/meta.yaml b/recipes/shorah/1.1.0/meta.yaml index af7ebe279f9bea..5a42bf9c1c0efb 100644 --- a/recipes/shorah/1.1.0/meta.yaml +++ b/recipes/shorah/1.1.0/meta.yaml @@ -3,7 +3,7 @@ package: version: "1.1.0" build: - number: 0 + number: 1 source: fn: shorah-1.1.0.tar.bz2 @@ -12,18 +12,18 @@ source: requirements: build: - - gcc # [linux] - - llvm # [osx] - - python - - gsl - - zlib + - gcc # [linux] + - llvm # [osx] + - python + - gsl {{CONDA_GSL}}* + - zlib {{CONDA_ZLIB}}* run: - - python - - samtools - - biopython - - numpy - - gsl - - zlib + - python + - samtools + - biopython + - numpy + - gsl {{CONDA_GSL}}* + - zlib {{CONDA_ZLIB}}* about: home: https://github.com/cbg-ethz/shorah diff --git a/recipes/shorah/1.1.3/meta.yaml b/recipes/shorah/1.1.3/meta.yaml index 43e1377808b632..2baad361e53675 100644 --- a/recipes/shorah/1.1.3/meta.yaml +++ b/recipes/shorah/1.1.3/meta.yaml @@ -13,7 +13,7 @@ package: version: {{ version }} build: - number: 0 + number: 1 source: fn: {{ name }}-{{ version }}.tar.bz2 diff --git a/recipes/short-read-connector/meta.yaml b/recipes/short-read-connector/meta.yaml index 007727409912b7..e9a48681647578 100644 --- a/recipes/short-read-connector/meta.yaml +++ b/recipes/short-read-connector/meta.yaml @@ -8,7 +8,7 @@ source: md5: "dfb9ea38a562df02c5046574d1bba1bb" build: - number: 0 + number: 1 requirements: build: diff --git a/recipes/shortstack/meta.yaml b/recipes/shortstack/meta.yaml index c348da47726773..9c5e6b9666c6d1 100644 --- a/recipes/shortstack/meta.yaml +++ b/recipes/shortstack/meta.yaml @@ -1,6 +1,6 @@ {% set name = "ShortStack" %} -{% set version = "3.8.3" %} -{% set sha256 = "7c76f51ed949ca95ec5df7cb54803ae2350658fd64c75909351d5a856abb0dbe" %} +{% set version = "3.8.5" %} +{% set sha256 = "3d947526b1953540dc0c486985772fa5fa6d57b28c966ca2d38e18cf8283bc3a" %} package: name: {{ name|lower }} diff --git a/recipes/sickle-trim/meta.yaml b/recipes/sickle-trim/meta.yaml index 02118cc7fd308a..31a849e690512c 100644 --- a/recipes/sickle-trim/meta.yaml +++ b/recipes/sickle-trim/meta.yaml @@ -11,13 +11,13 @@ source: sha256: {{ sha256 }} build: - number: 1 + number: 2 requirements: build: - - zlib 1.2.8 + - zlib {{CONDA_ZLIB}}* run: - - zlib 1.2.8 + - zlib {{CONDA_ZLIB}}* test: commands: diff --git a/recipes/slang/meta.yaml b/recipes/slang/meta.yaml index 5023004aa34c23..3b4c40eba92a49 100644 --- a/recipes/slang/meta.yaml +++ b/recipes/slang/meta.yaml @@ -1,5 +1,5 @@ build: - number: 0 + number: 1 skip: True # [osx] string: "ncurses{{CONDA_NCURSES}}_{{PKG_BUILDNUM}}" @@ -8,21 +8,21 @@ package: version: 2.3.0 source: - fn: slang-2.3.0.tar.bz2 - url: http://www.jedsoft.org/releases/slang/slang-2.3.0.tar.bz2 - sha1: 6e26e90307d4569e5feef195648c0858ba27f7ac + fn: slang-2.3.0.tar.bz + url: https://depot.galaxyproject.org/software/slang/slang_2.3.0_src_all.tar.bz2 + sha1: 34540ffc5331cc545c1035b06a72b4f8d375973d requirements: build: - readline - ncurses {{CONDA_NCURSES}}* - libpng - - zlib + - zlib {{CONDA_ZLIB}}* run: - readline - ncurses {{CONDA_NCURSES}}* - libpng - - zlib + - zlib {{CONDA_ZLIB}}* test: commands: diff --git a/recipes/slclust/meta.yaml b/recipes/slclust/meta.yaml index 461259279d43ef..3f9e0619d3db6c 100644 --- a/recipes/slclust/meta.yaml +++ b/recipes/slclust/meta.yaml @@ -8,16 +8,16 @@ source: sha256: 9e21b65288e7fc35647721380cfedffd68608e164b4240c692c511c18c1620f8 build: - number: 1 + number: 2 requirements: build: - gcc # [linux] - llvm # [osx] - - zlib + - zlib {{CONDA_ZLIB}}* run: - libgcc # [linux] - - zlib + - zlib {{CONDA_ZLIB}}* test: commands: diff --git a/recipes/smalt/meta.yaml b/recipes/smalt/meta.yaml index ffb73d966cb465..84138eb593fc6c 100644 --- a/recipes/smalt/meta.yaml +++ b/recipes/smalt/meta.yaml @@ -1,5 +1,5 @@ build: - number: 0 + number: 1 package: name: smalt @@ -15,12 +15,12 @@ requirements: - libtool - pkg-config - bambamc - - zlib + - zlib {{CONDA_ZLIB}}* - python >=2.6,<3 # used by 'make check' - samtools # used by 'make check' run: - bambamc - - zlib + - zlib {{CONDA_ZLIB}}* - libgcc test: commands: diff --git a/recipes/snakemake/meta.yaml b/recipes/snakemake/meta.yaml index e2150ade6447d9..53bd9b070c1b96 100644 --- a/recipes/snakemake/meta.yaml +++ b/recipes/snakemake/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "4.6.0" %} +{% set version = "4.7.0" %} package: name: snakemake @@ -7,7 +7,7 @@ package: source: fn: snakemake-{{ version }}.tar.gz url: https://pypi.io/packages/source/s/snakemake/snakemake-{{ version }}.tar.gz - sha256: c5e2e44ec59233a2763f54c9d534f7f580288ec135230bccd6d5ac7f6e25314b + sha256: a1c3245f47489219d212980f649ce435bc29b39638dade379e85f65a11c7e082 build: number: 0 @@ -26,12 +26,14 @@ requirements: - ratelimiter - configargparse - appdirs + - datrie run: - python - wrapt - requests - docutils - pyyaml + - datrie - requests >=2.8.1 # require this dropbox version to ensure that a conda doesn't pick up the # outdated version available diff --git a/recipes/sniffles/meta.yaml b/recipes/sniffles/meta.yaml index ce9fe528e4e05d..4b7948f7d87eeb 100644 --- a/recipes/sniffles/meta.yaml +++ b/recipes/sniffles/meta.yaml @@ -12,19 +12,20 @@ source: sha256: {{ hash }} build: - number: 0 + number: 1 + string: bamtools{{CONDA_BAMTOOLS}}_{{PKG_BUILDNUM}} requirements: build: - gcc - cmake - zlib {{CONDA_ZLIB}}* - - bamtools >=2.3.0 + - bamtools {{ CONDA_BAMTOOLS }}* - tclap >=1.2.1 run: - zlib {{CONDA_ZLIB}}* - libgcc - - bamtools >=2.3.0 + - bamtools {{ CONDA_BAMTOOLS }}* - tclap >=1.2.1 test: diff --git a/recipes/snippy/3.0/meta.yaml b/recipes/snippy/3.0/meta.yaml index faed7008b5fc3c..3dd1b2a948166d 100644 --- a/recipes/snippy/3.0/meta.yaml +++ b/recipes/snippy/3.0/meta.yaml @@ -13,7 +13,7 @@ build: requirements: build: - - perl-threaded + - perl - perl-bioperl - perl-app-cpanminus - perl-module-build @@ -25,7 +25,7 @@ requirements: - vcftools - snpeff run: - - perl-threaded + - perl - perl-bioperl - bwa - samtools diff --git a/recipes/snippy/meta.yaml b/recipes/snippy/meta.yaml index fb7d36147c87af..5b1f6c4544e508 100644 --- a/recipes/snippy/meta.yaml +++ b/recipes/snippy/meta.yaml @@ -12,7 +12,7 @@ source: url: https://github.com/tseemann/{{ name }}/archive/v{{ version }}.tar.gz build: - number: 0 + number: 1 requirements: run: @@ -24,9 +24,9 @@ requirements: - bwa >=0.7.12 - samtools >=1.3 - parallel >=20130422 - - freebayes + - freebayes >=1.1 - vcflib - - vcftools + - vcftools >=0.1.14 - snpeff >=4.3 test: diff --git a/recipes/snoscan/meta.yaml b/recipes/snoscan/meta.yaml index 9208b69f562bb8..e69d96b7d573ad 100644 --- a/recipes/snoscan/meta.yaml +++ b/recipes/snoscan/meta.yaml @@ -6,29 +6,29 @@ package: version: {{ version }} build: - number: 0 + number: 1 source: fn: {{ name|lower }}_{{ version }}.tar.gz - url: http://lowelab.ucsc.edu/software/snoscan-0.9.tar.gz + url: https://depot.galaxyproject.org/software/snoscan/snoscan_0.9b_src_all.tar.gz md5: 30719dc179f00c892d50ce070336d0a1 patches: - patches/sort-snos.patch - patches/sqio.c.patch - + requirements: build: - gcc # [not osx] - llvm # [osx] - - zlib + - zlib {{CONDA_ZLIB}}* - perl - perl-app-cpanminus - perl-module-build run: - libgcc # [not osx] - - zlib + - zlib {{CONDA_ZLIB}}* - perl test: @@ -40,4 +40,3 @@ about: home: http://lowelab.ucsc.edu/snoscan summary: Search for C/D box methylation guide snoRNA genes in a genomic sequence licence: GPL - diff --git a/recipes/snp-dists/meta.yaml b/recipes/snp-dists/meta.yaml index 4835fb669cb662..9896fad623bb72 100644 --- a/recipes/snp-dists/meta.yaml +++ b/recipes/snp-dists/meta.yaml @@ -6,7 +6,7 @@ package: version: {{ version }} build: - number: 0 + number: 1 source: fn: {{ name }}_v{{ version }}.tar.gz diff --git a/recipes/snp-sites/meta.yaml b/recipes/snp-sites/meta.yaml index 29268e1d207fad..9537c1f1ee8835 100644 --- a/recipes/snp-sites/meta.yaml +++ b/recipes/snp-sites/meta.yaml @@ -6,7 +6,7 @@ package: version: {{ version }} build: - number: 0 + number: 1 source: fn: {{ name|lower }}_{{ version }}.tar.gz @@ -22,11 +22,11 @@ requirements: - automake - autoconf - libtool - - zlib + - zlib {{CONDA_ZLIB}}* run: - libgcc [not osx] - - zlib + - zlib {{CONDA_ZLIB}}* test: commands: diff --git a/recipes/soapdenovo-trans/meta.yaml b/recipes/soapdenovo-trans/meta.yaml index 3775ca41bd7d7d..d0d62490ba113c 100644 --- a/recipes/soapdenovo-trans/meta.yaml +++ b/recipes/soapdenovo-trans/meta.yaml @@ -10,7 +10,7 @@ source: - makefile.patch build: - number: 0 + number: 1 # The source package includes a static library with ELF object files, which is linked during compilation. # The C source files aren't included, so rebuilding in Mach-O format isn't possible. skip: True # [osx] @@ -19,11 +19,11 @@ requirements: build: - gcc # [linux] - llvm # [osx] - - zlib + - zlib {{CONDA_ZLIB}}* run: - libgcc # [linux] - - zlib + - zlib {{CONDA_ZLIB}}* test: commands: diff --git a/recipes/soapdenovo2-errorcorrection/meta.yaml b/recipes/soapdenovo2-errorcorrection/meta.yaml index 6378559a4d8565..4607ba60692bae 100644 --- a/recipes/soapdenovo2-errorcorrection/meta.yaml +++ b/recipes/soapdenovo2-errorcorrection/meta.yaml @@ -4,20 +4,20 @@ about: summary: 'Error correction for soapdenovo2.' build: - number: 0 + number: 1 package: name: soapdenovo2-errorcorrection version: '2.0' requirements: - build: - - gcc # [linux] - - llvm # [osx] - - zlib - run: - - libgcc # [linux] - - zlib + build: + - gcc # [linux] + - llvm # [osx] + - zlib {{CONDA_ZLIB}}* + run: + - libgcc # [linux] + - zlib {{CONDA_ZLIB}}* source: fn: errorcorrection.tar.gz diff --git a/recipes/soapdenovo2-gapcloser/meta.yaml b/recipes/soapdenovo2-gapcloser/meta.yaml index 1b3e0fd98a8666..dae33198c42cb5 100644 --- a/recipes/soapdenovo2-gapcloser/meta.yaml +++ b/recipes/soapdenovo2-gapcloser/meta.yaml @@ -4,7 +4,7 @@ about: summary: 'a tool named GapCloser for SOAPdenovo.' build: - number: 0 + number: 1 package: name: soapdenovo2-gapcloser @@ -12,17 +12,17 @@ package: requirements: build: - - gcc # [linux] - - llvm # [osx] - - zlib + - gcc + - zlib {{CONDA_ZLIB}}* run: - - libgcc # [linux] - - zlib + - libgcc + - zlib {{CONDA_ZLIB}}* source: fn: gapcloser.tar.gz - url: https://sourceforge.net/projects/soapdenovo2/files/GapCloser/src/r6/GapCloser-src-v1.12-r6.tgz/download + url: https://sourceforge.net/projects/soapdenovo2/files/GapCloser/src/r6/GapCloser-src-v1.12-r6.tgz + sha256: a6d4b21c6da838bb4274b537c6625d4688624166673bc22c74eca00c061a6911 test: commands: - - GapCloser 2>&1 | grep 'input scaffold file name' + - GapCloser 2>&1 | grep "input scaffold file name" diff --git a/recipes/soapdenovo2-prepare/meta.yaml b/recipes/soapdenovo2-prepare/meta.yaml index 2bcfb7259605cf..8a4b45a9aa59fc 100644 --- a/recipes/soapdenovo2-prepare/meta.yaml +++ b/recipes/soapdenovo2-prepare/meta.yaml @@ -4,7 +4,7 @@ about: summary: 'SoapDenovo2 Data prepare module using assembled contig to do scaffold assembly' build: - number: 0 + number: 1 package: name: soapdenovo2-prepare @@ -14,10 +14,10 @@ requirements: build: - gcc # [linux] - llvm # [osx] - - zlib + - zlib {{CONDA_ZLIB}}* run: - libgcc # [linux] - - zlib + - zlib {{CONDA_ZLIB}}* source: fn: soapdenovo2-prepare.tar.gz diff --git a/recipes/soapdenovo2/meta.yaml b/recipes/soapdenovo2/meta.yaml index 5fd1e0a02075e9..3453aa9439d1ee 100644 --- a/recipes/soapdenovo2/meta.yaml +++ b/recipes/soapdenovo2/meta.yaml @@ -4,7 +4,7 @@ about: summary: 'SOAPdenovo is a novel short-read assembly method that can build a de novo draft assembly for the human-sized genomes.' build: - number: 0 + number: 1 package: name: soapdenovo2 @@ -14,11 +14,11 @@ requirements: build: - gcc # [linux] - llvm # [osx] - - zlib + - zlib {{CONDA_ZLIB}}* - samtools ==0.1.19 run: - libgcc # [linux] - - zlib + - zlib {{CONDA_ZLIB}}* - samtools ==0.1.19 source: diff --git a/recipes/soapec/build.sh b/recipes/soapec/build.sh index c8deded9e56b75..a885cbc4889559 100644 --- a/recipes/soapec/build.sh +++ b/recipes/soapec/build.sh @@ -8,10 +8,7 @@ export LIBRARY_PATH="${PREFIX}/lib" export LD_LIBRARY_PATH="${PREFIX}/lib" export LDFLAGS="-L${PREFIX}/lib" -export CPPFLAGS="-I${PREFIX}/include" - -export CXXFLAGS="-pthread" -export CFLAGS+="-pthread" +export CXXFLAGS="-I${PREFIX}/include" make PREFIX=$PREFIX/bin make install diff --git a/recipes/soapec/meta.yaml b/recipes/soapec/meta.yaml index 98de2f124e7870..be6039461ad344 100644 --- a/recipes/soapec/meta.yaml +++ b/recipes/soapec/meta.yaml @@ -4,7 +4,7 @@ about: summary: 'a correction tool for SOAPdenovo' build: - number: 1 + number: 2 skip: True # [osx] package: @@ -15,14 +15,14 @@ requirements: build: - gcc # [linux] - llvm # [osx] - - zlib + - zlib {{CONDA_ZLIB}}* run: - libgcc # [linux] - - zlib + - zlib {{CONDA_ZLIB}}* source: fn: soapec_v2.03.tar.gz - url: https://sourceforge.net/projects/soapdenovo2/files/ErrorCorrection/SOAPec_src_v2.03.tgz/download - + url: https://sourceforge.net/projects/soapdenovo2/files/ErrorCorrection/SOAPec_src_v2.03.tgz + sha256: d95faa1ebffc785bca134a72d88b336dd1a4797c526f5d66095db3d4c3ec3d24 test: commands: diff --git a/recipes/soapsplice/meta.yaml b/recipes/soapsplice/meta.yaml index 3b05b6d60dbbc6..c13b230bea2ee1 100644 --- a/recipes/soapsplice/meta.yaml +++ b/recipes/soapsplice/meta.yaml @@ -11,13 +11,13 @@ source: build: skip: True # [osx] - number: 0 + number: 1 requirements: build: - - zlib + - zlib {{CONDA_ZLIB}}* run: - - zlib + - zlib {{CONDA_ZLIB}}* test: commands: diff --git a/recipes/somatic-sniper/meta.yaml b/recipes/somatic-sniper/meta.yaml index 0955d58dde577e..b662df03fa7006 100644 --- a/recipes/somatic-sniper/meta.yaml +++ b/recipes/somatic-sniper/meta.yaml @@ -7,16 +7,16 @@ source: url: https://github.com/genome/somatic-sniper/archive/v1.0.5.0.tar.gz build: - number: 0 + number: 1 skip: False requirements: build: - cmake - gcc - - zlib + - zlib {{CONDA_ZLIB}}* run: - - zlib + - zlib {{CONDA_ZLIB}}* test: commands: diff --git a/recipes/sortmerna/2.0/meta.yaml b/recipes/sortmerna/2.0/meta.yaml index 49438df8e4ed23..c912fe4ab47ac9 100644 --- a/recipes/sortmerna/2.0/meta.yaml +++ b/recipes/sortmerna/2.0/meta.yaml @@ -8,16 +8,16 @@ source: md5: f233f7734105c75c14bd4c2fa4e2aefe build: - number: 1 + number: 2 requirements: build: - gcc # [not osx] - llvm # [osx] - - zlib + - zlib {{CONDA_ZLIB}}* run: - libgcc # [not osx] - - zlib + - zlib {{CONDA_ZLIB}}* test: commands: diff --git a/recipes/sortmerna/2.1b/meta.yaml b/recipes/sortmerna/2.1b/meta.yaml index da06e044612362..e857cb559ae9fb 100644 --- a/recipes/sortmerna/2.1b/meta.yaml +++ b/recipes/sortmerna/2.1b/meta.yaml @@ -8,16 +8,16 @@ source: sha256: b3d122776c323813971b35991cda21a2c2f3ce817daba68a4c4e09d4367c0abe build: - number: 1 + number: 2 requirements: build: - gcc # [not osx] - llvm # [osx] - - zlib + - zlib {{CONDA_ZLIB}}* run: - libgcc - - zlib + - zlib {{CONDA_ZLIB}}* test: commands: diff --git a/recipes/sourmash/meta.yaml b/recipes/sourmash/meta.yaml index 8a84707a457e38..edb8a026700d9d 100644 --- a/recipes/sourmash/meta.yaml +++ b/recipes/sourmash/meta.yaml @@ -1,6 +1,6 @@ {% set name = "sourmash" %} -{% set version = "2.0.0a3" %} -{% set hash = "e692c6be5f080cf3bbb26ec78b15b02c8dfe465208efb97f7f2fb3916b9477c0" %} +{% set version = "2.0.0a4" %} +{% set hash = "9ec94badf31c1fd9f7564008aafebbc3aea174add98efa8e6b2b7b42b662ffe1" %} package: name: {{ name|lower }} @@ -8,7 +8,7 @@ package: source: fn: {{ name|lower }}-{{ version }}.tar.gz - url: https://github.com/dib-lab/sourmash/archive/f469b5a2c6528ed9c641a3232968b91f8d3313a1.tar.gz + url: https://github.com/dib-lab/sourmash/archive/102b9eac5bf5bba41119fcf8b39bbebf4a09279a.tar.gz sha256: {{ hash }} patches: - sourmash.patch @@ -51,6 +51,7 @@ test: commands: - sourmash --help + - sourmash info about: home: https://github.com/dib-lab/sourmash diff --git a/recipes/spades/meta.yaml b/recipes/spades/meta.yaml index a108cf9d3a7121..8056461ea18a54 100644 --- a/recipes/spades/meta.yaml +++ b/recipes/spades/meta.yaml @@ -13,7 +13,7 @@ source: sha256: 3ab85d86bf7d595bd8adf11c971f5d258bbbd2574b7c1703b16d6639a725b474 # [linux] build: - number: 0 + number: 1 string: py{{CONDA_PY}}_zlib{{CONDA_ZLIB}}_{{PKG_BUILDNUM}} # [linux] requirements: @@ -21,13 +21,13 @@ requirements: - gcc >=4.8.2 # [linux] - cmake >=2.8.12 # [linux] - zlib {{CONDA_ZLIB}}* # [linux] - - bzip2 1.0.* # [linux] + - bzip2 {{CONDA_BZIP2}}* # [linux] run: - python - libgcc # [linux] - zlib {{CONDA_ZLIB}}* # [linux] - - bzip2 1.0.* # [linux] + - bzip2 {{CONDA_BZIP2}}* # [linux] test: commands: diff --git a/recipes/sparc/meta.yaml b/recipes/sparc/meta.yaml index fdc068a02bcaf7..79067cbdcd6f7b 100644 --- a/recipes/sparc/meta.yaml +++ b/recipes/sparc/meta.yaml @@ -6,7 +6,7 @@ package: version: {{ version }} build: - number: 0 + number: 1 script: "mkdir -p $PREFIX/bin; g++ -O3 -o Sparc *.cpp; mv Sparc $PREFIX/bin" source: @@ -15,13 +15,13 @@ source: requirements: build: - - gcc # [not osx] - - llvm # [osx] - - zlib + - gcc # [not osx] + - llvm # [osx] + - zlib {{CONDA_ZLIB}}* run: - - libgcc # [not osx] - - zlib + - libgcc # [not osx] + - zlib {{CONDA_ZLIB}}* test: commands: diff --git a/recipes/sparseassembler/meta.yaml b/recipes/sparseassembler/meta.yaml index 5cbf76e2bfb2cc..85f1d7131b4b20 100644 --- a/recipes/sparseassembler/meta.yaml +++ b/recipes/sparseassembler/meta.yaml @@ -6,7 +6,7 @@ package: version: {{ version }} build: - number: 1 + number: 2 script: "mkdir -p $PREFIX/bin; g++ -O3 -o SparseAssembler *.cpp; mv SparseAssembler $PREFIX/bin" source: @@ -18,11 +18,11 @@ requirements: build: - gcc # [not osx] - llvm # [osx] - - zlib + - zlib {{CONDA_ZLIB}}* run: - libgcc # [not osx] - - zlib + - zlib {{CONDA_ZLIB}}* test: commands: diff --git a/recipes/squeakr/meta.yaml b/recipes/squeakr/meta.yaml index c311794123c932..0d22d8a6c9f106 100644 --- a/recipes/squeakr/meta.yaml +++ b/recipes/squeakr/meta.yaml @@ -12,19 +12,19 @@ source: md5 : {{ md5 }} build: - number : 0 + number : 1 requirements: build: - gcc # [not osx] - llvm # [osx] - - bzip2 + - bzip2 {{CONDA_BZIP2}}* - zlib {{CONDA_ZLIB}}* - boost {{CONDA_BOOST}}* - openssl run: - libgcc # [not osx] - - bzip2 + - bzip2 {{CONDA_BZIP2}}* - zlib {{CONDA_ZLIB}}* - boost {{CONDA_BOOST}}* - openssl diff --git a/recipes/stacks/1.40/meta.yaml b/recipes/stacks/1.40/meta.yaml index 61077d93aca501..a2ecc33e78679d 100644 --- a/recipes/stacks/1.40/meta.yaml +++ b/recipes/stacks/1.40/meta.yaml @@ -2,7 +2,7 @@ package: name: stacks version: "1.40" build: - number: 1 + number: 2 skip: True # [osx] source: fn: stacks-1.40.tar.gz @@ -11,14 +11,14 @@ source: requirements: build: - gcc # [linux] - - zlib + - zlib {{CONDA_ZLIB}}* - samtools 0.1.19 - sparsehash run: - perl-threaded - velvet - libgcc # [linux] - - zlib + - zlib {{CONDA_ZLIB}}* - samtools 0.1.19 - sparsehash test: diff --git a/recipes/stacks/1.42/meta.yaml b/recipes/stacks/1.42/meta.yaml index 5de67afbd5a0bf..4762ef6d4e304c 100644 --- a/recipes/stacks/1.42/meta.yaml +++ b/recipes/stacks/1.42/meta.yaml @@ -2,7 +2,7 @@ package: name: stacks version: "1.42" build: - number: 3 + number: 4 skip: True # [osx] source: fn: stacks-1.42.tar.gz @@ -11,13 +11,13 @@ source: requirements: build: - gcc # [linux] - - zlib + - zlib {{CONDA_ZLIB}}* - sparsehash run: - perl-threaded - velvet - libgcc # [linux] - - zlib + - zlib {{CONDA_ZLIB}}* - sparsehash test: commands: diff --git a/recipes/stacks/1.43/meta.yaml b/recipes/stacks/1.43/meta.yaml index a294321963c80e..4b743ba4e330a0 100644 --- a/recipes/stacks/1.43/meta.yaml +++ b/recipes/stacks/1.43/meta.yaml @@ -2,7 +2,7 @@ package: name: stacks version: "1.43" build: - number: 0 + number: 1 skip: True # [osx] source: fn: stacks-1.43.tar.gz @@ -11,13 +11,13 @@ source: requirements: build: - gcc # [linux] - - zlib + - zlib {{CONDA_ZLIB}}* - sparsehash run: - perl-threaded - velvet - libgcc # [linux] - - zlib + - zlib {{CONDA_ZLIB}}* - sparsehash test: commands: diff --git a/recipes/stacks/1.44/meta.yaml b/recipes/stacks/1.44/meta.yaml index bcbe01d6a28f78..a0455dab5ea975 100644 --- a/recipes/stacks/1.44/meta.yaml +++ b/recipes/stacks/1.44/meta.yaml @@ -2,7 +2,7 @@ package: name: stacks version: "1.44" build: - number: 1 + number: 2 skip: True # [osx] source: fn: stacks-1.44.tar.gz @@ -11,13 +11,13 @@ source: requirements: build: - gcc # [linux] - - zlib + - zlib {{CONDA_ZLIB}}* - sparsehash run: - perl - velvet - libgcc # [linux] - - zlib + - zlib {{CONDA_ZLIB}}* - sparsehash test: commands: diff --git a/recipes/stacks/2.0/build.sh b/recipes/stacks/2.0/build.sh index 0b6e34e1954e01..8c4f85a1f0fdc5 100644 --- a/recipes/stacks/2.0/build.sh +++ b/recipes/stacks/2.0/build.sh @@ -1,15 +1,7 @@ #!/bin/bash -# Using --libdir doesn't work. -export LDFLAGS="-L${CONDA_PREFIX}/lib" # for both stacks and included htslib dependency -export CPATH=${CONDA_PREFIX}/include # for included htslib dependency +export CXXFLAGS="${CXXFLAGS} -std=c++11" ./configure --prefix=$PREFIX --enable-bam - -# Force included htslib library to use conda compiler toolsuite -sed -i "s|^CC *.*|CC = $CC|" htslib/Makefile -sed -i "s|^AR *.*|AR = $AR|" htslib/Makefile -sed -i "s|^RANLIB *.*|RANLIB = $RANLIB|" htslib/Makefile - make make install diff --git a/recipes/stacks/2.0/meta.yaml b/recipes/stacks/2.0/meta.yaml index baef6551b79ef5..bd5f93adda5d78 100644 --- a/recipes/stacks/2.0/meta.yaml +++ b/recipes/stacks/2.0/meta.yaml @@ -1,5 +1,8 @@ -{% set version="2.0Beta8" %} -{% set hash="1660bb4569dd6e427d5617977ef953d38f169b050ba475903a6419b82c055080" %} +{% set version="2.0Beta8c" %} +{% set hash="506ff10e93595237e9e74460d2d1113a367adf0ca320879fce0ba65481a34a38" %} +# `gxx_*`/`gcc_*`/`clang_*` below should be replaced by `compiler("cxx")` with conda-build 3 +{% set gxx_version = "7.2.0" %} +{% set clang_version = "4.0.1" %} package: @@ -7,10 +10,8 @@ package: version: {{ version }} build: - skip: True # [not linux] number: 0 - source: fn: stacks-{{ version }}.tar.gz sha256: {{ hash }} @@ -18,19 +19,22 @@ source: requirements: build: - - gcc_linux-64 # [linux64] - - gxx_linux-64 # [linux64] - - gcc_linux-32 # [linux32] - - gxx_linux-32 # [linux32] + - gcc_linux-64 {{ gxx_version }} # [linux64] + - gxx_linux-64 {{ gxx_version }} # [linux64] + - clangxx_osx-64 {{ clang_version }} # [osx] + - clang_osx-64 {{ clang_version }} # [osx] - zlib {{CONDA_ZLIB}}* - - openmp + - openmp # [linux] + - llvm-openmp # [osx] run: - perl - velvet - - libgcc # [linux] + - libgcc >={{ gxx_version }} # [linux] + - libcxx >={{ clang_version }} # [osx] - zlib {{CONDA_ZLIB}}* - - openmp + - openmp # [linux] + - llvm-openmp # [osx] test: commands: @@ -50,7 +54,7 @@ test: - command -v denovo_map.pl - command -v exec_velvet.pl - command -v export_sql.pl -# - extract_interpop_chars.pl +# - command -v extract_interpop_chars.pl - command -v index_radtags.pl - command -v integrate_alignments.py - command -v load_radtags.pl diff --git a/recipes/stacks/meta.yaml b/recipes/stacks/meta.yaml index db62c55352ab1d..1730e63d87823b 100644 --- a/recipes/stacks/meta.yaml +++ b/recipes/stacks/meta.yaml @@ -3,7 +3,7 @@ package: version: "1.47" build: - number: 0 + number: 1 skip: True # [osx] string: boost{{CONDA_BOOST}}_{{PKG_BUILDNUM}} diff --git a/recipes/stride/meta.yaml b/recipes/stride/meta.yaml index 365cb721fd33c7..3f3c6820cbb68c 100644 --- a/recipes/stride/meta.yaml +++ b/recipes/stride/meta.yaml @@ -7,7 +7,7 @@ package: version: {{ version }} build: - number: 2 + number: 3 skip: True # [osx] source: @@ -24,10 +24,10 @@ requirements: - automake - m4 - perl - - zlib + - zlib {{CONDA_ZLIB}}* run: - libgcc # [not osx] - + - zlib {{CONDA_ZLIB}}* test: commands: - stride 2>&1 | grep "stride" diff --git a/recipes/stringtie/0.97/build.sh b/recipes/stringtie/0.97/build.sh deleted file mode 100644 index 8eddff38b6f1b6..00000000000000 --- a/recipes/stringtie/0.97/build.sh +++ /dev/null @@ -1,4 +0,0 @@ -#!/bin/sh -make release -mkdir -p $PREFIX/bin -mv stringtie $PREFIX/bin diff --git a/recipes/stringtie/0.97/meta.yaml b/recipes/stringtie/0.97/meta.yaml deleted file mode 100644 index 6a2a15076423d4..00000000000000 --- a/recipes/stringtie/0.97/meta.yaml +++ /dev/null @@ -1,20 +0,0 @@ -about: - home: http://ccb.jhu.edu/software/stringtie/ - license: Artistic License 2.0 - summary: Transcriptome assembly and quantification for RNA-seq -build: - number: 0 - skip: True # [osx] -package: - name: stringtie - version: '0.97' -requirements: - build: [] - run: [] -source: - fn: stringtie-0.97.tar.gz - sha256: 8a8371827a123a94333036d482cc45ccd39d6dd54f6d394fb536853265241d1d - url: http://ccb.jhu.edu/software/stringtie/dl/stringtie-0.97.tar.gz -test: - commands: - - "stringtie 2>&1 | grep Assemble" diff --git a/recipes/stringtie/1.0.1/build.sh b/recipes/stringtie/1.0.1/build.sh deleted file mode 100644 index 55efc1f59e1049..00000000000000 --- a/recipes/stringtie/1.0.1/build.sh +++ /dev/null @@ -1,7 +0,0 @@ -#!/bin/sh - -sed -i 's/^LIBS.*/LIBS := -lbam -lz/g' Makefile - -make release -mkdir -p $PREFIX/bin -mv stringtie $PREFIX/bin diff --git a/recipes/stringtie/1.0.1/meta.yaml b/recipes/stringtie/1.0.1/meta.yaml deleted file mode 100644 index a73a8f02dcfd47..00000000000000 --- a/recipes/stringtie/1.0.1/meta.yaml +++ /dev/null @@ -1,21 +0,0 @@ -about: - home: http://ccb.jhu.edu/software/stringtie/ - license: Artistic License 2.0 - summary: Transcriptome assembly and quantification for RNA-seq -build: - number: 0 - skip: True # [osx] -package: - name: stringtie - version: 1.0.1 -requirements: - build: - - zlib - run: [] -source: - fn: stringtie-1.0.1.tar.gz - sha256: b0750b40214814270f7380d04efa350d57ef781eb67cf6f4cf168040e93fd98f - url: http://ccb.jhu.edu/software/stringtie/dl/stringtie-1.0.1.tar.gz -test: - commands: - - "stringtie 2>&1 | grep Assemble" diff --git a/recipes/stringtie/1.2.4/meta.yaml b/recipes/stringtie/1.2.4/meta.yaml index c573133b82536c..8cc0c1ede22f9a 100644 --- a/recipes/stringtie/1.2.4/meta.yaml +++ b/recipes/stringtie/1.2.4/meta.yaml @@ -3,7 +3,7 @@ about: license: Artistic License 2.0 summary: Transcriptome assembly and quantification for RNA-seq build: - number: 0 + number: 1 skip: True # [osx] package: name: stringtie @@ -12,10 +12,10 @@ requirements: build: - gcc # [linux] - llvm # [osx] - - zlib + - zlib {{CONDA_ZLIB}}* run: - libgcc # [linux] - - zlib + - zlib {{CONDA_ZLIB}}* source: fn: stringtie-1.2.4.tar.gz sha256: 7fcd64c3ad73816cdb446c5d703a1c46cf828db88871221267532355168b0dc9 diff --git a/recipes/stringtie/1.3.0/meta.yaml b/recipes/stringtie/1.3.0/meta.yaml index 6e05617415ffea..a1412bfd754e46 100644 --- a/recipes/stringtie/1.3.0/meta.yaml +++ b/recipes/stringtie/1.3.0/meta.yaml @@ -4,7 +4,7 @@ about: summary: Transcriptome assembly and quantification for RNA-seq build: - number: 0 + number: 1 package: name: stringtie @@ -14,10 +14,10 @@ requirements: build: - gcc # [linux] - llvm # [osx] - - zlib + - zlib {{CONDA_ZLIB}}* run: - libgcc # [linux] - - zlib + - zlib {{CONDA_ZLIB}}* source: fn: stringtie-1.3.0.tar.gz diff --git a/recipes/stringtie/meta.yaml b/recipes/stringtie/meta.yaml index 207a1fe4095402..b40e165c452c20 100644 --- a/recipes/stringtie/meta.yaml +++ b/recipes/stringtie/meta.yaml @@ -3,7 +3,7 @@ package: version: 1.3.3 build: - number: 2 + number: 3 requirements: build: diff --git a/recipes/subread/meta.yaml b/recipes/subread/meta.yaml index 763f5f35561da0..ba86c60ab808c4 100644 --- a/recipes/subread/meta.yaml +++ b/recipes/subread/meta.yaml @@ -7,7 +7,8 @@ package: version: 1.6.0 build: - number: 1 + number: 2 + source: fn: subread-1.6.0-source.tar.gz url: https://downloads.sourceforge.net/project/subread/subread-1.6.0/subread-1.6.0-source.tar.gz diff --git a/recipes/suma_package/meta.yaml b/recipes/suma_package/meta.yaml index d162a85052bb58..233ed43338d0b2 100644 --- a/recipes/suma_package/meta.yaml +++ b/recipes/suma_package/meta.yaml @@ -10,14 +10,17 @@ source: - ldflags.patch build: - number: 0 + number: 1 skip: True # [not linux64 or osx] requirements: build: - - zlib + - gcc # [not osx] + - llvm # [osx] + - zlib {{CONDA_ZLIB}}* run: - - zlib + - libgcc # [not osx] + - zlib {{CONDA_ZLIB}}* test: commands: diff --git a/recipes/svgwrite/build.sh b/recipes/svgwrite/build.sh deleted file mode 100644 index 4d7fc032b8cbea..00000000000000 --- a/recipes/svgwrite/build.sh +++ /dev/null @@ -1,9 +0,0 @@ -#!/bin/bash - -$PYTHON setup.py install - -# Add more build steps here, if they are necessary. - -# See -# http://docs.continuum.io/conda/build.html -# for a list of environment variables that are set during the build process. diff --git a/recipes/svgwrite/meta.yaml b/recipes/svgwrite/meta.yaml deleted file mode 100644 index 04833add6e006f..00000000000000 --- a/recipes/svgwrite/meta.yaml +++ /dev/null @@ -1,64 +0,0 @@ -package: - name: svgwrite - version: "1.1.6" - -source: - fn: svgwrite-1.1.6.tar.gz - url: https://pypi.python.org/packages/source/s/svgwrite/svgwrite-1.1.6.tar.gz - md5: 0d54ccf5584dd1f98fe22b7ac172bef1 -# patches: - # List any patch files here - # - fix.patch - -build: - skip: False - # noarch_python: True - # preserve_egg_dir: True - # entry_points: - # Put any entry points (scripts to be generated automatically) here. The - # syntax is module:function. For example - # - # - svgwrite = svgwrite:main - # - # Would create an entry point called svgwrite that calls svgwrite.main() - - - # If this is a new build for the same version, increment the build - # number. If you do not include this key, it defaults to 0. - # number: 1 - -requirements: - build: - - python - - setuptools - - pyparsing >=2.0.1 - - run: - - python - - pyparsing >=2.0.1 - -test: - # Python imports - imports: - - svgwrite - - # commands: - # You can put test commands to be run here. Use this to test that the - # entry points work. - - - # You can also put a file called run_test.py in the recipe that will be run - # at test time. - - # requires: - # Put any additional test requirements here. For example - # - nose - -about: - home: http://bitbucket.org/mozman/svgwrite - license: MIT License - summary: 'A Python library to create SVG drawings.' - -# See -# http://docs.continuum.io/conda/build.html for -# more information about meta.yaml diff --git a/recipes/swga/build.sh b/recipes/swga/build.sh index e2f5b4f64bebe5..ab74c583ecce99 100644 --- a/recipes/swga/build.sh +++ b/recipes/swga/build.sh @@ -1,6 +1,6 @@ #!/bin/bash -$PYTHON setup.py install +$PYTHON setup.py install --single-version-externally-managed --record=record.txt cp swga/bin/* $PREFIX/bin/ diff --git a/recipes/swga/meta.yaml b/recipes/swga/meta.yaml index 815cf2884a7403..427e30d4e43dbc 100644 --- a/recipes/swga/meta.yaml +++ b/recipes/swga/meta.yaml @@ -1,5 +1,5 @@ {% set name = "swga" %} -{% set version = "0.4.3.p1" %} +{% set version = "0.4.4" %} package: name: {{ name|lower }} @@ -7,8 +7,8 @@ package: source: fn: {{ name|lower }}_{{ version }}.tar.gz - url: https://github.com/eclarke/swga/archive/c91d2ff81349811369110df81219ec1036ba8129.tar.gz - md5: c71b533fed7037be59f852af90944c1d + url: https://github.com/eclarke/swga/archive/2f240cbb356d8c4b4130d9e442596d10227738ff.tar.gz + sha256: 28f6971234453f8ba91997c3203e71e94a4de5e37f7bcfd01096deb1fcb952c0 build: skip: true # [not py27] @@ -18,24 +18,19 @@ build: requirements: build: + - llvm # [osx] + - gcc # [not osx] - python - setuptools - - pyfaidx - - click - - peewee - - melt - - pytest - - argutils - - semantic_version - - workspace - - gcc run: + - libgcc # [not osx] - python - setuptools - - pyfaidx + - pyfaidx >0.4.5.2 - click - - peewee + - pyyaml + - peewee >=2.7.3,<3.0 - melt - pytest - argutils @@ -46,8 +41,7 @@ test: imports: - swga commands: - # click requires a unicode locale - - LANG=C.UTF-8 swga 2>&1 | grep Usage + - swga 2>&1 | grep Usage about: home: https://github.com/eclarke/swga diff --git a/recipes/t_coffee/meta.yaml b/recipes/t_coffee/meta.yaml index 75ffc8a3bfb87c..88aa85193788b2 100644 --- a/recipes/t_coffee/meta.yaml +++ b/recipes/t_coffee/meta.yaml @@ -8,7 +8,7 @@ source: md5: 2e375405c9ebb977adf87c145ca698bb build: - number: 2 + number: 3 skip: True # [osx] entry_points: - t_coffee = t_coffee.__main__:main @@ -18,13 +18,13 @@ requirements: - curl - openssl - python - - zlib + - zlib {{CONDA_ZLIB}}* run: - curl - openssl - - perl-threaded + - perl - python - - zlib + - zlib {{CONDA_ZLIB}}* test: imports: diff --git a/recipes/tabix/0.2.5/meta.yaml b/recipes/tabix/0.2.5/meta.yaml index 77383cfab75b3c..027109c1782f6b 100644 --- a/recipes/tabix/0.2.5/meta.yaml +++ b/recipes/tabix/0.2.5/meta.yaml @@ -7,15 +7,15 @@ source: sha256: 6ce0da41a7ef82aa34db413602cc7cd11c08d606f36ebba793da41ec402e2f86 build: - number: 0 + number: 1 requirements: build: - - zlib + - zlib {{CONDA_ZLIB}}* - gcc # [linux] - llvm # [osx] run: - - zlib + - zlib {{CONDA_ZLIB}}* - libgcc # [linux] test: diff --git a/recipes/tadarida-d/meta.yaml b/recipes/tadarida-d/meta.yaml index c311d5955c50fb..512749da5ee6fb 100644 --- a/recipes/tadarida-d/meta.yaml +++ b/recipes/tadarida-d/meta.yaml @@ -12,7 +12,7 @@ source: md5: {{ md5 }} build: - number: 0 + number: 1 skip: True # [osx] requirements: @@ -21,13 +21,13 @@ requirements: - fftw 3.3.4 - libsndfile 1.0.27 - gcc - - zlib + - zlib {{CONDA_ZLIB}}* run: - qt 4.8.7 - fftw 3.3.4 - libsndfile 1.0.27 - libgcc - - zlib + - zlib {{CONDA_ZLIB}}* - xorg-libsm - xorg-libxrender - xorg-libxext diff --git a/recipes/takeabreak/meta.yaml b/recipes/takeabreak/meta.yaml index dde161f6bbe293..0a56b4d3cb98a9 100644 --- a/recipes/takeabreak/meta.yaml +++ b/recipes/takeabreak/meta.yaml @@ -8,7 +8,7 @@ source: md5: "9170a6d61f51e53189822df830648fd0" build: - number: 0 + number: 1 requirements: build: diff --git a/recipes/tepid/meta.yaml b/recipes/tepid/meta.yaml index 62da1ea9dad762..0b9d14b32e45a8 100644 --- a/recipes/tepid/meta.yaml +++ b/recipes/tepid/meta.yaml @@ -25,7 +25,6 @@ requirements: - bedtools ==2.25.0 run: - libgcc - - zlib - python - pybedtools - numpy ==1.9.2 diff --git a/recipes/tesseract/3.04.01/meta.yaml b/recipes/tesseract/3.04.01/meta.yaml index bab56d65ed8d48..d0283fd68375af 100644 --- a/recipes/tesseract/3.04.01/meta.yaml +++ b/recipes/tesseract/3.04.01/meta.yaml @@ -2,7 +2,7 @@ package: name: tesseract version: 3.04.01 build: - number: 0 + number: 1 skip: True # [osx] source: fn: 3.04.01.tar.gz @@ -14,14 +14,17 @@ requirements: - libpng - jpeg - libtiff - - zlib + - automake + - autoconf + - libtool + - zlib {{CONDA_ZLIB}}* - leptonica run: - libgcc # [linux] - libpng - jpeg - libtiff - - zlib + - zlib {{CONDA_ZLIB}}* - leptonica test: commands: diff --git a/recipes/toil/build.sh b/recipes/toil/build.sh index b3be65fbf9cd80..f51640d7b5e1ce 100644 --- a/recipes/toil/build.sh +++ b/recipes/toil/build.sh @@ -12,10 +12,10 @@ sed -i.bak 's/docker==/docker>=/' setup.py sed -i.bak 's/galaxy-lib==/galaxy-lib>=/' setup.py sed -i.bak 's/requests==/requests>=/' setup.py -# Avoid needing git/.git for version prep -sed -i.bak 's/return _version()/return distVersion()/' version_template.py -sed -i.bak 's/return _version(shorten=True)/return distVersion()/' version_template.py -sed -i.bak 's/def currentCommit()/def _currentCommit()/' version_template.py -sed -i.bak 's/def dirty()/def _dirty()/' version_template.py +# For non-releases only: Avoid needing git/.git for version prep +#sed -i.bak 's/return _version()/return distVersion()/' version_template.py +#sed -i.bak 's/return _version(shorten=True)/return distVersion()/' version_template.py +#sed -i.bak 's/def currentCommit()/def _currentCommit()/' version_template.py +#sed -i.bak 's/def dirty()/def _dirty()/' version_template.py $PYTHON setup.py install --single-version-externally-managed --record=record.txt diff --git a/recipes/toil/meta.yaml b/recipes/toil/meta.yaml index 6a20e3baf01be9..377e741cf1f9b9 100644 --- a/recipes/toil/meta.yaml +++ b/recipes/toil/meta.yaml @@ -1,14 +1,14 @@ -{% set version="3.13.0a1" %} +{% set version="3.14.0" %} package: name: toil version: {{ version }} source: - #fn: toil-{{ version }}.tar.gz - #url: https://pypi.io/packages/source/t/toil/toil-{{ version }}.tar.gz - fn: toil-226abc7.tar.gz - url: https://github.com/BD2KGenomics/toil/archive/226abc7.tar.gz - md5: 95bef16fc4b6396bcdcda7149032dbaa + fn: toil-{{ version }}.tar.gz + url: https://pypi.io/packages/source/t/toil/toil-{{ version }}.tar.gz + #fn: toil-226abc7.tar.gz + #url: https://github.com/BD2KGenomics/toil/archive/226abc7.tar.gz + md5: 5c44aec8d5f12ae123fb77ef0f3a021f build: number: 0 @@ -24,10 +24,10 @@ requirements: - dill - psutil - cgcloud-lib - - boto ==2.38.0 + - boto >=2.38.0 - futures # [py27] - azure - - cwltool ==1.0.20170928192020 + - cwltool ==1.0.20180130110340 - gcs-oauth2-boto-plugin ==1.9 - pynacl ==1.1.2 - docker-py >=2.5.1 @@ -49,10 +49,10 @@ requirements: - dill - psutil - cgcloud-lib - - boto ==2.38.0 + - boto >=2.38.0 - futures # [py27] - azure - - cwltool ==1.0.20170928192020 + - cwltool ==1.0.20180130110340 - gcs-oauth2-boto-plugin ==1.9 - pynacl ==1.1.2 - docker-py >=2.5.1 @@ -68,7 +68,9 @@ requirements: test: commands: - - toil --help + # Bug in Toil --help in 3.14.0 release, missing __doc__ + # - toil --help + - toil --version - cwltoil --help about: diff --git a/recipes/transabyss/meta.yaml b/recipes/transabyss/meta.yaml index db6da4407de669..dff176380e6162 100644 --- a/recipes/transabyss/meta.yaml +++ b/recipes/transabyss/meta.yaml @@ -4,7 +4,8 @@ about: summary: 'de novo assembly of RNA-Seq data using ABySS' build: - number: 1 + skip: True # [py3k] + number: 2 package: name: transabyss @@ -12,7 +13,7 @@ package: requirements: build: - - python <3 + - python run: - zlib {{ CONDA_ZLIB }}* - abyss 1.5.2 @@ -20,7 +21,7 @@ requirements: - samtools 1.3.1 - bowtie2 - blat - - python <3 + - python - libiconv source: diff --git a/recipes/transcomb/meta.yaml b/recipes/transcomb/meta.yaml index 42d50be1c9db4e..8417320554c3fa 100644 --- a/recipes/transcomb/meta.yaml +++ b/recipes/transcomb/meta.yaml @@ -6,7 +6,8 @@ package: version: {{ version }} build: - number: 0 + number: 2 + string: bamtools{{CONDA_BAMTOOLS}}_boost{{CONDA_BOOST}}_{{PKG_BUILDNUM}} string: boost{{CONDA_BOOST}}_{{PKG_BUILDNUM}} source: @@ -18,20 +19,20 @@ source: requirements: build: - - gcc # [not osx] - - llvm # [osx] - - boost {{CONDA_BOOST}}* - - bamtools - - samtools ==0.1.19 - - zlib - - cmake + - gcc # [not osx] + - llvm # [osx] + - boost {{CONDA_BOOST}}* + - bamtools {{ CONDA_BAMTOOLS }}* + - samtools ==0.1.19 + - zlib {{CONDA_ZLIB}}* # [linux] + - cmake run: - - libgcc # [not osx] - - zlib - - boost {{CONDA_BOOST}}* - - bamtools - - samtools + - libgcc # [not osx] + - zlib {{CONDA_ZLIB}}* # [linux] + - boost {{CONDA_BOOST}}* + - bamtools {{ CONDA_BAMTOOLS }}* + - samtools test: commands: @@ -45,3 +46,4 @@ test: about: home: https://github.com/yechengxi/SparseAssembler summary: A sparse k-mer graph based, memory-efficient genome assembler + license: Unknown diff --git a/recipes/transrate-tools/meta.yaml b/recipes/transrate-tools/meta.yaml index ab215a829743cd..be7da9574cf30b 100644 --- a/recipes/transrate-tools/meta.yaml +++ b/recipes/transrate-tools/meta.yaml @@ -4,8 +4,8 @@ package: build: skip: True #[osx] - number: 0 - string: {{PKG_BUILDNUM}} + number: 2 + string: bamtools{{CONDA_BAMTOOLS}}_{{PKG_BUILDNUM}} source: fn: transrate-tools-1.0.0.tar.gz @@ -16,15 +16,16 @@ requirements: build: - gcc >=4.8 - libgcc - - bamtools - - zlib + - bamtools {{ CONDA_BAMTOOLS }}* + - zlib {{ CONDA_ZLIB }}* - cmake - make - gnu-wget run: - libgcc - - bamtools - - zlib + - bamtools {{ CONDA_BAMTOOLS }}* + - zlib {{ CONDA_ZLIB }}* + test: commands: - bam-read 2>&1 | grep "bam-read version" > /dev/null diff --git a/recipes/treekin/0.4.2/build.sh b/recipes/treekin/0.4.2/build.sh new file mode 100644 index 00000000000000..fc1b4c16cd14cd --- /dev/null +++ b/recipes/treekin/0.4.2/build.sh @@ -0,0 +1,5 @@ +#!/bin/sh + +./configure --prefix=$PREFIX && \ +make && \ +make install diff --git a/recipes/treekin/0.4.2/meta.yaml b/recipes/treekin/0.4.2/meta.yaml new file mode 100644 index 00000000000000..b28ff70f50df53 --- /dev/null +++ b/recipes/treekin/0.4.2/meta.yaml @@ -0,0 +1,38 @@ +{% set name = "treekin" %} +{% set version = "0.4.2" %} +{% set sha256 = "093bbafa28c1b2a00482eddb1379a80ac60d7f7f6c0abf638e3827499d8dbb03" %} + +package: + name: {{ name }} + version: {{ version }} + +about: + home: https://www.tbi.univie.ac.at/RNA/Barriers/ + license: GPL + license_file: COPYING + summary: "Compute folding dynamics on coarse grained version of an energy landscape by numeric integration of a Markov process" + +build: + number: 0 + +source: + fn: Treekin-0.4.2.tar.gz + url: http://lindor.tbi.univie.ac.at/fileadmin/media/software/Treekin-0.4.2.tar.gz + sha256: {{ sha256 }} + +requirements: + build: + - lapack + - blas + - libcxx # [osx] + - llvm # [osx] + - gcc # [linux] + run: + - lapack + - blas + - libcxx # [osx] + - libgcc # [linux] + +test: + commands: + - treekin --version diff --git a/recipes/treemix/meta.yaml b/recipes/treemix/meta.yaml index 92d4e76fd808fc..a9807a088f3bde 100644 --- a/recipes/treemix/meta.yaml +++ b/recipes/treemix/meta.yaml @@ -3,7 +3,7 @@ package: version: 1.12 build: - number: 0 + number: 1 skip: True # [osx] string: boost{{CONDA_BOOST}}__gsl{{CONDA_GSL}}_{{PKG_BUILDNUM}} @@ -16,13 +16,13 @@ source: requirements: build: - gcc - - zlib + - zlib {{CONDA_ZLIB}}* - gsl {{CONDA_GSL}}* - boost {{CONDA_BOOST}}* run: - libgcc - - zlib + - zlib {{CONDA_ZLIB}}* - gsl {{CONDA_GSL}}* about: diff --git a/recipes/trim_galore/build.sh b/recipes/trim-galore/0.4.1/build.sh similarity index 100% rename from recipes/trim_galore/build.sh rename to recipes/trim-galore/0.4.1/build.sh diff --git a/recipes/trim_galore/0.4.1/meta.yaml b/recipes/trim-galore/0.4.1/meta.yaml similarity index 65% rename from recipes/trim_galore/0.4.1/meta.yaml rename to recipes/trim-galore/0.4.1/meta.yaml index 1e20b56134b184..edd74f9db5c9bc 100644 --- a/recipes/trim_galore/0.4.1/meta.yaml +++ b/recipes/trim-galore/0.4.1/meta.yaml @@ -1,21 +1,30 @@ +{% set version = "0.4.1" %} +{% set sha256 = "7e7609c68c54032e985eedf36d3b810f39e5bd3d1003a3686f2a34f532ae5d3d" %} + package: name: trim-galore - version: "0.4.1" + version: {{ version }} + build: number: 0 skip: True # [osx] + source: - fn: trim_galore_v0.4.1.zip - url: http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/trim_galore_v0.4.1.zip + fn: trim_galore_v{{ version }}.zip + url: http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/trim_galore_v{{ version }}.zip + sha256: {{ sha256 }} + requirements: build: run: - - perl-threaded + - perl - fastqc - cutadapt + test: commands: - trim_galore --help | grep trim_galore > /dev/null + about: home: http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/ license: GPL diff --git a/recipes/trim-galore/build.sh b/recipes/trim-galore/build.sh new file mode 100644 index 00000000000000..fac1df761c65cb --- /dev/null +++ b/recipes/trim-galore/build.sh @@ -0,0 +1,8 @@ +#!/bin/bash + +mkdir -p $PREFIX/bin +chmod a+x trim_galore +#/usr/bin/perl is hardcoded, need to point to env +sed -i.bak 's/perl/env perl/g' trim_galore + +cp trim_galore $PREFIX/bin diff --git a/recipes/trim_galore/meta.yaml b/recipes/trim-galore/meta.yaml similarity index 98% rename from recipes/trim_galore/meta.yaml rename to recipes/trim-galore/meta.yaml index eb348591485ebb..3bec51a36130ff 100644 --- a/recipes/trim_galore/meta.yaml +++ b/recipes/trim-galore/meta.yaml @@ -7,7 +7,7 @@ package: version: {{ version }} build: - number: 0 + number: 1 skip: False source: diff --git a/recipes/trim_galore/0.4.1/build.sh b/recipes/trim_galore/0.4.1/build.sh deleted file mode 100644 index 454f1ba3aef0ba..00000000000000 --- a/recipes/trim_galore/0.4.1/build.sh +++ /dev/null @@ -1,5 +0,0 @@ -#!/bin/bash - -mkdir -p $PREFIX/bin -chmod a+x trim_galore -cp trim_galore $PREFIX/bin diff --git a/recipes/trimadap/meta.yaml b/recipes/trimadap/meta.yaml index 603845c9cc9228..14a66b85532f66 100644 --- a/recipes/trimadap/meta.yaml +++ b/recipes/trimadap/meta.yaml @@ -3,7 +3,7 @@ package: version: "r10" build: - number: 0 + number: 1 source: fn: trimadap_r10.tar.gz @@ -12,13 +12,13 @@ source: requirements: build: - - gcc # [not osx] - - llvm # [osx] - - zlib + - gcc # [not osx] + - llvm # [osx] + - zlib {{CONDA_ZLIB}}* run: - - libgcc # [not osx] - - zlib + - libgcc # [not osx] + - zlib {{CONDA_ZLIB}}* test: commands: diff --git a/recipes/trimmomatic/0.33/build.sh b/recipes/trimmomatic/0.33/build.sh new file mode 100644 index 00000000000000..57ce1a3ea822e0 --- /dev/null +++ b/recipes/trimmomatic/0.33/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash + +outdir=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $outdir +mkdir -p $PREFIX/bin +cp -R ./* $outdir/ +mv $outdir/trimmomatic-$PKG_VERSION.jar $outdir/trimmomatic.jar +cp $RECIPE_DIR/trimmomatic.sh $outdir/trimmomatic +chmod +x $outdir/trimmomatic + +ln -s $outdir/trimmomatic $PREFIX/bin diff --git a/recipes/trimmomatic/0.33/meta.yaml b/recipes/trimmomatic/0.33/meta.yaml new file mode 100644 index 00000000000000..c861c41dae800b --- /dev/null +++ b/recipes/trimmomatic/0.33/meta.yaml @@ -0,0 +1,27 @@ +about: + home: 'http://www.usadellab.org/cms/?page=trimmomatic' + license: "GPLv3" + summary: "A flexible read trimming tool for Illumina NGS data" + +package: + name: trimmomatic + version: '0.33' + +build: + number: 0 + skip: False + +source: + fn: Trimmomatic-0.33.zip + md5: 924fc8eb38fdff71740a0e05d32d6a2b + url: http://www.usadellab.org/cms/uploads/supplementary/Trimmomatic/Trimmomatic-0.33.zip + +requirements: + run: + - openjdk >=8 + +test: + commands: + #- trimmomatic -version # trimmomatic currently lacks a simple argument that gives + # a zero exit code, so... + - 'trimmomatic 2>&1 | grep "^Usage:"' diff --git a/recipes/trimmomatic/0.33/trimmomatic.sh b/recipes/trimmomatic/0.33/trimmomatic.sh new file mode 100644 index 00000000000000..a27e43f8c981a2 --- /dev/null +++ b/recipes/trimmomatic/0.33/trimmomatic.sh @@ -0,0 +1,62 @@ +#!/bin/bash +# trimmomatic executable shell script, adapted from VarScan shell script +set -eu -o pipefail + +set -o pipefail +export LC_ALL=en_US.UTF-8 + +# Find original directory of bash script, resovling symlinks +# http://stackoverflow.com/questions/59895/can-a-bash-script-tell-what-directory-its-stored-in/246128#246128 +SOURCE="${BASH_SOURCE[0]}" +while [ -h "$SOURCE" ]; do # resolve $SOURCE until the file is no longer a symlink + DIR="$( cd -P "$( dirname "$SOURCE" )" && pwd )" + SOURCE="$(readlink "$SOURCE")" + [[ $SOURCE != /* ]] && SOURCE="$DIR/$SOURCE" # if $SOURCE was a relative symlink, we need to resolve it relative to the path where the symlink file was located +done +DIR="$( cd -P "$( dirname "$SOURCE" )" && pwd )" + +JAR_DIR=$DIR + +java=java + +if [ -z "${JAVA_HOME:=}" ]; then + if [ -e "$JAVA_HOME/bin/java" ]; then + java="$JAVA_HOME/bin/java" + fi +fi + +# extract memory and system property Java arguments from the list of provided arguments +# http://java.dzone.com/articles/better-java-shell-script +default_jvm_mem_opts="-Xms512m -Xmx1g" +jvm_mem_opts="" +jvm_prop_opts="" +pass_args="" +for arg in "$@"; do + case $arg in + '-D'*) + jvm_prop_opts="$jvm_prop_opts $arg" + ;; + '-XX'*) + jvm_prop_opts="$jvm_prop_opts $arg" + ;; + '-Xm'*) + jvm_mem_opts="$jvm_mem_opts $arg" + ;; + *) + pass_args="$pass_args $arg" + ;; + esac +done + +if [ "$jvm_mem_opts" == "" ]; then + jvm_mem_opts="$default_jvm_mem_opts" +fi + +pass_arr=($pass_args) +if [[ ${pass_arr[0]:=} == org* ]] +then + eval "$java" $jvm_mem_opts $jvm_prop_opts -cp "$JAR_DIR/trimmomatic.jar" $pass_args +else + eval "$java" $jvm_mem_opts $jvm_prop_opts -jar "$JAR_DIR/trimmomatic.jar" $pass_args +fi +exit diff --git a/recipes/trinity/2.1.1/date.2011_11_26/meta.yaml b/recipes/trinity/2.1.1/date.2011_11_26/meta.yaml index 59c0c1330dd00f..df56fa7e430bbd 100644 --- a/recipes/trinity/2.1.1/date.2011_11_26/meta.yaml +++ b/recipes/trinity/2.1.1/date.2011_11_26/meta.yaml @@ -3,7 +3,7 @@ about: license: "https://raw.githubusercontent.com/trinityrnaseq/trinityrnaseq/master/LICENSE.txt" summary: "Trinity assembles transcript sequences from Illumina RNA-Seq data" build: - number: 4 + number: 5 string: ncurses{{CONDA_NCURSES}}_{{PKG_BUILDNUM}} package: name: trinity @@ -18,18 +18,18 @@ source: - samtools_makefile.patch # patch samtools Makefile due to missing curses.h requirements: build: - - perl-threaded + - perl - gcc - java-jdk >=6 - - bzip2 - - zlib + - bzip2 {{CONDA_BZIP2}}* + - zlib {{CONDA_ZLIB}}* - ncurses {{CONDA_NCURSES}}* run: - - perl-threaded + - perl - libgcc - java-jdk >=6 - - bzip2 - - zlib + - bzip2 {{CONDA_BZIP2}}* + - zlib {{CONDA_ZLIB}}* - ncurses {{CONDA_NCURSES}}* extra: notes: "Trinity version date.2011_11_26 relies on a custom wrapper script, symlinked to bin/: Trinity-runner.sh. This script changes the current working directory to that of the Trinity.pl perl script before calling Trinity, so relative paths work as expected (particularly for Trinity plugins). All arguments are passed to Trinity.pl (via $@)" diff --git a/recipes/trinity/2.1.1/meta.yaml b/recipes/trinity/2.1.1/meta.yaml index 18551c41f0320b..143dc52e70628c 100644 --- a/recipes/trinity/2.1.1/meta.yaml +++ b/recipes/trinity/2.1.1/meta.yaml @@ -3,34 +3,34 @@ about: license: "https://raw.githubusercontent.com/trinityrnaseq/trinityrnaseq/master/LICENSE.txt" summary: "Trinity assembles transcript sequences from Illumina RNA-Seq data" build: - number: 6 + number: 7 skip: True # [osx] package: name: trinity version: '2.1.1' source: fn: v2.1.1.tar.gz - md5: 45c1ad13c331d6a1976f6a9b5b015daa + md5: 5cc37d847abc8022d588d0c36b83344f url: https://github.com/trinityrnaseq/trinityrnaseq/archive/v2.1.1.tar.gz requirements: build: - - perl-threaded - - java-jdk + - perl + - openjdk - trimmomatic - samtools - jellyfish - - htslib + - htslib {{ CONDA_HTSLIB }}* - collectl - fastool - parafly - slclust run: - - perl-threaded - - java-jdk + - perl + - openjdk - trimmomatic - samtools - jellyfish - - htslib + - htslib {{ CONDA_HTSLIB }}* - collectl - fastool - parafly diff --git a/recipes/trinity/2.2.0/meta.yaml b/recipes/trinity/2.2.0/meta.yaml index 9425f4d98dd713..8fe23ccb55376f 100644 --- a/recipes/trinity/2.2.0/meta.yaml +++ b/recipes/trinity/2.2.0/meta.yaml @@ -4,7 +4,7 @@ about: summary: 'Trinity RNA-Seq de novo transcriptome assembly' build: - number: 6 + number: 7 skip: True # [osx] @@ -20,7 +20,7 @@ requirements: - perl-module-build - perl-file-find-rule - java-jdk - - zlib + - zlib {{CONDA_ZLIB}}* - jellyfish 2.2.3 - samtools 0.1.19 - trimmomatic @@ -33,7 +33,7 @@ requirements: - perl-module-build - perl-file-find-rule - java-jdk - - zlib + - zlib {{CONDA_ZLIB}}* - jellyfish 2.2.3 - samtools 0.1.19 - trimmomatic diff --git a/recipes/trinity/2.3.2/meta.yaml b/recipes/trinity/2.3.2/meta.yaml index 8e173e98c3ef2d..c4c87b2f1957a3 100644 --- a/recipes/trinity/2.3.2/meta.yaml +++ b/recipes/trinity/2.3.2/meta.yaml @@ -6,7 +6,7 @@ package: version: {{ version }} build: - number: 1 + number: 2 skip: True # [osx] source: @@ -23,7 +23,7 @@ requirements: - perl-module-build - perl-file-find-rule - java-jdk - - zlib + - zlib {{CONDA_ZLIB}}* - jellyfish 2.2.3 - samtools 0.1.19 - trimmomatic @@ -39,7 +39,7 @@ requirements: - perl-module-build - perl-file-find-rule - java-jdk - - zlib + - zlib {{CONDA_ZLIB}}* - jellyfish 2.2.3 - samtools 0.1.19 - trimmomatic diff --git a/recipes/trinity/date.2011_11_26/meta.yaml b/recipes/trinity/date.2011_11_26/meta.yaml index 5b09e724e611c9..0e0a3a12db8055 100644 --- a/recipes/trinity/date.2011_11_26/meta.yaml +++ b/recipes/trinity/date.2011_11_26/meta.yaml @@ -3,7 +3,7 @@ about: license: "https://raw.githubusercontent.com/trinityrnaseq/trinityrnaseq/master/LICENSE.txt" summary: "Trinity assembles transcript sequences from Illumina RNA-Seq data" build: - number: 7 + number: 8 string: ncurses{{CONDA_NCURSES}}_{{PKG_BUILDNUM}} package: name: trinity @@ -25,15 +25,15 @@ requirements: - perl - gcc - openjdk >=6 - - bzip2 - - zlib + - bzip2 {{CONDA_BZIP2}}* + - zlib {{CONDA_ZLIB}}* - ncurses {{CONDA_NCURSES}}* run: - perl - libgcc - openjdk >=6 - - bzip2 - - zlib + - bzip2 {{CONDA_BZIP2}}* + - zlib {{CONDA_ZLIB}}* - ncurses {{CONDA_NCURSES}}* extra: notes: "Trinity version date.2011_11_26 relies on a custom wrapper script, symlinked to bin/: Trinity-runner.sh. This script changes the current working directory to that of the Trinity.pl perl script before calling Trinity, so relative paths work as expected (particularly for Trinity plugins). All arguments are passed to Trinity.pl (via $@)" diff --git a/recipes/trinity/meta.yaml b/recipes/trinity/meta.yaml index 3e11c6475729cd..64570e44349557 100644 --- a/recipes/trinity/meta.yaml +++ b/recipes/trinity/meta.yaml @@ -1,5 +1,5 @@ build: - number: 0 + number: 1 # OSX build skipped because of this error: https://gist.github.com/pvanheus/2fbce93b326a3edb1a57aaebc8ca749e skip: True # [osx] @@ -21,7 +21,7 @@ requirements: - samtools >=1.3 - slclust - trimmomatic >=0.36 - - zlib + - zlib {{CONDA_ZLIB}}* run: - bowtie @@ -37,7 +37,7 @@ requirements: - samtools >=1.3 - slclust - trimmomatic >=0.36 - - zlib + - zlib {{CONDA_ZLIB}}* source: fn: Trinity-v2.5.1.tar.gz diff --git a/recipes/ucsc-addcols/meta.yaml b/recipes/ucsc-addcols/meta.yaml index ef6099652ae0cf..d30f09dd95470d 100644 --- a/recipes/ucsc-addcols/meta.yaml +++ b/recipes/ucsc-addcols/meta.yaml @@ -18,7 +18,7 @@ source: fn: "{{ program }}" # [osx] build: - number: 0 + number: 1 requirements: build: @@ -27,7 +27,7 @@ requirements: - libuuid # [linux] - mysql-connector-c # [linux] - openssl # [linux] - - zlib # [linux] + - zlib {{CONDA_ZLIB}}* # [linux] run: - libgcc # [linux] @@ -35,7 +35,7 @@ requirements: - libuuid # [linux] - mysql-connector-c # [linux] - openssl # [linux] - - zlib # [linux] + - zlib {{CONDA_ZLIB}}* # [linux] test: commands: diff --git a/recipes/ucsc-ameme/meta.yaml b/recipes/ucsc-ameme/meta.yaml index 7bc18315c45ccf..6568126f8d96ab 100644 --- a/recipes/ucsc-ameme/meta.yaml +++ b/recipes/ucsc-ameme/meta.yaml @@ -18,7 +18,7 @@ source: fn: "{{ program }}" # [osx] build: - number: 0 + number: 1 requirements: build: @@ -27,7 +27,7 @@ requirements: - libuuid # [linux] - mysql-connector-c # [linux] - openssl # [linux] - - zlib # [linux] + - zlib {{CONDA_ZLIB}}* # [linux] run: - libgcc # [linux] @@ -35,7 +35,7 @@ requirements: - libuuid # [linux] - mysql-connector-c # [linux] - openssl # [linux] - - zlib # [linux] + - zlib {{CONDA_ZLIB}}* # [linux] test: commands: diff --git a/recipes/ucsc-autodtd/meta.yaml b/recipes/ucsc-autodtd/meta.yaml index f06354a23f49b0..10d76bc76fb889 100644 --- a/recipes/ucsc-autodtd/meta.yaml +++ b/recipes/ucsc-autodtd/meta.yaml @@ -18,7 +18,7 @@ source: fn: "{{ program }}" # [osx] build: - number: 0 + number: 1 requirements: build: @@ -27,7 +27,7 @@ requirements: - libuuid # [linux] - mysql-connector-c # [linux] - openssl # [linux] - - zlib # [linux] + - zlib {{CONDA_ZLIB}}* # [linux] run: - libgcc # [linux] @@ -35,7 +35,7 @@ requirements: - libuuid # [linux] - mysql-connector-c # [linux] - openssl # [linux] - - zlib # [linux] + - zlib {{CONDA_ZLIB}}* # [linux] test: commands: diff --git a/recipes/ucsc-autosql/meta.yaml b/recipes/ucsc-autosql/meta.yaml index 40d8d2a4c7efad..5389c4de5482ed 100644 --- a/recipes/ucsc-autosql/meta.yaml +++ b/recipes/ucsc-autosql/meta.yaml @@ -18,7 +18,7 @@ source: fn: "{{ program }}" # [osx] build: - number: 0 + number: 1 requirements: build: @@ -27,7 +27,7 @@ requirements: - libuuid # [linux] - mysql-connector-c # [linux] - openssl # [linux] - - zlib # [linux] + - zlib {{CONDA_ZLIB}}* # [linux] run: - libgcc # [linux] @@ -35,7 +35,7 @@ requirements: - libuuid # [linux] - mysql-connector-c # [linux] - openssl # [linux] - - zlib # [linux] + - zlib {{CONDA_ZLIB}}* # [linux] test: commands: diff --git a/recipes/ucsc-autoxml/meta.yaml b/recipes/ucsc-autoxml/meta.yaml index 468a5a8a5df31f..3db948419df9eb 100644 --- a/recipes/ucsc-autoxml/meta.yaml +++ b/recipes/ucsc-autoxml/meta.yaml @@ -18,7 +18,7 @@ source: fn: "{{ program }}" # [osx] build: - number: 0 + number: 1 requirements: build: @@ -27,7 +27,7 @@ requirements: - libuuid # [linux] - mysql-connector-c # [linux] - openssl # [linux] - - zlib # [linux] + - zlib {{CONDA_ZLIB}}* # [linux] run: - libgcc # [linux] @@ -35,7 +35,7 @@ requirements: - libuuid # [linux] - mysql-connector-c # [linux] - openssl # [linux] - - zlib # [linux] + - zlib {{CONDA_ZLIB}}* # [linux] test: commands: diff --git a/recipes/ucsc-avecols/meta.yaml b/recipes/ucsc-avecols/meta.yaml index fa088b366c9b6d..bcaed58518a737 100644 --- a/recipes/ucsc-avecols/meta.yaml +++ b/recipes/ucsc-avecols/meta.yaml @@ -18,7 +18,7 @@ source: fn: "{{ program }}" # [osx] build: - number: 0 + number: 1 requirements: build: @@ -27,7 +27,7 @@ requirements: - libuuid # [linux] - mysql-connector-c # [linux] - openssl # [linux] - - zlib # [linux] + - zlib {{CONDA_ZLIB}}* # [linux] run: - libgcc # [linux] @@ -35,7 +35,7 @@ requirements: - libuuid # [linux] - mysql-connector-c # [linux] - openssl # [linux] - - zlib # [linux] + - zlib {{CONDA_ZLIB}}* # [linux] test: commands: diff --git a/recipes/ucsc-axtchain/meta.yaml b/recipes/ucsc-axtchain/meta.yaml index 09cd4960ece365..4d10180f2d48fa 100644 --- a/recipes/ucsc-axtchain/meta.yaml +++ b/recipes/ucsc-axtchain/meta.yaml @@ -18,7 +18,7 @@ source: fn: "{{ program }}" # [osx] build: - number: 0 + number: 1 requirements: build: @@ -27,7 +27,7 @@ requirements: - libuuid # [linux] - mysql-connector-c # [linux] - openssl # [linux] - - zlib # [linux] + - zlib {{CONDA_ZLIB}}* # [linux] run: - libgcc # [linux] @@ -35,7 +35,7 @@ requirements: - libuuid # [linux] - mysql-connector-c # [linux] - openssl # [linux] - - zlib # [linux] + - zlib {{CONDA_ZLIB}}* # [linux] test: commands: diff --git a/recipes/ucsc-axtsort/meta.yaml b/recipes/ucsc-axtsort/meta.yaml index a0a30a78d42544..ae29ea817a99d5 100644 --- a/recipes/ucsc-axtsort/meta.yaml +++ b/recipes/ucsc-axtsort/meta.yaml @@ -18,7 +18,7 @@ source: fn: "{{ program }}" # [osx] build: - number: 0 + number: 1 requirements: build: @@ -27,7 +27,7 @@ requirements: - libuuid # [linux] - mysql-connector-c # [linux] - openssl # [linux] - - zlib # [linux] + - zlib {{CONDA_ZLIB}}* # [linux] run: - libgcc # [linux] @@ -35,7 +35,7 @@ requirements: - libuuid # [linux] - mysql-connector-c # [linux] - openssl # [linux] - - zlib # [linux] + - zlib {{CONDA_ZLIB}}* # [linux] test: commands: diff --git a/recipes/ucsc-axtswap/meta.yaml b/recipes/ucsc-axtswap/meta.yaml index f2a0a2ff9c4f7b..400fea3079a81e 100644 --- a/recipes/ucsc-axtswap/meta.yaml +++ b/recipes/ucsc-axtswap/meta.yaml @@ -18,7 +18,7 @@ source: fn: "{{ program }}" # [osx] build: - number: 0 + number: 1 requirements: build: @@ -27,7 +27,7 @@ requirements: - libuuid # [linux] - mysql-connector-c # [linux] - openssl # [linux] - - zlib # [linux] + - zlib {{ CONDA_ZLIB }}* # [linux] run: - libgcc # [linux] @@ -35,7 +35,7 @@ requirements: - libuuid # [linux] - mysql-connector-c # [linux] - openssl # [linux] - - zlib # [linux] + - zlib {{ CONDA_ZLIB }}* # [linux] test: commands: diff --git a/recipes/ucsc-axttomaf/meta.yaml b/recipes/ucsc-axttomaf/meta.yaml index fce51fc2ce32ed..bc62a05d7739d0 100644 --- a/recipes/ucsc-axttomaf/meta.yaml +++ b/recipes/ucsc-axttomaf/meta.yaml @@ -18,7 +18,7 @@ source: fn: "{{ program }}" # [osx] build: - number: 0 + number: 1 requirements: build: @@ -27,7 +27,7 @@ requirements: - libuuid # [linux] - mysql-connector-c # [linux] - openssl # [linux] - - zlib # [linux] + - zlib {{CONDA_ZLIB}}* # [linux] run: - libgcc # [linux] @@ -35,7 +35,7 @@ requirements: - libuuid # [linux] - mysql-connector-c # [linux] - openssl # [linux] - - zlib # [linux] + - zlib {{CONDA_ZLIB}}* # [linux] test: commands: diff --git a/recipes/ucsc-axttopsl/meta.yaml b/recipes/ucsc-axttopsl/meta.yaml index 04b8a8a84497e5..572fb058d1f50c 100644 --- a/recipes/ucsc-axttopsl/meta.yaml +++ b/recipes/ucsc-axttopsl/meta.yaml @@ -18,7 +18,7 @@ source: fn: "{{ program }}" # [osx] build: - number: 0 + number: 1 requirements: build: @@ -27,7 +27,7 @@ requirements: - libuuid # [linux] - mysql-connector-c # [linux] - openssl # [linux] - - zlib # [linux] + - zlib {{CONDA_ZLIB}}* # [linux] run: - libgcc # [linux] @@ -35,7 +35,7 @@ requirements: - libuuid # [linux] - mysql-connector-c # [linux] - openssl # [linux] - - zlib # [linux] + - zlib {{CONDA_ZLIB}}* # [linux] test: commands: diff --git a/recipes/ucsc-bamtopsl/meta.yaml b/recipes/ucsc-bamtopsl/meta.yaml index fe4263aff29989..48d19f870bd582 100644 --- a/recipes/ucsc-bamtopsl/meta.yaml +++ b/recipes/ucsc-bamtopsl/meta.yaml @@ -18,7 +18,7 @@ source: fn: "{{ program }}" # [osx] build: - number: 0 + number: 1 requirements: build: @@ -27,7 +27,7 @@ requirements: - libuuid # [linux] - mysql-connector-c # [linux] - openssl # [linux] - - zlib # [linux] + - zlib {{CONDA_ZLIB}}* # [linux] run: - libgcc # [linux] @@ -35,7 +35,7 @@ requirements: - libuuid # [linux] - mysql-connector-c # [linux] - openssl # [linux] - - zlib # [linux] + - zlib {{CONDA_ZLIB}}* # [linux] test: commands: diff --git a/recipes/ucsc-bedclip/meta.yaml b/recipes/ucsc-bedclip/meta.yaml index b8a836739ad82c..ddd92fd216af39 100644 --- a/recipes/ucsc-bedclip/meta.yaml +++ b/recipes/ucsc-bedclip/meta.yaml @@ -18,7 +18,7 @@ source: fn: "{{ program }}" # [osx] build: - number: 0 + number: 1 requirements: build: @@ -27,7 +27,7 @@ requirements: - libuuid # [linux] - mysql-connector-c # [linux] - openssl # [linux] - - zlib # [linux] + - zlib {{CONDA_ZLIB}}* # [linux] run: - libgcc # [linux] @@ -35,7 +35,7 @@ requirements: - libuuid # [linux] - mysql-connector-c # [linux] - openssl # [linux] - - zlib # [linux] + - zlib {{CONDA_ZLIB}}* # [linux] test: commands: diff --git a/recipes/ucsc-bedcommonregions/meta.yaml b/recipes/ucsc-bedcommonregions/meta.yaml index 8a25bfc23a07a6..a18a8009a97391 100644 --- a/recipes/ucsc-bedcommonregions/meta.yaml +++ b/recipes/ucsc-bedcommonregions/meta.yaml @@ -18,7 +18,7 @@ source: fn: "{{ program }}" # [osx] build: - number: 0 + number: 1 requirements: build: @@ -27,7 +27,7 @@ requirements: - libuuid # [linux] - mysql-connector-c # [linux] - openssl # [linux] - - zlib # [linux] + - zlib {{CONDA_ZLIB}}* # [linux] run: - libgcc # [linux] @@ -35,7 +35,7 @@ requirements: - libuuid # [linux] - mysql-connector-c # [linux] - openssl # [linux] - - zlib # [linux] + - zlib {{CONDA_ZLIB}}* # [linux] test: commands: diff --git a/recipes/ucsc-bedcoverage/meta.yaml b/recipes/ucsc-bedcoverage/meta.yaml index c4f2a1d5b66de9..62ac3088793dea 100644 --- a/recipes/ucsc-bedcoverage/meta.yaml +++ b/recipes/ucsc-bedcoverage/meta.yaml @@ -18,7 +18,7 @@ source: fn: "{{ program }}" # [osx] build: - number: 0 + number: 1 requirements: build: @@ -27,7 +27,7 @@ requirements: - libuuid # [linux] - mysql-connector-c # [linux] - openssl # [linux] - - zlib # [linux] + - zlib {{CONDA_ZLIB}}* # [linux] run: - libgcc # [linux] @@ -35,7 +35,7 @@ requirements: - libuuid # [linux] - mysql-connector-c # [linux] - openssl # [linux] - - zlib # [linux] + - zlib {{CONDA_ZLIB}}* # [linux] test: commands: diff --git a/recipes/ucsc-bedextendranges/meta.yaml b/recipes/ucsc-bedextendranges/meta.yaml index 31b78be78aeb4b..e44c79cae060b7 100644 --- a/recipes/ucsc-bedextendranges/meta.yaml +++ b/recipes/ucsc-bedextendranges/meta.yaml @@ -18,7 +18,7 @@ source: fn: "{{ program }}" # [osx] build: - number: 0 + number: 1 requirements: build: @@ -27,7 +27,7 @@ requirements: - libuuid # [linux] - mysql-connector-c # [linux] - openssl # [linux] - - zlib # [linux] + - zlib {{CONDA_ZLIB}}* # [linux] run: - libgcc # [linux] @@ -35,7 +35,7 @@ requirements: - libuuid # [linux] - mysql-connector-c # [linux] - openssl # [linux] - - zlib # [linux] + - zlib {{CONDA_ZLIB}}* # [linux] test: commands: diff --git a/recipes/ucsc-bedgeneparts/meta.yaml b/recipes/ucsc-bedgeneparts/meta.yaml index 2d3a4bdc63207b..3fb9c1697da78a 100644 --- a/recipes/ucsc-bedgeneparts/meta.yaml +++ b/recipes/ucsc-bedgeneparts/meta.yaml @@ -18,7 +18,7 @@ source: fn: "{{ program }}" # [osx] build: - number: 0 + number: 1 requirements: build: @@ -27,7 +27,7 @@ requirements: - libuuid # [linux] - mysql-connector-c # [linux] - openssl # [linux] - - zlib # [linux] + - zlib {{CONDA_ZLIB}}* # [linux] run: - libgcc # [linux] @@ -35,7 +35,7 @@ requirements: - libuuid # [linux] - mysql-connector-c # [linux] - openssl # [linux] - - zlib # [linux] + - zlib {{CONDA_ZLIB}}* # [linux] test: commands: diff --git a/recipes/ucsc-bedgraphpack/meta.yaml b/recipes/ucsc-bedgraphpack/meta.yaml index e8c1df2d66de0a..71e295597dd2c2 100644 --- a/recipes/ucsc-bedgraphpack/meta.yaml +++ b/recipes/ucsc-bedgraphpack/meta.yaml @@ -18,7 +18,7 @@ source: fn: "{{ program }}" # [osx] build: - number: 0 + number: 1 requirements: build: @@ -27,7 +27,7 @@ requirements: - libuuid # [linux] - mysql-connector-c # [linux] - openssl # [linux] - - zlib # [linux] + - zlib {{CONDA_ZLIB}}* # [linux] run: - libgcc # [linux] @@ -35,7 +35,7 @@ requirements: - libuuid # [linux] - mysql-connector-c # [linux] - openssl # [linux] - - zlib # [linux] + - zlib {{CONDA_ZLIB}}* # [linux] test: commands: diff --git a/recipes/ucsc-bedgraphtobigwig/meta.yaml b/recipes/ucsc-bedgraphtobigwig/meta.yaml index 1115d120fce7dc..92a27f91daf6d1 100644 --- a/recipes/ucsc-bedgraphtobigwig/meta.yaml +++ b/recipes/ucsc-bedgraphtobigwig/meta.yaml @@ -18,7 +18,7 @@ source: fn: "{{ program }}" # [osx] build: - number: 0 + number: 1 requirements: build: @@ -27,7 +27,7 @@ requirements: - libuuid # [linux] - mysql-connector-c # [linux] - openssl # [linux] - - zlib # [linux] + - zlib {{ CONDA_ZLIB }}* # [linux] run: - libgcc # [linux] @@ -35,7 +35,7 @@ requirements: - libuuid # [linux] - mysql-connector-c # [linux] - openssl # [linux] - - zlib # [linux] + - zlib {{ CONDA_ZLIB }}* # [linux] test: commands: diff --git a/recipes/ucsc-bedintersect/meta.yaml b/recipes/ucsc-bedintersect/meta.yaml index 7a7bba36209465..c8e11ba7c6b0c2 100644 --- a/recipes/ucsc-bedintersect/meta.yaml +++ b/recipes/ucsc-bedintersect/meta.yaml @@ -18,7 +18,7 @@ source: fn: "{{ program }}" # [osx] build: - number: 0 + number: 1 requirements: build: @@ -27,7 +27,7 @@ requirements: - libuuid # [linux] - mysql-connector-c # [linux] - openssl # [linux] - - zlib # [linux] + - zlib {{CONDA_ZLIB}}* # [linux] run: - libgcc # [linux] @@ -35,7 +35,7 @@ requirements: - libuuid # [linux] - mysql-connector-c # [linux] - openssl # [linux] - - zlib # [linux] + - zlib {{CONDA_ZLIB}}* # [linux] test: commands: diff --git a/recipes/ucsc-beditemoverlapcount/meta.yaml b/recipes/ucsc-beditemoverlapcount/meta.yaml index f8ce0849e76360..00bbc80873bb41 100644 --- a/recipes/ucsc-beditemoverlapcount/meta.yaml +++ b/recipes/ucsc-beditemoverlapcount/meta.yaml @@ -18,7 +18,7 @@ source: fn: "{{ program }}" # [osx] build: - number: 0 + number: 1 requirements: build: @@ -27,7 +27,7 @@ requirements: - libuuid # [linux] - mysql-connector-c # [linux] - openssl # [linux] - - zlib # [linux] + - zlib {{CONDA_ZLIB}}* # [linux] run: - libgcc # [linux] @@ -35,7 +35,7 @@ requirements: - libuuid # [linux] - mysql-connector-c # [linux] - openssl # [linux] - - zlib # [linux] + - zlib {{CONDA_ZLIB}}* # [linux] test: commands: diff --git a/recipes/ucsc-bedpileups/meta.yaml b/recipes/ucsc-bedpileups/meta.yaml index 4735bb847cc2e1..4ae3404db56142 100644 --- a/recipes/ucsc-bedpileups/meta.yaml +++ b/recipes/ucsc-bedpileups/meta.yaml @@ -18,7 +18,7 @@ source: fn: "{{ program }}" # [osx] build: - number: 0 + number: 1 requirements: build: @@ -27,7 +27,7 @@ requirements: - libuuid # [linux] - mysql-connector-c # [linux] - openssl # [linux] - - zlib # [linux] + - zlib {{CONDA_ZLIB}}* # [linux] run: - libgcc # [linux] @@ -35,7 +35,7 @@ requirements: - libuuid # [linux] - mysql-connector-c # [linux] - openssl # [linux] - - zlib # [linux] + - zlib {{CONDA_ZLIB}}* # [linux] test: commands: diff --git a/recipes/ucsc-bedremoveoverlap/meta.yaml b/recipes/ucsc-bedremoveoverlap/meta.yaml index 8d6adb4c2f0e7f..15a4cb839ace5d 100644 --- a/recipes/ucsc-bedremoveoverlap/meta.yaml +++ b/recipes/ucsc-bedremoveoverlap/meta.yaml @@ -18,7 +18,7 @@ source: fn: "{{ program }}" # [osx] build: - number: 0 + number: 1 requirements: build: @@ -27,7 +27,7 @@ requirements: - libuuid # [linux] - mysql-connector-c # [linux] - openssl # [linux] - - zlib # [linux] + - zlib {{CONDA_ZLIB}}* # [linux] run: - libgcc # [linux] @@ -35,7 +35,7 @@ requirements: - libuuid # [linux] - mysql-connector-c # [linux] - openssl # [linux] - - zlib # [linux] + - zlib {{CONDA_ZLIB}}* # [linux] test: commands: diff --git a/recipes/ucsc-bedrestricttopositions/meta.yaml b/recipes/ucsc-bedrestricttopositions/meta.yaml index 2f72c96933707c..54dc7601bc8522 100644 --- a/recipes/ucsc-bedrestricttopositions/meta.yaml +++ b/recipes/ucsc-bedrestricttopositions/meta.yaml @@ -18,7 +18,7 @@ source: fn: "{{ program }}" # [osx] build: - number: 0 + number: 1 requirements: build: @@ -27,7 +27,7 @@ requirements: - libuuid # [linux] - mysql-connector-c # [linux] - openssl # [linux] - - zlib # [linux] + - zlib {{CONDA_ZLIB}}* # [linux] run: - libgcc # [linux] @@ -35,7 +35,7 @@ requirements: - libuuid # [linux] - mysql-connector-c # [linux] - openssl # [linux] - - zlib # [linux] + - zlib {{CONDA_ZLIB}}* # [linux] test: commands: diff --git a/recipes/ucsc-bedsort/meta.yaml b/recipes/ucsc-bedsort/meta.yaml index 99ad61b73203bb..16e94938158949 100644 --- a/recipes/ucsc-bedsort/meta.yaml +++ b/recipes/ucsc-bedsort/meta.yaml @@ -18,7 +18,7 @@ source: fn: "{{ program }}" # [osx] build: - number: 0 + number: 1 requirements: build: @@ -27,7 +27,7 @@ requirements: - libuuid # [linux] - mysql-connector-c # [linux] - openssl # [linux] - - zlib # [linux] + - zlib {{CONDA_ZLIB}}* # [linux] run: - libgcc # [linux] @@ -35,7 +35,7 @@ requirements: - libuuid # [linux] - mysql-connector-c # [linux] - openssl # [linux] - - zlib # [linux] + - zlib {{CONDA_ZLIB}}* # [linux] test: commands: diff --git a/recipes/ucsc-bedtobigbed/meta.yaml b/recipes/ucsc-bedtobigbed/meta.yaml index 3238b596082388..02b59eef5950f7 100644 --- a/recipes/ucsc-bedtobigbed/meta.yaml +++ b/recipes/ucsc-bedtobigbed/meta.yaml @@ -18,7 +18,7 @@ source: fn: "{{ program }}" # [osx] build: - number: 0 + number: 1 requirements: build: @@ -27,7 +27,7 @@ requirements: - libuuid # [linux] - mysql-connector-c # [linux] - openssl # [linux] - - zlib # [linux] + - zlib {{CONDA_ZLIB}}* # [linux] run: - libgcc # [linux] @@ -35,7 +35,7 @@ requirements: - libuuid # [linux] - mysql-connector-c # [linux] - openssl # [linux] - - zlib # [linux] + - zlib {{CONDA_ZLIB}}* # [linux] test: commands: diff --git a/recipes/ucsc-bedtogenepred/meta.yaml b/recipes/ucsc-bedtogenepred/meta.yaml index 85d0fb291d8f01..e034217ed72d55 100644 --- a/recipes/ucsc-bedtogenepred/meta.yaml +++ b/recipes/ucsc-bedtogenepred/meta.yaml @@ -18,7 +18,7 @@ source: fn: "{{ program }}" # [osx] build: - number: 0 + number: 1 requirements: build: @@ -27,7 +27,7 @@ requirements: - libuuid # [linux] - mysql-connector-c # [linux] - openssl # [linux] - - zlib # [linux] + - zlib {{CONDA_ZLIB}}* # [linux] run: - libgcc # [linux] @@ -35,7 +35,7 @@ requirements: - libuuid # [linux] - mysql-connector-c # [linux] - openssl # [linux] - - zlib # [linux] + - zlib {{CONDA_ZLIB}}* # [linux] test: commands: diff --git a/recipes/ucsc-bedtopsl/meta.yaml b/recipes/ucsc-bedtopsl/meta.yaml index ecea64e3b591ce..78e0b7998428bb 100644 --- a/recipes/ucsc-bedtopsl/meta.yaml +++ b/recipes/ucsc-bedtopsl/meta.yaml @@ -18,7 +18,7 @@ source: fn: "{{ program }}" # [osx] build: - number: 0 + number: 1 requirements: build: @@ -27,7 +27,7 @@ requirements: - libuuid # [linux] - mysql-connector-c # [linux] - openssl # [linux] - - zlib # [linux] + - zlib {{CONDA_ZLIB}}* # [linux] run: - libgcc # [linux] @@ -35,7 +35,7 @@ requirements: - libuuid # [linux] - mysql-connector-c # [linux] - openssl # [linux] - - zlib # [linux] + - zlib {{CONDA_ZLIB}}* # [linux] test: commands: diff --git a/recipes/ucsc-bedweedoverlapping/meta.yaml b/recipes/ucsc-bedweedoverlapping/meta.yaml index 885c4ebf4723e4..6666947a50a9ae 100644 --- a/recipes/ucsc-bedweedoverlapping/meta.yaml +++ b/recipes/ucsc-bedweedoverlapping/meta.yaml @@ -18,7 +18,7 @@ source: fn: "{{ program }}" # [osx] build: - number: 0 + number: 1 requirements: build: @@ -27,7 +27,7 @@ requirements: - libuuid # [linux] - mysql-connector-c # [linux] - openssl # [linux] - - zlib # [linux] + - zlib {{CONDA_ZLIB}}* # [linux] run: - libgcc # [linux] @@ -35,7 +35,7 @@ requirements: - libuuid # [linux] - mysql-connector-c # [linux] - openssl # [linux] - - zlib # [linux] + - zlib {{CONDA_ZLIB}}* # [linux] test: commands: diff --git a/recipes/ucsc-bigbedinfo/meta.yaml b/recipes/ucsc-bigbedinfo/meta.yaml index 2c8a15506efce4..522182e04e9988 100644 --- a/recipes/ucsc-bigbedinfo/meta.yaml +++ b/recipes/ucsc-bigbedinfo/meta.yaml @@ -18,7 +18,7 @@ source: fn: "{{ program }}" # [osx] build: - number: 0 + number: 1 requirements: build: @@ -27,7 +27,7 @@ requirements: - libuuid # [linux] - mysql-connector-c # [linux] - openssl # [linux] - - zlib # [linux] + - zlib {{CONDA_ZLIB}}* # [linux] run: - libgcc # [linux] @@ -35,7 +35,7 @@ requirements: - libuuid # [linux] - mysql-connector-c # [linux] - openssl # [linux] - - zlib # [linux] + - zlib {{CONDA_ZLIB}}* # [linux] test: commands: diff --git a/recipes/ucsc-bigbednameditems/meta.yaml b/recipes/ucsc-bigbednameditems/meta.yaml index 34ba4fc067ea6c..0392bf57df97e7 100644 --- a/recipes/ucsc-bigbednameditems/meta.yaml +++ b/recipes/ucsc-bigbednameditems/meta.yaml @@ -18,7 +18,7 @@ source: fn: "{{ program }}" # [osx] build: - number: 0 + number: 1 requirements: build: @@ -27,7 +27,7 @@ requirements: - libuuid # [linux] - mysql-connector-c # [linux] - openssl # [linux] - - zlib # [linux] + - zlib {{CONDA_ZLIB}}* # [linux] run: - libgcc # [linux] @@ -35,7 +35,7 @@ requirements: - libuuid # [linux] - mysql-connector-c # [linux] - openssl # [linux] - - zlib # [linux] + - zlib {{CONDA_ZLIB}}* # [linux] test: commands: diff --git a/recipes/ucsc-bigbedsummary/meta.yaml b/recipes/ucsc-bigbedsummary/meta.yaml index 8c65e747749262..6554d7210f6f33 100644 --- a/recipes/ucsc-bigbedsummary/meta.yaml +++ b/recipes/ucsc-bigbedsummary/meta.yaml @@ -18,7 +18,7 @@ source: fn: "{{ program }}" # [osx] build: - number: 0 + number: 1 requirements: build: @@ -27,7 +27,7 @@ requirements: - libuuid # [linux] - mysql-connector-c # [linux] - openssl # [linux] - - zlib # [linux] + - zlib {{CONDA_ZLIB}}* # [linux] run: - libgcc # [linux] @@ -35,7 +35,7 @@ requirements: - libuuid # [linux] - mysql-connector-c # [linux] - openssl # [linux] - - zlib # [linux] + - zlib {{CONDA_ZLIB}}* # [linux] test: commands: diff --git a/recipes/ucsc-bigbedtobed/meta.yaml b/recipes/ucsc-bigbedtobed/meta.yaml index 7eab4de1f4466d..6c9f325f75b402 100644 --- a/recipes/ucsc-bigbedtobed/meta.yaml +++ b/recipes/ucsc-bigbedtobed/meta.yaml @@ -18,7 +18,7 @@ source: fn: "{{ program }}" # [osx] build: - number: 0 + number: 1 requirements: build: @@ -27,7 +27,7 @@ requirements: - libuuid # [linux] - mysql-connector-c # [linux] - openssl # [linux] - - zlib # [linux] + - zlib {{CONDA_ZLIB}}* # [linux] run: - libgcc # [linux] @@ -35,7 +35,7 @@ requirements: - libuuid # [linux] - mysql-connector-c # [linux] - openssl # [linux] - - zlib # [linux] + - zlib {{CONDA_ZLIB}}* # [linux] test: commands: diff --git a/recipes/ucsc-bigmaftomaf/meta.yaml b/recipes/ucsc-bigmaftomaf/meta.yaml index cd6a999aa5d6b3..5885285a9e273a 100644 --- a/recipes/ucsc-bigmaftomaf/meta.yaml +++ b/recipes/ucsc-bigmaftomaf/meta.yaml @@ -18,7 +18,7 @@ source: fn: "{{ program }}" # [osx] build: - number: 0 + number: 1 requirements: build: @@ -27,7 +27,7 @@ requirements: - libuuid # [linux] - mysql-connector-c # [linux] - openssl # [linux] - - zlib # [linux] + - zlib {{CONDA_ZLIB}}* # [linux] run: - libgcc # [linux] @@ -35,7 +35,7 @@ requirements: - libuuid # [linux] - mysql-connector-c # [linux] - openssl # [linux] - - zlib # [linux] + - zlib {{CONDA_ZLIB}}* # [linux] test: commands: diff --git a/recipes/ucsc-bigpsltopsl/meta.yaml b/recipes/ucsc-bigpsltopsl/meta.yaml index c1ab2d3eb04f9b..6158c668c2305d 100644 --- a/recipes/ucsc-bigpsltopsl/meta.yaml +++ b/recipes/ucsc-bigpsltopsl/meta.yaml @@ -18,7 +18,7 @@ source: fn: "{{ program }}" # [osx] build: - number: 0 + number: 1 requirements: build: @@ -27,7 +27,7 @@ requirements: - libuuid # [linux] - mysql-connector-c # [linux] - openssl # [linux] - - zlib # [linux] + - zlib {{CONDA_ZLIB}}* # [linux] run: - libgcc # [linux] @@ -35,7 +35,7 @@ requirements: - libuuid # [linux] - mysql-connector-c # [linux] - openssl # [linux] - - zlib # [linux] + - zlib {{CONDA_ZLIB}}* # [linux] test: commands: diff --git a/recipes/ucsc-bigwigaverageoverbed/meta.yaml b/recipes/ucsc-bigwigaverageoverbed/meta.yaml index 6a22edb10f8b51..c3a177b11bb895 100644 --- a/recipes/ucsc-bigwigaverageoverbed/meta.yaml +++ b/recipes/ucsc-bigwigaverageoverbed/meta.yaml @@ -18,7 +18,7 @@ source: fn: "{{ program }}" # [osx] build: - number: 0 + number: 1 requirements: build: @@ -27,7 +27,7 @@ requirements: - libuuid # [linux] - mysql-connector-c # [linux] - openssl # [linux] - - zlib # [linux] + - zlib {{CONDA_ZLIB}}* # [linux] run: - libgcc # [linux] @@ -35,7 +35,7 @@ requirements: - libuuid # [linux] - mysql-connector-c # [linux] - openssl # [linux] - - zlib # [linux] + - zlib {{CONDA_ZLIB}}* # [linux] test: commands: diff --git a/recipes/ucsc-bigwigcat/meta.yaml b/recipes/ucsc-bigwigcat/meta.yaml index 12de04a26fef05..07a09d5b685248 100644 --- a/recipes/ucsc-bigwigcat/meta.yaml +++ b/recipes/ucsc-bigwigcat/meta.yaml @@ -18,7 +18,7 @@ source: fn: "{{ program }}" # [osx] build: - number: 0 + number: 1 requirements: build: @@ -27,7 +27,7 @@ requirements: - libuuid # [linux] - mysql-connector-c # [linux] - openssl # [linux] - - zlib # [linux] + - zlib {{CONDA_ZLIB}}* # [linux] run: - libgcc # [linux] @@ -35,7 +35,7 @@ requirements: - libuuid # [linux] - mysql-connector-c # [linux] - openssl # [linux] - - zlib # [linux] + - zlib {{CONDA_ZLIB}}* # [linux] test: commands: diff --git a/recipes/ucsc-bigwigcluster/meta.yaml b/recipes/ucsc-bigwigcluster/meta.yaml index c79e10028bb238..a67a4cd2449070 100644 --- a/recipes/ucsc-bigwigcluster/meta.yaml +++ b/recipes/ucsc-bigwigcluster/meta.yaml @@ -18,7 +18,7 @@ source: fn: "{{ program }}" # [osx] build: - number: 0 + number: 1 requirements: build: @@ -27,7 +27,7 @@ requirements: - libuuid # [linux] - mysql-connector-c # [linux] - openssl # [linux] - - zlib # [linux] + - zlib {{CONDA_ZLIB}}* # [linux] run: - libgcc # [linux] @@ -35,7 +35,7 @@ requirements: - libuuid # [linux] - mysql-connector-c # [linux] - openssl # [linux] - - zlib # [linux] + - zlib {{CONDA_ZLIB}}* # [linux] test: commands: diff --git a/recipes/ucsc-bigwigcorrelate/meta.yaml b/recipes/ucsc-bigwigcorrelate/meta.yaml index 7cb2d3b66266af..18d481837fa5a1 100644 --- a/recipes/ucsc-bigwigcorrelate/meta.yaml +++ b/recipes/ucsc-bigwigcorrelate/meta.yaml @@ -18,7 +18,7 @@ source: fn: "{{ program }}" # [osx] build: - number: 0 + number: 1 requirements: build: @@ -27,7 +27,7 @@ requirements: - libuuid # [linux] - mysql-connector-c # [linux] - openssl # [linux] - - zlib # [linux] + - zlib {{CONDA_ZLIB}}* # [linux] run: - libgcc # [linux] @@ -35,7 +35,7 @@ requirements: - libuuid # [linux] - mysql-connector-c # [linux] - openssl # [linux] - - zlib # [linux] + - zlib {{CONDA_ZLIB}}* # [linux] test: commands: diff --git a/recipes/ucsc-bigwiginfo/meta.yaml b/recipes/ucsc-bigwiginfo/meta.yaml index 859033ac857a4e..ad3381803e1382 100644 --- a/recipes/ucsc-bigwiginfo/meta.yaml +++ b/recipes/ucsc-bigwiginfo/meta.yaml @@ -18,7 +18,7 @@ source: fn: "{{ program }}" # [osx] build: - number: 0 + number: 1 requirements: build: @@ -27,7 +27,7 @@ requirements: - libuuid # [linux] - mysql-connector-c # [linux] - openssl # [linux] - - zlib # [linux] + - zlib {{CONDA_ZLIB}}* # [linux] run: - libgcc # [linux] @@ -35,7 +35,7 @@ requirements: - libuuid # [linux] - mysql-connector-c # [linux] - openssl # [linux] - - zlib # [linux] + - zlib {{CONDA_ZLIB}}* # [linux] test: commands: diff --git a/recipes/ucsc-bigwigmerge/meta.yaml b/recipes/ucsc-bigwigmerge/meta.yaml index 4f682d0fea1229..50764037081760 100644 --- a/recipes/ucsc-bigwigmerge/meta.yaml +++ b/recipes/ucsc-bigwigmerge/meta.yaml @@ -18,7 +18,7 @@ source: fn: "{{ program }}" # [osx] build: - number: 0 + number: 1 requirements: build: @@ -27,7 +27,7 @@ requirements: - libuuid # [linux] - mysql-connector-c # [linux] - openssl # [linux] - - zlib # [linux] + - zlib {{CONDA_ZLIB}}* # [linux] run: - libgcc # [linux] @@ -35,7 +35,7 @@ requirements: - libuuid # [linux] - mysql-connector-c # [linux] - openssl # [linux] - - zlib # [linux] + - zlib {{CONDA_ZLIB}}* # [linux] test: commands: diff --git a/recipes/ucsc-bigwigsummary/meta.yaml b/recipes/ucsc-bigwigsummary/meta.yaml index 1c61e61518a141..916ba05c7601ae 100644 --- a/recipes/ucsc-bigwigsummary/meta.yaml +++ b/recipes/ucsc-bigwigsummary/meta.yaml @@ -18,7 +18,7 @@ source: fn: "{{ program }}" # [osx] build: - number: 0 + number: 1 requirements: build: @@ -27,7 +27,7 @@ requirements: - libuuid # [linux] - mysql-connector-c # [linux] - openssl # [linux] - - zlib # [linux] + - zlib {{CONDA_ZLIB}}* # [linux] run: - libgcc # [linux] @@ -35,7 +35,7 @@ requirements: - libuuid # [linux] - mysql-connector-c # [linux] - openssl # [linux] - - zlib # [linux] + - zlib {{CONDA_ZLIB}}* # [linux] test: commands: diff --git a/recipes/ucsc-bigwigtobedgraph/meta.yaml b/recipes/ucsc-bigwigtobedgraph/meta.yaml index 776a5170752580..1b550210623914 100644 --- a/recipes/ucsc-bigwigtobedgraph/meta.yaml +++ b/recipes/ucsc-bigwigtobedgraph/meta.yaml @@ -18,7 +18,7 @@ source: fn: "{{ program }}" # [osx] build: - number: 0 + number: 1 requirements: build: @@ -27,7 +27,7 @@ requirements: - libuuid # [linux] - mysql-connector-c # [linux] - openssl # [linux] - - zlib # [linux] + - zlib {{CONDA_ZLIB}}* # [linux] run: - libgcc # [linux] @@ -35,7 +35,7 @@ requirements: - libuuid # [linux] - mysql-connector-c # [linux] - openssl # [linux] - - zlib # [linux] + - zlib {{CONDA_ZLIB}}* # [linux] test: commands: diff --git a/recipes/ucsc-bigwigtowig/meta.yaml b/recipes/ucsc-bigwigtowig/meta.yaml index 82e8e511d34ccb..3c6c245ef0bcf2 100644 --- a/recipes/ucsc-bigwigtowig/meta.yaml +++ b/recipes/ucsc-bigwigtowig/meta.yaml @@ -18,7 +18,7 @@ source: fn: "{{ program }}" # [osx] build: - number: 0 + number: 1 requirements: build: @@ -27,7 +27,7 @@ requirements: - libuuid # [linux] - mysql-connector-c # [linux] - openssl # [linux] - - zlib # [linux] + - zlib {{CONDA_ZLIB}}* # [linux] run: - libgcc # [linux] @@ -35,7 +35,7 @@ requirements: - libuuid # [linux] - mysql-connector-c # [linux] - openssl # [linux] - - zlib # [linux] + - zlib {{CONDA_ZLIB}}* # [linux] test: commands: diff --git a/recipes/ucsc-blasttopsl/meta.yaml b/recipes/ucsc-blasttopsl/meta.yaml index 70b953be4470a7..3f1136d4281c94 100644 --- a/recipes/ucsc-blasttopsl/meta.yaml +++ b/recipes/ucsc-blasttopsl/meta.yaml @@ -18,7 +18,7 @@ source: fn: "{{ program }}" # [osx] build: - number: 0 + number: 1 requirements: build: @@ -27,7 +27,7 @@ requirements: - libuuid # [linux] - mysql-connector-c # [linux] - openssl # [linux] - - zlib # [linux] + - zlib {{CONDA_ZLIB}}* # [linux] run: - libgcc # [linux] @@ -35,7 +35,7 @@ requirements: - libuuid # [linux] - mysql-connector-c # [linux] - openssl # [linux] - - zlib # [linux] + - zlib {{CONDA_ZLIB}}* # [linux] test: commands: diff --git a/recipes/ucsc-blat/meta.yaml b/recipes/ucsc-blat/meta.yaml index a9655233646b68..da21feffdcd685 100644 --- a/recipes/ucsc-blat/meta.yaml +++ b/recipes/ucsc-blat/meta.yaml @@ -18,7 +18,7 @@ source: fn: "{{ program }}" # [osx] build: - number: 0 + number: 1 requirements: build: @@ -27,7 +27,7 @@ requirements: - libuuid # [linux] - mysql-connector-c # [linux] - openssl # [linux] - - zlib # [linux] + - zlib {{CONDA_ZLIB}}* # [linux] run: - libgcc # [linux] @@ -35,7 +35,7 @@ requirements: - libuuid # [linux] - mysql-connector-c # [linux] - openssl # [linux] - - zlib # [linux] + - zlib {{CONDA_ZLIB}}* # [linux] test: commands: diff --git a/recipes/ucsc-catdir/meta.yaml b/recipes/ucsc-catdir/meta.yaml index cad4945642a987..ee46ba64545b1a 100644 --- a/recipes/ucsc-catdir/meta.yaml +++ b/recipes/ucsc-catdir/meta.yaml @@ -18,7 +18,7 @@ source: fn: "{{ program }}" # [osx] build: - number: 0 + number: 1 requirements: build: @@ -27,7 +27,7 @@ requirements: - libuuid # [linux] - mysql-connector-c # [linux] - openssl # [linux] - - zlib # [linux] + - zlib {{CONDA_ZLIB}}* # [linux] run: - libgcc # [linux] @@ -35,7 +35,7 @@ requirements: - libuuid # [linux] - mysql-connector-c # [linux] - openssl # [linux] - - zlib # [linux] + - zlib {{CONDA_ZLIB}}* # [linux] test: commands: diff --git a/recipes/ucsc-catuncomment/meta.yaml b/recipes/ucsc-catuncomment/meta.yaml index a055a7f939dbec..0f85435733ae86 100644 --- a/recipes/ucsc-catuncomment/meta.yaml +++ b/recipes/ucsc-catuncomment/meta.yaml @@ -18,7 +18,7 @@ source: fn: "{{ program }}" # [osx] build: - number: 0 + number: 1 requirements: build: @@ -27,7 +27,7 @@ requirements: - libuuid # [linux] - mysql-connector-c # [linux] - openssl # [linux] - - zlib # [linux] + - zlib {{CONDA_ZLIB}}* # [linux] run: - libgcc # [linux] @@ -35,7 +35,7 @@ requirements: - libuuid # [linux] - mysql-connector-c # [linux] - openssl # [linux] - - zlib # [linux] + - zlib {{CONDA_ZLIB}}* # [linux] test: commands: diff --git a/recipes/ucsc-chainantirepeat/meta.yaml b/recipes/ucsc-chainantirepeat/meta.yaml index bec60b5f4cd9ee..9d219cbd3e89a5 100644 --- a/recipes/ucsc-chainantirepeat/meta.yaml +++ b/recipes/ucsc-chainantirepeat/meta.yaml @@ -18,7 +18,7 @@ source: fn: "{{ program }}" # [osx] build: - number: 0 + number: 1 requirements: build: @@ -27,7 +27,7 @@ requirements: - libuuid # [linux] - mysql-connector-c # [linux] - openssl # [linux] - - zlib # [linux] + - zlib {{CONDA_ZLIB}}* # [linux] run: - libgcc # [linux] @@ -35,7 +35,7 @@ requirements: - libuuid # [linux] - mysql-connector-c # [linux] - openssl # [linux] - - zlib # [linux] + - zlib {{CONDA_ZLIB}}* # [linux] test: commands: diff --git a/recipes/ucsc-chainfilter/meta.yaml b/recipes/ucsc-chainfilter/meta.yaml index c3e230b861e420..ea94030b760f68 100644 --- a/recipes/ucsc-chainfilter/meta.yaml +++ b/recipes/ucsc-chainfilter/meta.yaml @@ -18,7 +18,7 @@ source: fn: "{{ program }}" # [osx] build: - number: 0 + number: 1 requirements: build: @@ -27,7 +27,7 @@ requirements: - libuuid # [linux] - mysql-connector-c # [linux] - openssl # [linux] - - zlib # [linux] + - zlib {{CONDA_ZLIB}}* # [linux] run: - libgcc # [linux] @@ -35,7 +35,7 @@ requirements: - libuuid # [linux] - mysql-connector-c # [linux] - openssl # [linux] - - zlib # [linux] + - zlib {{CONDA_ZLIB}}* # [linux] test: commands: diff --git a/recipes/ucsc-chainmergesort/meta.yaml b/recipes/ucsc-chainmergesort/meta.yaml index 98426b3c194cab..eac7f1616874f9 100644 --- a/recipes/ucsc-chainmergesort/meta.yaml +++ b/recipes/ucsc-chainmergesort/meta.yaml @@ -18,7 +18,7 @@ source: fn: "{{ program }}" # [osx] build: - number: 0 + number: 1 requirements: build: @@ -27,7 +27,7 @@ requirements: - libuuid # [linux] - mysql-connector-c # [linux] - openssl # [linux] - - zlib # [linux] + - zlib {{CONDA_ZLIB}}* # [linux] run: - libgcc # [linux] @@ -35,7 +35,7 @@ requirements: - libuuid # [linux] - mysql-connector-c # [linux] - openssl # [linux] - - zlib # [linux] + - zlib {{CONDA_ZLIB}}* # [linux] test: commands: diff --git a/recipes/ucsc-chainnet/meta.yaml b/recipes/ucsc-chainnet/meta.yaml index a6d31aca16e1ac..5e8a094ac9dd55 100644 --- a/recipes/ucsc-chainnet/meta.yaml +++ b/recipes/ucsc-chainnet/meta.yaml @@ -18,7 +18,7 @@ source: fn: "{{ program }}" # [osx] build: - number: 0 + number: 1 requirements: build: @@ -27,7 +27,7 @@ requirements: - libuuid # [linux] - mysql-connector-c # [linux] - openssl # [linux] - - zlib # [linux] + - zlib {{CONDA_ZLIB}}* # [linux] run: - libgcc # [linux] @@ -35,7 +35,7 @@ requirements: - libuuid # [linux] - mysql-connector-c # [linux] - openssl # [linux] - - zlib # [linux] + - zlib {{CONDA_ZLIB}}* # [linux] test: commands: diff --git a/recipes/ucsc-chainprenet/meta.yaml b/recipes/ucsc-chainprenet/meta.yaml index 908817a5ff389d..89c8b0956fd34d 100644 --- a/recipes/ucsc-chainprenet/meta.yaml +++ b/recipes/ucsc-chainprenet/meta.yaml @@ -18,7 +18,7 @@ source: fn: "{{ program }}" # [osx] build: - number: 0 + number: 1 requirements: build: @@ -27,7 +27,7 @@ requirements: - libuuid # [linux] - mysql-connector-c # [linux] - openssl # [linux] - - zlib # [linux] + - zlib {{CONDA_ZLIB}}* # [linux] run: - libgcc # [linux] @@ -35,7 +35,7 @@ requirements: - libuuid # [linux] - mysql-connector-c # [linux] - openssl # [linux] - - zlib # [linux] + - zlib {{CONDA_ZLIB}}* # [linux] test: commands: diff --git a/recipes/ucsc-chainsort/meta.yaml b/recipes/ucsc-chainsort/meta.yaml index e8a48768d48e05..d02667b5327d54 100644 --- a/recipes/ucsc-chainsort/meta.yaml +++ b/recipes/ucsc-chainsort/meta.yaml @@ -18,7 +18,7 @@ source: fn: "{{ program }}" # [osx] build: - number: 0 + number: 1 requirements: build: @@ -27,7 +27,7 @@ requirements: - libuuid # [linux] - mysql-connector-c # [linux] - openssl # [linux] - - zlib # [linux] + - zlib {{CONDA_ZLIB}}* # [linux] run: - libgcc # [linux] @@ -35,7 +35,7 @@ requirements: - libuuid # [linux] - mysql-connector-c # [linux] - openssl # [linux] - - zlib # [linux] + - zlib {{CONDA_ZLIB}}* # [linux] test: commands: diff --git a/recipes/ucsc-chainsplit/meta.yaml b/recipes/ucsc-chainsplit/meta.yaml index e2581aa8d57893..6e61862334b372 100644 --- a/recipes/ucsc-chainsplit/meta.yaml +++ b/recipes/ucsc-chainsplit/meta.yaml @@ -18,7 +18,7 @@ source: fn: "{{ program }}" # [osx] build: - number: 0 + number: 1 requirements: build: @@ -27,7 +27,7 @@ requirements: - libuuid # [linux] - mysql-connector-c # [linux] - openssl # [linux] - - zlib # [linux] + - zlib {{CONDA_ZLIB}}* # [linux] run: - libgcc # [linux] @@ -35,7 +35,7 @@ requirements: - libuuid # [linux] - mysql-connector-c # [linux] - openssl # [linux] - - zlib # [linux] + - zlib {{CONDA_ZLIB}}* # [linux] test: commands: diff --git a/recipes/ucsc-chainstitchid/meta.yaml b/recipes/ucsc-chainstitchid/meta.yaml index 5a18ed40cd0986..038772ad655915 100644 --- a/recipes/ucsc-chainstitchid/meta.yaml +++ b/recipes/ucsc-chainstitchid/meta.yaml @@ -18,7 +18,7 @@ source: fn: "{{ program }}" # [osx] build: - number: 0 + number: 1 requirements: build: @@ -27,7 +27,7 @@ requirements: - libuuid # [linux] - mysql-connector-c # [linux] - openssl # [linux] - - zlib # [linux] + - zlib {{CONDA_ZLIB}}* # [linux] run: - libgcc # [linux] @@ -35,7 +35,7 @@ requirements: - libuuid # [linux] - mysql-connector-c # [linux] - openssl # [linux] - - zlib # [linux] + - zlib {{CONDA_ZLIB}}* # [linux] test: commands: diff --git a/recipes/ucsc-chainswap/meta.yaml b/recipes/ucsc-chainswap/meta.yaml index 91622196da274f..88b316021b6dc1 100644 --- a/recipes/ucsc-chainswap/meta.yaml +++ b/recipes/ucsc-chainswap/meta.yaml @@ -18,7 +18,7 @@ source: fn: "{{ program }}" # [osx] build: - number: 0 + number: 1 requirements: build: @@ -27,7 +27,7 @@ requirements: - libuuid # [linux] - mysql-connector-c # [linux] - openssl # [linux] - - zlib # [linux] + - zlib {{CONDA_ZLIB}}* # [linux] run: - libgcc # [linux] @@ -35,7 +35,7 @@ requirements: - libuuid # [linux] - mysql-connector-c # [linux] - openssl # [linux] - - zlib # [linux] + - zlib {{CONDA_ZLIB}}* # [linux] test: commands: diff --git a/recipes/ucsc-chaintoaxt/meta.yaml b/recipes/ucsc-chaintoaxt/meta.yaml index 3193a2aec8c242..e6e769576d3bc0 100644 --- a/recipes/ucsc-chaintoaxt/meta.yaml +++ b/recipes/ucsc-chaintoaxt/meta.yaml @@ -18,7 +18,7 @@ source: fn: "{{ program }}" # [osx] build: - number: 0 + number: 1 requirements: build: @@ -27,7 +27,7 @@ requirements: - libuuid # [linux] - mysql-connector-c # [linux] - openssl # [linux] - - zlib # [linux] + - zlib {{CONDA_ZLIB}}* # [linux] run: - libgcc # [linux] @@ -35,7 +35,7 @@ requirements: - libuuid # [linux] - mysql-connector-c # [linux] - openssl # [linux] - - zlib # [linux] + - zlib {{CONDA_ZLIB}}* # [linux] test: commands: diff --git a/recipes/ucsc-chaintopsl/meta.yaml b/recipes/ucsc-chaintopsl/meta.yaml index 798caa00bd4580..f0d0daca7db88f 100644 --- a/recipes/ucsc-chaintopsl/meta.yaml +++ b/recipes/ucsc-chaintopsl/meta.yaml @@ -18,7 +18,7 @@ source: fn: "{{ program }}" # [osx] build: - number: 0 + number: 1 requirements: build: @@ -27,7 +27,7 @@ requirements: - libuuid # [linux] - mysql-connector-c # [linux] - openssl # [linux] - - zlib # [linux] + - zlib {{CONDA_ZLIB}}* # [linux] run: - libgcc # [linux] @@ -35,7 +35,7 @@ requirements: - libuuid # [linux] - mysql-connector-c # [linux] - openssl # [linux] - - zlib # [linux] + - zlib {{CONDA_ZLIB}}* # [linux] test: commands: diff --git a/recipes/ucsc-chaintopslbasic/meta.yaml b/recipes/ucsc-chaintopslbasic/meta.yaml index 6aea6552ac0ce5..1cd3d0bce5bf3a 100644 --- a/recipes/ucsc-chaintopslbasic/meta.yaml +++ b/recipes/ucsc-chaintopslbasic/meta.yaml @@ -18,7 +18,7 @@ source: fn: "{{ program }}" # [osx] build: - number: 0 + number: 1 requirements: build: @@ -27,7 +27,7 @@ requirements: - libuuid # [linux] - mysql-connector-c # [linux] - openssl # [linux] - - zlib # [linux] + - zlib {{CONDA_ZLIB}}* # [linux] run: - libgcc # [linux] @@ -35,7 +35,7 @@ requirements: - libuuid # [linux] - mysql-connector-c # [linux] - openssl # [linux] - - zlib # [linux] + - zlib {{CONDA_ZLIB}}* # [linux] test: commands: diff --git a/recipes/ucsc-checkagpandfa/meta.yaml b/recipes/ucsc-checkagpandfa/meta.yaml index b751de1cac1f92..964b3cf39c984f 100644 --- a/recipes/ucsc-checkagpandfa/meta.yaml +++ b/recipes/ucsc-checkagpandfa/meta.yaml @@ -18,7 +18,7 @@ source: fn: "{{ program }}" # [osx] build: - number: 0 + number: 1 requirements: build: @@ -27,7 +27,7 @@ requirements: - libuuid # [linux] - mysql-connector-c # [linux] - openssl # [linux] - - zlib # [linux] + - zlib {{CONDA_ZLIB}}* # [linux] run: - libgcc # [linux] @@ -35,7 +35,7 @@ requirements: - libuuid # [linux] - mysql-connector-c # [linux] - openssl # [linux] - - zlib # [linux] + - zlib {{CONDA_ZLIB}}* # [linux] test: commands: diff --git a/recipes/ucsc-checkcoveragegaps/meta.yaml b/recipes/ucsc-checkcoveragegaps/meta.yaml index 8749d2670d6ddc..b81ea39fc41240 100644 --- a/recipes/ucsc-checkcoveragegaps/meta.yaml +++ b/recipes/ucsc-checkcoveragegaps/meta.yaml @@ -18,7 +18,7 @@ source: fn: "{{ program }}" # [osx] build: - number: 0 + number: 1 requirements: build: @@ -27,7 +27,7 @@ requirements: - libuuid # [linux] - mysql-connector-c # [linux] - openssl # [linux] - - zlib # [linux] + - zlib {{CONDA_ZLIB}}* # [linux] run: - libgcc # [linux] @@ -35,7 +35,7 @@ requirements: - libuuid # [linux] - mysql-connector-c # [linux] - openssl # [linux] - - zlib # [linux] + - zlib {{CONDA_ZLIB}}* # [linux] test: commands: diff --git a/recipes/ucsc-checkhgfindspec/meta.yaml b/recipes/ucsc-checkhgfindspec/meta.yaml index 8cb6017e473a9f..71c26012fff9e8 100644 --- a/recipes/ucsc-checkhgfindspec/meta.yaml +++ b/recipes/ucsc-checkhgfindspec/meta.yaml @@ -18,7 +18,7 @@ source: fn: "{{ program }}" # [osx] build: - number: 0 + number: 1 requirements: build: @@ -27,7 +27,7 @@ requirements: - libuuid # [linux] - mysql-connector-c # [linux] - openssl # [linux] - - zlib # [linux] + - zlib {{CONDA_ZLIB}}* # [linux] run: - libgcc # [linux] @@ -35,7 +35,7 @@ requirements: - libuuid # [linux] - mysql-connector-c # [linux] - openssl # [linux] - - zlib # [linux] + - zlib {{CONDA_ZLIB}}* # [linux] test: commands: diff --git a/recipes/ucsc-checktablecoords/meta.yaml b/recipes/ucsc-checktablecoords/meta.yaml index 1cce3c934e66a7..474fb83f880e3b 100644 --- a/recipes/ucsc-checktablecoords/meta.yaml +++ b/recipes/ucsc-checktablecoords/meta.yaml @@ -18,7 +18,7 @@ source: fn: "{{ program }}" # [osx] build: - number: 0 + number: 1 requirements: build: @@ -27,7 +27,7 @@ requirements: - libuuid # [linux] - mysql-connector-c # [linux] - openssl # [linux] - - zlib # [linux] + - zlib {{CONDA_ZLIB}}* # [linux] run: - libgcc # [linux] @@ -35,7 +35,7 @@ requirements: - libuuid # [linux] - mysql-connector-c # [linux] - openssl # [linux] - - zlib # [linux] + - zlib {{CONDA_ZLIB}}* # [linux] test: commands: diff --git a/recipes/ucsc-chopfalines/meta.yaml b/recipes/ucsc-chopfalines/meta.yaml index a07a3b2efaec37..4d5c6f38ba2838 100644 --- a/recipes/ucsc-chopfalines/meta.yaml +++ b/recipes/ucsc-chopfalines/meta.yaml @@ -18,7 +18,7 @@ source: fn: "{{ program }}" # [osx] build: - number: 0 + number: 1 requirements: build: @@ -27,7 +27,7 @@ requirements: - libuuid # [linux] - mysql-connector-c # [linux] - openssl # [linux] - - zlib # [linux] + - zlib {{CONDA_ZLIB}}* # [linux] run: - libgcc # [linux] @@ -35,7 +35,7 @@ requirements: - libuuid # [linux] - mysql-connector-c # [linux] - openssl # [linux] - - zlib # [linux] + - zlib {{CONDA_ZLIB}}* # [linux] test: commands: diff --git a/recipes/ucsc-chromgraphfrombin/meta.yaml b/recipes/ucsc-chromgraphfrombin/meta.yaml index 0245e5af876f89..2d8a73ccba2a23 100644 --- a/recipes/ucsc-chromgraphfrombin/meta.yaml +++ b/recipes/ucsc-chromgraphfrombin/meta.yaml @@ -18,7 +18,7 @@ source: fn: "{{ program }}" # [osx] build: - number: 0 + number: 1 requirements: build: @@ -27,7 +27,7 @@ requirements: - libuuid # [linux] - mysql-connector-c # [linux] - openssl # [linux] - - zlib # [linux] + - zlib {{CONDA_ZLIB}}* # [linux] run: - libgcc # [linux] @@ -35,7 +35,7 @@ requirements: - libuuid # [linux] - mysql-connector-c # [linux] - openssl # [linux] - - zlib # [linux] + - zlib {{CONDA_ZLIB}}* # [linux] test: commands: diff --git a/recipes/ucsc-chromgraphtobin/meta.yaml b/recipes/ucsc-chromgraphtobin/meta.yaml index 35585e38ad9887..76e7601fe5d90d 100644 --- a/recipes/ucsc-chromgraphtobin/meta.yaml +++ b/recipes/ucsc-chromgraphtobin/meta.yaml @@ -18,7 +18,7 @@ source: fn: "{{ program }}" # [osx] build: - number: 0 + number: 1 requirements: build: @@ -27,7 +27,7 @@ requirements: - libuuid # [linux] - mysql-connector-c # [linux] - openssl # [linux] - - zlib # [linux] + - zlib {{CONDA_ZLIB}}* # [linux] run: - libgcc # [linux] @@ -35,7 +35,7 @@ requirements: - libuuid # [linux] - mysql-connector-c # [linux] - openssl # [linux] - - zlib # [linux] + - zlib {{CONDA_ZLIB}}* # [linux] test: commands: diff --git a/recipes/ucsc-coltransform/meta.yaml b/recipes/ucsc-coltransform/meta.yaml index b4f00d89880a87..60a3be577ceced 100644 --- a/recipes/ucsc-coltransform/meta.yaml +++ b/recipes/ucsc-coltransform/meta.yaml @@ -18,7 +18,7 @@ source: fn: "{{ program }}" # [osx] build: - number: 0 + number: 1 requirements: build: @@ -27,7 +27,7 @@ requirements: - libuuid # [linux] - mysql-connector-c # [linux] - openssl # [linux] - - zlib # [linux] + - zlib {{CONDA_ZLIB}}* # [linux] run: - libgcc # [linux] @@ -35,7 +35,7 @@ requirements: - libuuid # [linux] - mysql-connector-c # [linux] - openssl # [linux] - - zlib # [linux] + - zlib {{CONDA_ZLIB}}* # [linux] test: commands: diff --git a/recipes/ucsc-countchars/meta.yaml b/recipes/ucsc-countchars/meta.yaml index f9dcfcf2eda060..e594a9c995b0e2 100644 --- a/recipes/ucsc-countchars/meta.yaml +++ b/recipes/ucsc-countchars/meta.yaml @@ -18,7 +18,7 @@ source: fn: "{{ program }}" # [osx] build: - number: 0 + number: 1 requirements: build: @@ -27,7 +27,7 @@ requirements: - libuuid # [linux] - mysql-connector-c # [linux] - openssl # [linux] - - zlib # [linux] + - zlib {{CONDA_ZLIB}}* # [linux] run: - libgcc # [linux] @@ -35,7 +35,7 @@ requirements: - libuuid # [linux] - mysql-connector-c # [linux] - openssl # [linux] - - zlib # [linux] + - zlib {{CONDA_ZLIB}}* # [linux] test: commands: diff --git a/recipes/ucsc-crtreeindexbed/meta.yaml b/recipes/ucsc-crtreeindexbed/meta.yaml index 32a7515221a1c6..39bac2d6ae7c63 100644 --- a/recipes/ucsc-crtreeindexbed/meta.yaml +++ b/recipes/ucsc-crtreeindexbed/meta.yaml @@ -18,7 +18,7 @@ source: fn: "{{ program }}" # [osx] build: - number: 0 + number: 1 requirements: build: @@ -27,7 +27,7 @@ requirements: - libuuid # [linux] - mysql-connector-c # [linux] - openssl # [linux] - - zlib # [linux] + - zlib {{CONDA_ZLIB}}* # [linux] run: - libgcc # [linux] @@ -35,7 +35,7 @@ requirements: - libuuid # [linux] - mysql-connector-c # [linux] - openssl # [linux] - - zlib # [linux] + - zlib {{CONDA_ZLIB}}* # [linux] test: commands: diff --git a/recipes/ucsc-crtreesearchbed/meta.yaml b/recipes/ucsc-crtreesearchbed/meta.yaml index fa13c09a3570e8..c659025642d518 100644 --- a/recipes/ucsc-crtreesearchbed/meta.yaml +++ b/recipes/ucsc-crtreesearchbed/meta.yaml @@ -18,7 +18,7 @@ source: fn: "{{ program }}" # [osx] build: - number: 0 + number: 1 requirements: build: @@ -27,7 +27,7 @@ requirements: - libuuid # [linux] - mysql-connector-c # [linux] - openssl # [linux] - - zlib # [linux] + - zlib {{CONDA_ZLIB}}* # [linux] run: - libgcc # [linux] @@ -35,7 +35,7 @@ requirements: - libuuid # [linux] - mysql-connector-c # [linux] - openssl # [linux] - - zlib # [linux] + - zlib {{CONDA_ZLIB}}* # [linux] test: commands: diff --git a/recipes/ucsc-dbsnoop/meta.yaml b/recipes/ucsc-dbsnoop/meta.yaml index 15e6f46a8d7bb2..b55bddb13a52c9 100644 --- a/recipes/ucsc-dbsnoop/meta.yaml +++ b/recipes/ucsc-dbsnoop/meta.yaml @@ -18,7 +18,7 @@ source: fn: "{{ program }}" # [osx] build: - number: 0 + number: 1 requirements: build: @@ -27,7 +27,7 @@ requirements: - libuuid # [linux] - mysql-connector-c # [linux] - openssl # [linux] - - zlib # [linux] + - zlib {{CONDA_ZLIB}}* # [linux] run: - libgcc # [linux] @@ -35,7 +35,7 @@ requirements: - libuuid # [linux] - mysql-connector-c # [linux] - openssl # [linux] - - zlib # [linux] + - zlib {{CONDA_ZLIB}}* # [linux] test: commands: diff --git a/recipes/ucsc-dbtrash/meta.yaml b/recipes/ucsc-dbtrash/meta.yaml index e3ce911309f384..ebe56990ce5974 100644 --- a/recipes/ucsc-dbtrash/meta.yaml +++ b/recipes/ucsc-dbtrash/meta.yaml @@ -18,7 +18,7 @@ source: fn: "{{ program }}" # [osx] build: - number: 0 + number: 1 requirements: build: @@ -27,7 +27,7 @@ requirements: - libuuid # [linux] - mysql-connector-c # [linux] - openssl # [linux] - - zlib # [linux] + - zlib {{CONDA_ZLIB}}* # [linux] run: - libgcc # [linux] @@ -35,7 +35,7 @@ requirements: - libuuid # [linux] - mysql-connector-c # [linux] - openssl # [linux] - - zlib # [linux] + - zlib {{CONDA_ZLIB}}* # [linux] test: commands: diff --git a/recipes/ucsc-estorient/meta.yaml b/recipes/ucsc-estorient/meta.yaml index 9e8a7123a6defb..95db61771c1865 100644 --- a/recipes/ucsc-estorient/meta.yaml +++ b/recipes/ucsc-estorient/meta.yaml @@ -18,7 +18,7 @@ source: fn: "{{ program }}" # [osx] build: - number: 0 + number: 1 requirements: build: @@ -27,7 +27,7 @@ requirements: - libuuid # [linux] - mysql-connector-c # [linux] - openssl # [linux] - - zlib # [linux] + - zlib {{CONDA_ZLIB}}* # [linux] run: - libgcc # [linux] @@ -35,7 +35,7 @@ requirements: - libuuid # [linux] - mysql-connector-c # [linux] - openssl # [linux] - - zlib # [linux] + - zlib {{CONDA_ZLIB}}* # [linux] test: commands: diff --git a/recipes/ucsc-expmatrixtobarchartbed/meta.yaml b/recipes/ucsc-expmatrixtobarchartbed/meta.yaml index 009f62d0d0ae48..452e0ca80fe5e0 100644 --- a/recipes/ucsc-expmatrixtobarchartbed/meta.yaml +++ b/recipes/ucsc-expmatrixtobarchartbed/meta.yaml @@ -19,7 +19,7 @@ source: fn: "{{ program }}" # [osx] build: - number: 0 + number: 1 requirements: build: @@ -28,7 +28,7 @@ requirements: - libuuid # [linux] - mysql-connector-c # [linux] - openssl # [linux] - - zlib # [linux] + - zlib {{CONDA_ZLIB}}* # [linux] run: - libgcc # [linux] @@ -37,7 +37,7 @@ requirements: - mysql-connector-c # [linux] - openssl # [linux] - python # [linux] - - zlib # [linux] + - zlib {{CONDA_ZLIB}}* # [linux] test: commands: diff --git a/recipes/ucsc-faalign/meta.yaml b/recipes/ucsc-faalign/meta.yaml index 5765c1e2f345c2..c48f81f660a421 100644 --- a/recipes/ucsc-faalign/meta.yaml +++ b/recipes/ucsc-faalign/meta.yaml @@ -18,7 +18,7 @@ source: fn: "{{ program }}" # [osx] build: - number: 0 + number: 1 requirements: build: @@ -27,7 +27,7 @@ requirements: - libuuid # [linux] - mysql-connector-c # [linux] - openssl # [linux] - - zlib # [linux] + - zlib {{CONDA_ZLIB}}* # [linux] run: - libgcc # [linux] @@ -35,7 +35,7 @@ requirements: - libuuid # [linux] - mysql-connector-c # [linux] - openssl # [linux] - - zlib # [linux] + - zlib {{CONDA_ZLIB}}* # [linux] test: commands: diff --git a/recipes/ucsc-facmp/meta.yaml b/recipes/ucsc-facmp/meta.yaml index 1cc0e6ff230eea..e688b7dcc7698a 100644 --- a/recipes/ucsc-facmp/meta.yaml +++ b/recipes/ucsc-facmp/meta.yaml @@ -18,7 +18,7 @@ source: fn: "{{ program }}" # [osx] build: - number: 0 + number: 1 requirements: build: @@ -27,7 +27,7 @@ requirements: - libuuid # [linux] - mysql-connector-c # [linux] - openssl # [linux] - - zlib # [linux] + - zlib {{CONDA_ZLIB}}* # [linux] run: - libgcc # [linux] @@ -35,7 +35,7 @@ requirements: - libuuid # [linux] - mysql-connector-c # [linux] - openssl # [linux] - - zlib # [linux] + - zlib {{CONDA_ZLIB}}* # [linux] test: commands: diff --git a/recipes/ucsc-facount/meta.yaml b/recipes/ucsc-facount/meta.yaml index 65957e4a81ff11..cb7686eb8546d9 100644 --- a/recipes/ucsc-facount/meta.yaml +++ b/recipes/ucsc-facount/meta.yaml @@ -18,7 +18,7 @@ source: fn: "{{ program }}" # [osx] build: - number: 0 + number: 1 requirements: build: @@ -27,7 +27,7 @@ requirements: - libuuid # [linux] - mysql-connector-c # [linux] - openssl # [linux] - - zlib # [linux] + - zlib {{CONDA_ZLIB}}* # [linux] run: - libgcc # [linux] @@ -35,7 +35,7 @@ requirements: - libuuid # [linux] - mysql-connector-c # [linux] - openssl # [linux] - - zlib # [linux] + - zlib {{CONDA_ZLIB}}* # [linux] test: commands: diff --git a/recipes/ucsc-fafilter/meta.yaml b/recipes/ucsc-fafilter/meta.yaml index 65d9da2c8164d1..cc30056de80ab2 100644 --- a/recipes/ucsc-fafilter/meta.yaml +++ b/recipes/ucsc-fafilter/meta.yaml @@ -18,7 +18,7 @@ source: fn: "{{ program }}" # [osx] build: - number: 0 + number: 1 requirements: build: @@ -27,7 +27,7 @@ requirements: - libuuid # [linux] - mysql-connector-c # [linux] - openssl # [linux] - - zlib # [linux] + - zlib {{CONDA_ZLIB}}* # [linux] run: - libgcc # [linux] @@ -35,7 +35,7 @@ requirements: - libuuid # [linux] - mysql-connector-c # [linux] - openssl # [linux] - - zlib # [linux] + - zlib {{CONDA_ZLIB}}* # [linux] test: commands: diff --git a/recipes/ucsc-fafiltern/meta.yaml b/recipes/ucsc-fafiltern/meta.yaml index b73fe4c6eeffbf..5b2a80ca907864 100644 --- a/recipes/ucsc-fafiltern/meta.yaml +++ b/recipes/ucsc-fafiltern/meta.yaml @@ -18,7 +18,7 @@ source: fn: "{{ program }}" # [osx] build: - number: 0 + number: 1 requirements: build: @@ -27,7 +27,7 @@ requirements: - libuuid # [linux] - mysql-connector-c # [linux] - openssl # [linux] - - zlib # [linux] + - zlib {{CONDA_ZLIB}}* # [linux] run: - libgcc # [linux] @@ -35,7 +35,7 @@ requirements: - libuuid # [linux] - mysql-connector-c # [linux] - openssl # [linux] - - zlib # [linux] + - zlib {{CONDA_ZLIB}}* # [linux] test: commands: diff --git a/recipes/ucsc-fafrag/meta.yaml b/recipes/ucsc-fafrag/meta.yaml index e8245cb07cd488..f09d24a8435da7 100644 --- a/recipes/ucsc-fafrag/meta.yaml +++ b/recipes/ucsc-fafrag/meta.yaml @@ -18,7 +18,7 @@ source: fn: "{{ program }}" # [osx] build: - number: 0 + number: 1 requirements: build: @@ -27,7 +27,7 @@ requirements: - libuuid # [linux] - mysql-connector-c # [linux] - openssl # [linux] - - zlib # [linux] + - zlib {{CONDA_ZLIB}}* # [linux] run: - libgcc # [linux] @@ -35,7 +35,7 @@ requirements: - libuuid # [linux] - mysql-connector-c # [linux] - openssl # [linux] - - zlib # [linux] + - zlib {{CONDA_ZLIB}}* # [linux] test: commands: diff --git a/recipes/ucsc-fanoise/meta.yaml b/recipes/ucsc-fanoise/meta.yaml index 1e6addbc264854..bb733b3b2a5b41 100644 --- a/recipes/ucsc-fanoise/meta.yaml +++ b/recipes/ucsc-fanoise/meta.yaml @@ -18,7 +18,7 @@ source: fn: "{{ program }}" # [osx] build: - number: 0 + number: 1 requirements: build: @@ -27,7 +27,7 @@ requirements: - libuuid # [linux] - mysql-connector-c # [linux] - openssl # [linux] - - zlib # [linux] + - zlib {{CONDA_ZLIB}}* # [linux] run: - libgcc # [linux] @@ -35,7 +35,7 @@ requirements: - libuuid # [linux] - mysql-connector-c # [linux] - openssl # [linux] - - zlib # [linux] + - zlib {{CONDA_ZLIB}}* # [linux] test: commands: diff --git a/recipes/ucsc-faonerecord/meta.yaml b/recipes/ucsc-faonerecord/meta.yaml index 009af246af8e89..254d96698ce54f 100644 --- a/recipes/ucsc-faonerecord/meta.yaml +++ b/recipes/ucsc-faonerecord/meta.yaml @@ -18,7 +18,7 @@ source: fn: "{{ program }}" # [osx] build: - number: 0 + number: 1 requirements: build: @@ -27,7 +27,7 @@ requirements: - libuuid # [linux] - mysql-connector-c # [linux] - openssl # [linux] - - zlib # [linux] + - zlib {{CONDA_ZLIB}}* # [linux] run: - libgcc # [linux] @@ -35,7 +35,7 @@ requirements: - libuuid # [linux] - mysql-connector-c # [linux] - openssl # [linux] - - zlib # [linux] + - zlib {{CONDA_ZLIB}}* # [linux] test: commands: diff --git a/recipes/ucsc-fapolyasizes/meta.yaml b/recipes/ucsc-fapolyasizes/meta.yaml index 4fb02a1b63da05..9a068b7645cb2a 100644 --- a/recipes/ucsc-fapolyasizes/meta.yaml +++ b/recipes/ucsc-fapolyasizes/meta.yaml @@ -18,7 +18,7 @@ source: fn: "{{ program }}" # [osx] build: - number: 0 + number: 1 requirements: build: @@ -27,7 +27,7 @@ requirements: - libuuid # [linux] - mysql-connector-c # [linux] - openssl # [linux] - - zlib # [linux] + - zlib {{CONDA_ZLIB}}* # [linux] run: - libgcc # [linux] @@ -35,7 +35,7 @@ requirements: - libuuid # [linux] - mysql-connector-c # [linux] - openssl # [linux] - - zlib # [linux] + - zlib {{CONDA_ZLIB}}* # [linux] test: commands: diff --git a/recipes/ucsc-farandomize/meta.yaml b/recipes/ucsc-farandomize/meta.yaml index 4b92134c563a35..b3d717832e323c 100644 --- a/recipes/ucsc-farandomize/meta.yaml +++ b/recipes/ucsc-farandomize/meta.yaml @@ -18,7 +18,7 @@ source: fn: "{{ program }}" # [osx] build: - number: 0 + number: 1 requirements: build: @@ -27,7 +27,7 @@ requirements: - libuuid # [linux] - mysql-connector-c # [linux] - openssl # [linux] - - zlib # [linux] + - zlib {{ CONDA_ZLIB }}* # [linux] run: - libgcc # [linux] @@ -35,7 +35,7 @@ requirements: - libuuid # [linux] - mysql-connector-c # [linux] - openssl # [linux] - - zlib # [linux] + - zlib {{ CONDA_ZLIB }}* # [linux] test: commands: diff --git a/recipes/ucsc-farc/meta.yaml b/recipes/ucsc-farc/meta.yaml index 4e754a3ac23dee..b571b17d416364 100644 --- a/recipes/ucsc-farc/meta.yaml +++ b/recipes/ucsc-farc/meta.yaml @@ -18,7 +18,7 @@ source: fn: "{{ program }}" # [osx] build: - number: 0 + number: 1 requirements: build: @@ -27,7 +27,7 @@ requirements: - libuuid # [linux] - mysql-connector-c # [linux] - openssl # [linux] - - zlib # [linux] + - zlib {{CONDA_ZLIB}}* # [linux] run: - libgcc # [linux] @@ -35,7 +35,7 @@ requirements: - libuuid # [linux] - mysql-connector-c # [linux] - openssl # [linux] - - zlib # [linux] + - zlib {{CONDA_ZLIB}}* # [linux] test: commands: diff --git a/recipes/ucsc-fasize/meta.yaml b/recipes/ucsc-fasize/meta.yaml index 28c204cf1c250d..be55b0b535edd2 100644 --- a/recipes/ucsc-fasize/meta.yaml +++ b/recipes/ucsc-fasize/meta.yaml @@ -18,7 +18,7 @@ source: fn: "{{ program }}" # [osx] build: - number: 0 + number: 1 requirements: build: @@ -27,7 +27,7 @@ requirements: - libuuid # [linux] - mysql-connector-c # [linux] - openssl # [linux] - - zlib # [linux] + - zlib {{CONDA_ZLIB}}* # [linux] run: - libgcc # [linux] @@ -35,7 +35,7 @@ requirements: - libuuid # [linux] - mysql-connector-c # [linux] - openssl # [linux] - - zlib # [linux] + - zlib {{CONDA_ZLIB}}* # [linux] test: commands: diff --git a/recipes/ucsc-fasomerecords/meta.yaml b/recipes/ucsc-fasomerecords/meta.yaml index a7ef05769a793c..e699684a3b4c68 100644 --- a/recipes/ucsc-fasomerecords/meta.yaml +++ b/recipes/ucsc-fasomerecords/meta.yaml @@ -18,7 +18,7 @@ source: fn: "{{ program }}" # [osx] build: - number: 0 + number: 1 requirements: build: @@ -27,7 +27,7 @@ requirements: - libuuid # [linux] - mysql-connector-c # [linux] - openssl # [linux] - - zlib # [linux] + - zlib {{CONDA_ZLIB}}* # [linux] run: - libgcc # [linux] @@ -35,7 +35,7 @@ requirements: - libuuid # [linux] - mysql-connector-c # [linux] - openssl # [linux] - - zlib # [linux] + - zlib {{CONDA_ZLIB}}* # [linux] test: commands: diff --git a/recipes/ucsc-fasplit/meta.yaml b/recipes/ucsc-fasplit/meta.yaml index ddea7cb7a581db..d5cebd6ad16256 100644 --- a/recipes/ucsc-fasplit/meta.yaml +++ b/recipes/ucsc-fasplit/meta.yaml @@ -18,7 +18,7 @@ source: fn: "{{ program }}" # [osx] build: - number: 0 + number: 1 requirements: build: @@ -27,7 +27,7 @@ requirements: - libuuid # [linux] - mysql-connector-c # [linux] - openssl # [linux] - - zlib # [linux] + - zlib {{ CONDA_ZLIB }}* # [linux] run: - libgcc # [linux] @@ -35,7 +35,7 @@ requirements: - libuuid # [linux] - mysql-connector-c # [linux] - openssl # [linux] - - zlib # [linux] + - zlib {{ CONDA_ZLIB }}* # [linux] test: commands: diff --git a/recipes/ucsc-fastqstatsandsubsample/meta.yaml b/recipes/ucsc-fastqstatsandsubsample/meta.yaml index b674b5adbad1c9..eaee6951fb3e06 100644 --- a/recipes/ucsc-fastqstatsandsubsample/meta.yaml +++ b/recipes/ucsc-fastqstatsandsubsample/meta.yaml @@ -18,7 +18,7 @@ source: fn: "{{ program }}" # [osx] build: - number: 0 + number: 1 requirements: build: @@ -27,7 +27,7 @@ requirements: - libuuid # [linux] - mysql-connector-c # [linux] - openssl # [linux] - - zlib # [linux] + - zlib {{CONDA_ZLIB}}* # [linux] run: - libgcc # [linux] @@ -35,7 +35,7 @@ requirements: - libuuid # [linux] - mysql-connector-c # [linux] - openssl # [linux] - - zlib # [linux] + - zlib {{CONDA_ZLIB}}* # [linux] test: commands: diff --git a/recipes/ucsc-fastqtofa/meta.yaml b/recipes/ucsc-fastqtofa/meta.yaml index a2f7160d4877bf..442566a07714e1 100644 --- a/recipes/ucsc-fastqtofa/meta.yaml +++ b/recipes/ucsc-fastqtofa/meta.yaml @@ -18,7 +18,7 @@ source: fn: "{{ program }}" # [osx] build: - number: 0 + number: 1 requirements: build: @@ -27,7 +27,7 @@ requirements: - libuuid # [linux] - mysql-connector-c # [linux] - openssl # [linux] - - zlib # [linux] + - zlib {{CONDA_ZLIB}}* # [linux] run: - libgcc # [linux] @@ -35,7 +35,7 @@ requirements: - libuuid # [linux] - mysql-connector-c # [linux] - openssl # [linux] - - zlib # [linux] + - zlib {{CONDA_ZLIB}}* # [linux] test: commands: diff --git a/recipes/ucsc-fatofastq/meta.yaml b/recipes/ucsc-fatofastq/meta.yaml index 9bfcb89cb80133..3ea0792b773a55 100644 --- a/recipes/ucsc-fatofastq/meta.yaml +++ b/recipes/ucsc-fatofastq/meta.yaml @@ -18,7 +18,7 @@ source: fn: "{{ program }}" # [osx] build: - number: 0 + number: 1 requirements: build: @@ -27,7 +27,7 @@ requirements: - libuuid # [linux] - mysql-connector-c # [linux] - openssl # [linux] - - zlib # [linux] + - zlib {{CONDA_ZLIB}}* # [linux] run: - libgcc # [linux] @@ -35,7 +35,7 @@ requirements: - libuuid # [linux] - mysql-connector-c # [linux] - openssl # [linux] - - zlib # [linux] + - zlib {{CONDA_ZLIB}}* # [linux] test: commands: diff --git a/recipes/ucsc-fatotab/meta.yaml b/recipes/ucsc-fatotab/meta.yaml index 57075e7b8cccd9..d40445f8fad7b6 100644 --- a/recipes/ucsc-fatotab/meta.yaml +++ b/recipes/ucsc-fatotab/meta.yaml @@ -18,7 +18,7 @@ source: fn: "{{ program }}" # [osx] build: - number: 0 + number: 1 requirements: build: @@ -27,7 +27,7 @@ requirements: - libuuid # [linux] - mysql-connector-c # [linux] - openssl # [linux] - - zlib # [linux] + - zlib {{CONDA_ZLIB}}* # [linux] run: - libgcc # [linux] @@ -35,7 +35,7 @@ requirements: - libuuid # [linux] - mysql-connector-c # [linux] - openssl # [linux] - - zlib # [linux] + - zlib {{CONDA_ZLIB}}* # [linux] test: commands: diff --git a/recipes/ucsc-fatotwobit/meta.yaml b/recipes/ucsc-fatotwobit/meta.yaml index e8cd7e22af2c58..0747dcdfbe62a9 100644 --- a/recipes/ucsc-fatotwobit/meta.yaml +++ b/recipes/ucsc-fatotwobit/meta.yaml @@ -18,7 +18,7 @@ source: fn: "{{ program }}" # [osx] build: - number: 0 + number: 1 requirements: build: @@ -27,7 +27,7 @@ requirements: - libuuid # [linux] - mysql-connector-c # [linux] - openssl # [linux] - - zlib # [linux] + - zlib {{CONDA_ZLIB}}* # [linux] run: - libgcc # [linux] @@ -35,7 +35,7 @@ requirements: - libuuid # [linux] - mysql-connector-c # [linux] - openssl # [linux] - - zlib # [linux] + - zlib {{CONDA_ZLIB}}* # [linux] test: commands: diff --git a/recipes/ucsc-fatrans/meta.yaml b/recipes/ucsc-fatrans/meta.yaml index 6cc5e268e81282..5f5aba9be1a8fe 100644 --- a/recipes/ucsc-fatrans/meta.yaml +++ b/recipes/ucsc-fatrans/meta.yaml @@ -18,7 +18,7 @@ source: fn: "{{ program }}" # [osx] build: - number: 0 + number: 1 requirements: build: @@ -27,7 +27,7 @@ requirements: - libuuid # [linux] - mysql-connector-c # [linux] - openssl # [linux] - - zlib # [linux] + - zlib {{CONDA_ZLIB}}* # [linux] run: - libgcc # [linux] @@ -35,7 +35,7 @@ requirements: - libuuid # [linux] - mysql-connector-c # [linux] - openssl # [linux] - - zlib # [linux] + - zlib {{CONDA_ZLIB}}* # [linux] test: commands: diff --git a/recipes/ucsc-featurebits/meta.yaml b/recipes/ucsc-featurebits/meta.yaml index 657ff4720ebaee..011f7835cfc92d 100644 --- a/recipes/ucsc-featurebits/meta.yaml +++ b/recipes/ucsc-featurebits/meta.yaml @@ -18,7 +18,7 @@ source: fn: "{{ program }}" # [osx] build: - number: 0 + number: 1 requirements: build: @@ -27,7 +27,7 @@ requirements: - libuuid # [linux] - mysql-connector-c # [linux] - openssl # [linux] - - zlib # [linux] + - zlib {{CONDA_ZLIB}}* # [linux] run: - libgcc # [linux] @@ -35,7 +35,7 @@ requirements: - libuuid # [linux] - mysql-connector-c # [linux] - openssl # [linux] - - zlib # [linux] + - zlib {{CONDA_ZLIB}}* # [linux] test: commands: diff --git a/recipes/ucsc-fetchchromsizes/meta.yaml b/recipes/ucsc-fetchchromsizes/meta.yaml index 88a186d6ee2abe..91c5af62cbcb37 100644 --- a/recipes/ucsc-fetchchromsizes/meta.yaml +++ b/recipes/ucsc-fetchchromsizes/meta.yaml @@ -18,7 +18,7 @@ source: fn: "{{ program }}" # [osx] build: - number: 0 + number: 1 requirements: build: @@ -27,7 +27,7 @@ requirements: - libuuid # [linux] - mysql-connector-c # [linux] - openssl # [linux] - - zlib # [linux] + - zlib {{CONDA_ZLIB}}* # [linux] run: - libgcc # [linux] @@ -35,7 +35,7 @@ requirements: - libuuid # [linux] - mysql-connector-c # [linux] - openssl # [linux] - - zlib # [linux] + - zlib {{CONDA_ZLIB}}* # [linux] test: commands: diff --git a/recipes/ucsc-findmotif/meta.yaml b/recipes/ucsc-findmotif/meta.yaml index ace6fba17934f1..27516ff8038e1d 100644 --- a/recipes/ucsc-findmotif/meta.yaml +++ b/recipes/ucsc-findmotif/meta.yaml @@ -18,7 +18,7 @@ source: fn: "{{ program }}" # [osx] build: - number: 0 + number: 1 requirements: build: @@ -27,7 +27,7 @@ requirements: - libuuid # [linux] - mysql-connector-c # [linux] - openssl # [linux] - - zlib # [linux] + - zlib {{CONDA_ZLIB}}* # [linux] run: - libgcc # [linux] @@ -35,7 +35,7 @@ requirements: - libuuid # [linux] - mysql-connector-c # [linux] - openssl # [linux] - - zlib # [linux] + - zlib {{CONDA_ZLIB}}* # [linux] test: commands: diff --git a/recipes/ucsc-gaptolift/meta.yaml b/recipes/ucsc-gaptolift/meta.yaml index e4d24a806b61a7..3827102ad0d08c 100644 --- a/recipes/ucsc-gaptolift/meta.yaml +++ b/recipes/ucsc-gaptolift/meta.yaml @@ -18,7 +18,7 @@ source: fn: "{{ program }}" # [osx] build: - number: 0 + number: 1 requirements: build: @@ -27,7 +27,7 @@ requirements: - libuuid # [linux] - mysql-connector-c # [linux] - openssl # [linux] - - zlib # [linux] + - zlib {{CONDA_ZLIB}}* # [linux] run: - libgcc # [linux] @@ -35,7 +35,7 @@ requirements: - libuuid # [linux] - mysql-connector-c # [linux] - openssl # [linux] - - zlib # [linux] + - zlib {{CONDA_ZLIB}}* # [linux] test: commands: diff --git a/recipes/ucsc-genepredcheck/meta.yaml b/recipes/ucsc-genepredcheck/meta.yaml index 6436313805afd2..9008ad4eef4d51 100644 --- a/recipes/ucsc-genepredcheck/meta.yaml +++ b/recipes/ucsc-genepredcheck/meta.yaml @@ -18,7 +18,7 @@ source: fn: "{{ program }}" # [osx] build: - number: 0 + number: 1 requirements: build: @@ -27,7 +27,7 @@ requirements: - libuuid # [linux] - mysql-connector-c # [linux] - openssl # [linux] - - zlib # [linux] + - zlib {{CONDA_ZLIB}}* # [linux] run: - libgcc # [linux] @@ -35,7 +35,7 @@ requirements: - libuuid # [linux] - mysql-connector-c # [linux] - openssl # [linux] - - zlib # [linux] + - zlib {{CONDA_ZLIB}}* # [linux] test: commands: diff --git a/recipes/ucsc-genepredfilter/meta.yaml b/recipes/ucsc-genepredfilter/meta.yaml index 56393a6c8ec6cc..3e24db54d8e97f 100644 --- a/recipes/ucsc-genepredfilter/meta.yaml +++ b/recipes/ucsc-genepredfilter/meta.yaml @@ -18,7 +18,7 @@ source: fn: "{{ program }}" # [osx] build: - number: 0 + number: 1 requirements: build: @@ -27,7 +27,7 @@ requirements: - libuuid # [linux] - mysql-connector-c # [linux] - openssl # [linux] - - zlib # [linux] + - zlib {{CONDA_ZLIB}}* # [linux] run: - libgcc # [linux] @@ -35,7 +35,7 @@ requirements: - libuuid # [linux] - mysql-connector-c # [linux] - openssl # [linux] - - zlib # [linux] + - zlib {{CONDA_ZLIB}}* # [linux] test: commands: diff --git a/recipes/ucsc-genepredhisto/meta.yaml b/recipes/ucsc-genepredhisto/meta.yaml index d3efdaf7ec6536..0e1f12f3776472 100644 --- a/recipes/ucsc-genepredhisto/meta.yaml +++ b/recipes/ucsc-genepredhisto/meta.yaml @@ -18,7 +18,7 @@ source: fn: "{{ program }}" # [osx] build: - number: 0 + number: 1 requirements: build: @@ -27,7 +27,7 @@ requirements: - libuuid # [linux] - mysql-connector-c # [linux] - openssl # [linux] - - zlib # [linux] + - zlib {{CONDA_ZLIB}}* # [linux] run: - libgcc # [linux] @@ -35,7 +35,7 @@ requirements: - libuuid # [linux] - mysql-connector-c # [linux] - openssl # [linux] - - zlib # [linux] + - zlib {{CONDA_ZLIB}}* # [linux] test: commands: diff --git a/recipes/ucsc-genepredsinglecover/meta.yaml b/recipes/ucsc-genepredsinglecover/meta.yaml index 47f7a0d8064d6d..cdd08e44142063 100644 --- a/recipes/ucsc-genepredsinglecover/meta.yaml +++ b/recipes/ucsc-genepredsinglecover/meta.yaml @@ -18,7 +18,7 @@ source: fn: "{{ program }}" # [osx] build: - number: 0 + number: 1 requirements: build: @@ -27,7 +27,7 @@ requirements: - libuuid # [linux] - mysql-connector-c # [linux] - openssl # [linux] - - zlib # [linux] + - zlib {{CONDA_ZLIB}}* # [linux] run: - libgcc # [linux] @@ -35,7 +35,7 @@ requirements: - libuuid # [linux] - mysql-connector-c # [linux] - openssl # [linux] - - zlib # [linux] + - zlib {{CONDA_ZLIB}}* # [linux] test: commands: diff --git a/recipes/ucsc-genepredtobed/meta.yaml b/recipes/ucsc-genepredtobed/meta.yaml index 7100c956c2bee8..af49a871ee1759 100644 --- a/recipes/ucsc-genepredtobed/meta.yaml +++ b/recipes/ucsc-genepredtobed/meta.yaml @@ -18,7 +18,7 @@ source: fn: "{{ program }}" # [osx] build: - number: 0 + number: 1 requirements: build: @@ -27,7 +27,7 @@ requirements: - libuuid # [linux] - mysql-connector-c # [linux] - openssl # [linux] - - zlib # [linux] + - zlib {{CONDA_ZLIB}}* # [linux] run: - libgcc # [linux] @@ -35,7 +35,7 @@ requirements: - libuuid # [linux] - mysql-connector-c # [linux] - openssl # [linux] - - zlib # [linux] + - zlib {{CONDA_ZLIB}}* # [linux] test: commands: diff --git a/recipes/ucsc-genepredtobiggenepred/meta.yaml b/recipes/ucsc-genepredtobiggenepred/meta.yaml index 99592640c1eea7..5faddf80d5c123 100644 --- a/recipes/ucsc-genepredtobiggenepred/meta.yaml +++ b/recipes/ucsc-genepredtobiggenepred/meta.yaml @@ -18,7 +18,7 @@ source: fn: "{{ program }}" # [osx] build: - number: 0 + number: 1 requirements: build: @@ -27,7 +27,7 @@ requirements: - libuuid # [linux] - mysql-connector-c # [linux] - openssl # [linux] - - zlib # [linux] + - zlib {{CONDA_ZLIB}}* # [linux] run: - libgcc # [linux] @@ -35,7 +35,7 @@ requirements: - libuuid # [linux] - mysql-connector-c # [linux] - openssl # [linux] - - zlib # [linux] + - zlib {{CONDA_ZLIB}}* # [linux] test: commands: diff --git a/recipes/ucsc-genepredtofakepsl/meta.yaml b/recipes/ucsc-genepredtofakepsl/meta.yaml index 1550a4d2ed0ef6..01b548e228f22b 100644 --- a/recipes/ucsc-genepredtofakepsl/meta.yaml +++ b/recipes/ucsc-genepredtofakepsl/meta.yaml @@ -18,7 +18,7 @@ source: fn: "{{ program }}" # [osx] build: - number: 0 + number: 1 requirements: build: @@ -27,7 +27,7 @@ requirements: - libuuid # [linux] - mysql-connector-c # [linux] - openssl # [linux] - - zlib # [linux] + - zlib {{CONDA_ZLIB}}* # [linux] run: - libgcc # [linux] @@ -35,7 +35,7 @@ requirements: - libuuid # [linux] - mysql-connector-c # [linux] - openssl # [linux] - - zlib # [linux] + - zlib {{CONDA_ZLIB}}* # [linux] test: commands: diff --git a/recipes/ucsc-genepredtogtf/meta.yaml b/recipes/ucsc-genepredtogtf/meta.yaml index 07660475811c82..398e13320a0163 100644 --- a/recipes/ucsc-genepredtogtf/meta.yaml +++ b/recipes/ucsc-genepredtogtf/meta.yaml @@ -18,7 +18,7 @@ source: fn: "{{ program }}" # [osx] build: - number: 0 + number: 1 requirements: build: @@ -27,7 +27,7 @@ requirements: - libuuid # [linux] - mysql-connector-c # [linux] - openssl # [linux] - - zlib # [linux] + - zlib {{CONDA_ZLIB}}* # [linux] run: - libgcc # [linux] @@ -35,7 +35,7 @@ requirements: - libuuid # [linux] - mysql-connector-c # [linux] - openssl # [linux] - - zlib # [linux] + - zlib {{CONDA_ZLIB}}* # [linux] test: commands: diff --git a/recipes/ucsc-genepredtomafframes/meta.yaml b/recipes/ucsc-genepredtomafframes/meta.yaml index fab7a0e5ef8ee3..95188f558a4b62 100644 --- a/recipes/ucsc-genepredtomafframes/meta.yaml +++ b/recipes/ucsc-genepredtomafframes/meta.yaml @@ -18,7 +18,7 @@ source: fn: "{{ program }}" # [osx] build: - number: 0 + number: 1 requirements: build: @@ -27,7 +27,7 @@ requirements: - libuuid # [linux] - mysql-connector-c # [linux] - openssl # [linux] - - zlib # [linux] + - zlib {{CONDA_ZLIB}}* # [linux] run: - libgcc # [linux] @@ -35,7 +35,7 @@ requirements: - libuuid # [linux] - mysql-connector-c # [linux] - openssl # [linux] - - zlib # [linux] + - zlib {{CONDA_ZLIB}}* # [linux] test: commands: diff --git a/recipes/ucsc-genepredtoprot/meta.yaml b/recipes/ucsc-genepredtoprot/meta.yaml index b5c59f4cf2c226..39848c69467672 100644 --- a/recipes/ucsc-genepredtoprot/meta.yaml +++ b/recipes/ucsc-genepredtoprot/meta.yaml @@ -18,7 +18,7 @@ source: fn: "{{ program }}" # [osx] build: - number: 0 + number: 1 requirements: build: @@ -27,7 +27,7 @@ requirements: - libuuid # [linux] - mysql-connector-c # [linux] - openssl # [linux] - - zlib # [linux] + - zlib {{CONDA_ZLIB}}* # [linux] run: - libgcc # [linux] @@ -35,7 +35,7 @@ requirements: - libuuid # [linux] - mysql-connector-c # [linux] - openssl # [linux] - - zlib # [linux] + - zlib {{CONDA_ZLIB}}* # [linux] test: commands: diff --git a/recipes/ucsc-getrna/meta.yaml b/recipes/ucsc-getrna/meta.yaml index d254f3840c6c47..d97ade1b7c05ce 100644 --- a/recipes/ucsc-getrna/meta.yaml +++ b/recipes/ucsc-getrna/meta.yaml @@ -18,7 +18,7 @@ source: fn: "{{ program }}" # [osx] build: - number: 0 + number: 1 requirements: build: @@ -27,7 +27,7 @@ requirements: - libuuid # [linux] - mysql-connector-c # [linux] - openssl # [linux] - - zlib # [linux] + - zlib {{CONDA_ZLIB}}* # [linux] run: - libgcc # [linux] @@ -35,7 +35,7 @@ requirements: - libuuid # [linux] - mysql-connector-c # [linux] - openssl # [linux] - - zlib # [linux] + - zlib {{CONDA_ZLIB}}* # [linux] test: commands: diff --git a/recipes/ucsc-getrnapred/meta.yaml b/recipes/ucsc-getrnapred/meta.yaml index 14f880b1448082..09372a2190ba9c 100644 --- a/recipes/ucsc-getrnapred/meta.yaml +++ b/recipes/ucsc-getrnapred/meta.yaml @@ -18,7 +18,7 @@ source: fn: "{{ program }}" # [osx] build: - number: 0 + number: 1 requirements: build: @@ -27,7 +27,7 @@ requirements: - libuuid # [linux] - mysql-connector-c # [linux] - openssl # [linux] - - zlib # [linux] + - zlib {{CONDA_ZLIB}}* # [linux] run: - libgcc # [linux] @@ -35,7 +35,7 @@ requirements: - libuuid # [linux] - mysql-connector-c # [linux] - openssl # [linux] - - zlib # [linux] + - zlib {{CONDA_ZLIB}}* # [linux] test: commands: diff --git a/recipes/ucsc-gff3togenepred/meta.yaml b/recipes/ucsc-gff3togenepred/meta.yaml index 892e9290dd67c7..926ed47307b94d 100644 --- a/recipes/ucsc-gff3togenepred/meta.yaml +++ b/recipes/ucsc-gff3togenepred/meta.yaml @@ -18,7 +18,7 @@ source: fn: "{{ program }}" # [osx] build: - number: 0 + number: 1 requirements: build: @@ -27,7 +27,7 @@ requirements: - libuuid # [linux] - mysql-connector-c # [linux] - openssl # [linux] - - zlib # [linux] + - zlib {{CONDA_ZLIB}}* # [linux] run: - libgcc # [linux] @@ -35,7 +35,7 @@ requirements: - libuuid # [linux] - mysql-connector-c # [linux] - openssl # [linux] - - zlib # [linux] + - zlib {{CONDA_ZLIB}}* # [linux] test: commands: diff --git a/recipes/ucsc-gff3topsl/meta.yaml b/recipes/ucsc-gff3topsl/meta.yaml index 28b1bfea5fae51..ec7c910dcb649a 100644 --- a/recipes/ucsc-gff3topsl/meta.yaml +++ b/recipes/ucsc-gff3topsl/meta.yaml @@ -18,7 +18,7 @@ source: fn: "{{ program }}" # [osx] build: - number: 0 + number: 1 requirements: build: @@ -27,7 +27,7 @@ requirements: - libuuid # [linux] - mysql-connector-c # [linux] - openssl # [linux] - - zlib # [linux] + - zlib {{CONDA_ZLIB}}* # [linux] run: - libgcc # [linux] @@ -35,7 +35,7 @@ requirements: - libuuid # [linux] - mysql-connector-c # [linux] - openssl # [linux] - - zlib # [linux] + - zlib {{CONDA_ZLIB}}* # [linux] test: commands: diff --git a/recipes/ucsc-gmtime/meta.yaml b/recipes/ucsc-gmtime/meta.yaml index 38b4518896ad36..b6d08c98192c32 100644 --- a/recipes/ucsc-gmtime/meta.yaml +++ b/recipes/ucsc-gmtime/meta.yaml @@ -18,7 +18,7 @@ source: fn: "{{ program }}" # [osx] build: - number: 0 + number: 1 requirements: build: @@ -27,7 +27,7 @@ requirements: - libuuid # [linux] - mysql-connector-c # [linux] - openssl # [linux] - - zlib # [linux] + - zlib {{CONDA_ZLIB}}* # [linux] run: - libgcc # [linux] @@ -35,7 +35,7 @@ requirements: - libuuid # [linux] - mysql-connector-c # [linux] - openssl # [linux] - - zlib # [linux] + - zlib {{CONDA_ZLIB}}* # [linux] test: commands: diff --git a/recipes/ucsc-gtftogenepred/meta.yaml b/recipes/ucsc-gtftogenepred/meta.yaml index 3966635fb1661d..aa48910e490d0b 100644 --- a/recipes/ucsc-gtftogenepred/meta.yaml +++ b/recipes/ucsc-gtftogenepred/meta.yaml @@ -18,7 +18,7 @@ source: fn: "{{ program }}" # [osx] build: - number: 0 + number: 1 requirements: build: @@ -27,7 +27,7 @@ requirements: - libuuid # [linux] - mysql-connector-c # [linux] - openssl # [linux] - - zlib # [linux] + - zlib {{CONDA_ZLIB}}* # [linux] run: - libgcc # [linux] @@ -35,7 +35,7 @@ requirements: - libuuid # [linux] - mysql-connector-c # [linux] - openssl # [linux] - - zlib # [linux] + - zlib {{CONDA_ZLIB}}* # [linux] test: commands: diff --git a/recipes/ucsc-headrest/meta.yaml b/recipes/ucsc-headrest/meta.yaml index aaf4d3d1ec0c4d..33214b5ad0101b 100644 --- a/recipes/ucsc-headrest/meta.yaml +++ b/recipes/ucsc-headrest/meta.yaml @@ -18,7 +18,7 @@ source: fn: "{{ program }}" # [osx] build: - number: 0 + number: 1 requirements: build: @@ -27,7 +27,7 @@ requirements: - libuuid # [linux] - mysql-connector-c # [linux] - openssl # [linux] - - zlib # [linux] + - zlib {{CONDA_ZLIB}}* # [linux] run: - libgcc # [linux] @@ -35,7 +35,7 @@ requirements: - libuuid # [linux] - mysql-connector-c # [linux] - openssl # [linux] - - zlib # [linux] + - zlib {{CONDA_ZLIB}}* # [linux] test: commands: diff --git a/recipes/ucsc-hgbbidblink/meta.yaml b/recipes/ucsc-hgbbidblink/meta.yaml index efbd0f496bd1cb..e2942655918eb8 100644 --- a/recipes/ucsc-hgbbidblink/meta.yaml +++ b/recipes/ucsc-hgbbidblink/meta.yaml @@ -18,7 +18,7 @@ source: fn: "{{ program }}" # [osx] build: - number: 0 + number: 1 requirements: build: @@ -27,7 +27,7 @@ requirements: - libuuid # [linux] - mysql-connector-c # [linux] - openssl # [linux] - - zlib # [linux] + - zlib {{CONDA_ZLIB}}* # [linux] run: - libgcc # [linux] @@ -35,7 +35,7 @@ requirements: - libuuid # [linux] - mysql-connector-c # [linux] - openssl # [linux] - - zlib # [linux] + - zlib {{CONDA_ZLIB}}* # [linux] test: commands: diff --git a/recipes/ucsc-hgfakeagp/meta.yaml b/recipes/ucsc-hgfakeagp/meta.yaml index 3647d04eb41326..ea7e619ca70a36 100644 --- a/recipes/ucsc-hgfakeagp/meta.yaml +++ b/recipes/ucsc-hgfakeagp/meta.yaml @@ -18,7 +18,7 @@ source: fn: "{{ program }}" # [osx] build: - number: 0 + number: 1 requirements: build: @@ -27,7 +27,7 @@ requirements: - libuuid # [linux] - mysql-connector-c # [linux] - openssl # [linux] - - zlib # [linux] + - zlib {{CONDA_ZLIB}}* # [linux] run: - libgcc # [linux] @@ -35,7 +35,7 @@ requirements: - libuuid # [linux] - mysql-connector-c # [linux] - openssl # [linux] - - zlib # [linux] + - zlib {{CONDA_ZLIB}}* # [linux] test: commands: diff --git a/recipes/ucsc-hgfindspec/meta.yaml b/recipes/ucsc-hgfindspec/meta.yaml index 83926a24be66a4..70398c3a9ece76 100644 --- a/recipes/ucsc-hgfindspec/meta.yaml +++ b/recipes/ucsc-hgfindspec/meta.yaml @@ -18,7 +18,7 @@ source: fn: "{{ program }}" # [osx] build: - number: 0 + number: 1 requirements: build: @@ -27,7 +27,7 @@ requirements: - libuuid # [linux] - mysql-connector-c # [linux] - openssl # [linux] - - zlib # [linux] + - zlib {{CONDA_ZLIB}}* # [linux] run: - libgcc # [linux] @@ -35,7 +35,7 @@ requirements: - libuuid # [linux] - mysql-connector-c # [linux] - openssl # [linux] - - zlib # [linux] + - zlib {{CONDA_ZLIB}}* # [linux] test: commands: diff --git a/recipes/ucsc-hggcpercent/meta.yaml b/recipes/ucsc-hggcpercent/meta.yaml index 440c1b5d8c7bee..69a3eb715353b7 100644 --- a/recipes/ucsc-hggcpercent/meta.yaml +++ b/recipes/ucsc-hggcpercent/meta.yaml @@ -18,7 +18,7 @@ source: fn: "{{ program }}" # [osx] build: - number: 0 + number: 1 requirements: build: @@ -27,7 +27,7 @@ requirements: - libuuid # [linux] - mysql-connector-c # [linux] - openssl # [linux] - - zlib # [linux] + - zlib {{CONDA_ZLIB}}* # [linux] run: - libgcc # [linux] @@ -35,7 +35,7 @@ requirements: - libuuid # [linux] - mysql-connector-c # [linux] - openssl # [linux] - - zlib # [linux] + - zlib {{CONDA_ZLIB}}* # [linux] test: commands: diff --git a/recipes/ucsc-hgloadbed/meta.yaml b/recipes/ucsc-hgloadbed/meta.yaml index 5083f442d7de69..b7168dd3ad5a2c 100644 --- a/recipes/ucsc-hgloadbed/meta.yaml +++ b/recipes/ucsc-hgloadbed/meta.yaml @@ -18,7 +18,7 @@ source: fn: "{{ program }}" # [osx] build: - number: 0 + number: 1 requirements: build: @@ -27,7 +27,7 @@ requirements: - libuuid # [linux] - mysql-connector-c # [linux] - openssl # [linux] - - zlib # [linux] + - zlib {{CONDA_ZLIB}}* # [linux] run: - libgcc # [linux] @@ -35,7 +35,7 @@ requirements: - libuuid # [linux] - mysql-connector-c # [linux] - openssl # [linux] - - zlib # [linux] + - zlib {{CONDA_ZLIB}}* # [linux] test: commands: diff --git a/recipes/ucsc-hgloadchain/meta.yaml b/recipes/ucsc-hgloadchain/meta.yaml index 1c5f19cfccccae..18f1033615a9bb 100644 --- a/recipes/ucsc-hgloadchain/meta.yaml +++ b/recipes/ucsc-hgloadchain/meta.yaml @@ -18,7 +18,7 @@ source: fn: "{{ program }}" # [osx] build: - number: 0 + number: 1 requirements: build: @@ -27,7 +27,7 @@ requirements: - libuuid # [linux] - mysql-connector-c # [linux] - openssl # [linux] - - zlib # [linux] + - zlib {{CONDA_ZLIB}}* # [linux] run: - libgcc # [linux] @@ -35,7 +35,7 @@ requirements: - libuuid # [linux] - mysql-connector-c # [linux] - openssl # [linux] - - zlib # [linux] + - zlib {{CONDA_ZLIB}}* # [linux] test: commands: diff --git a/recipes/ucsc-hgloadmaf/meta.yaml b/recipes/ucsc-hgloadmaf/meta.yaml index 26252c440d507c..4ecf44cad5aee2 100644 --- a/recipes/ucsc-hgloadmaf/meta.yaml +++ b/recipes/ucsc-hgloadmaf/meta.yaml @@ -18,7 +18,7 @@ source: fn: "{{ program }}" # [osx] build: - number: 0 + number: 1 requirements: build: @@ -27,7 +27,7 @@ requirements: - libuuid # [linux] - mysql-connector-c # [linux] - openssl # [linux] - - zlib # [linux] + - zlib {{CONDA_ZLIB}}* # [linux] run: - libgcc # [linux] @@ -35,7 +35,7 @@ requirements: - libuuid # [linux] - mysql-connector-c # [linux] - openssl # [linux] - - zlib # [linux] + - zlib {{CONDA_ZLIB}}* # [linux] test: commands: diff --git a/recipes/ucsc-hgloadnet/meta.yaml b/recipes/ucsc-hgloadnet/meta.yaml index e67c9921168780..5f348633b1c2fb 100644 --- a/recipes/ucsc-hgloadnet/meta.yaml +++ b/recipes/ucsc-hgloadnet/meta.yaml @@ -18,7 +18,7 @@ source: fn: "{{ program }}" # [osx] build: - number: 0 + number: 1 requirements: build: @@ -27,7 +27,7 @@ requirements: - libuuid # [linux] - mysql-connector-c # [linux] - openssl # [linux] - - zlib # [linux] + - zlib {{CONDA_ZLIB}}* # [linux] run: - libgcc # [linux] @@ -35,7 +35,7 @@ requirements: - libuuid # [linux] - mysql-connector-c # [linux] - openssl # [linux] - - zlib # [linux] + - zlib {{CONDA_ZLIB}}* # [linux] test: commands: diff --git a/recipes/ucsc-hgloadout/meta.yaml b/recipes/ucsc-hgloadout/meta.yaml index 879c429525c527..10fd3df44c2096 100644 --- a/recipes/ucsc-hgloadout/meta.yaml +++ b/recipes/ucsc-hgloadout/meta.yaml @@ -18,7 +18,7 @@ source: fn: "{{ program }}" # [osx] build: - number: 0 + number: 1 requirements: build: @@ -27,7 +27,7 @@ requirements: - libuuid # [linux] - mysql-connector-c # [linux] - openssl # [linux] - - zlib # [linux] + - zlib {{CONDA_ZLIB}}* # [linux] run: - libgcc # [linux] @@ -35,7 +35,7 @@ requirements: - libuuid # [linux] - mysql-connector-c # [linux] - openssl # [linux] - - zlib # [linux] + - zlib {{CONDA_ZLIB}}* # [linux] test: commands: diff --git a/recipes/ucsc-hgloadoutjoined/meta.yaml b/recipes/ucsc-hgloadoutjoined/meta.yaml index c46ba92cc52600..595aaf4dd89807 100644 --- a/recipes/ucsc-hgloadoutjoined/meta.yaml +++ b/recipes/ucsc-hgloadoutjoined/meta.yaml @@ -18,7 +18,7 @@ source: fn: "{{ program }}" # [osx] build: - number: 0 + number: 1 requirements: build: @@ -27,7 +27,7 @@ requirements: - libuuid # [linux] - mysql-connector-c # [linux] - openssl # [linux] - - zlib # [linux] + - zlib {{CONDA_ZLIB}}* # [linux] run: - libgcc # [linux] @@ -35,7 +35,7 @@ requirements: - libuuid # [linux] - mysql-connector-c # [linux] - openssl # [linux] - - zlib # [linux] + - zlib {{CONDA_ZLIB}}* # [linux] test: commands: diff --git a/recipes/ucsc-hgloadwiggle/meta.yaml b/recipes/ucsc-hgloadwiggle/meta.yaml index 514641aaa2168f..dee709e97ce0c1 100644 --- a/recipes/ucsc-hgloadwiggle/meta.yaml +++ b/recipes/ucsc-hgloadwiggle/meta.yaml @@ -18,7 +18,7 @@ source: fn: "{{ program }}" # [osx] build: - number: 0 + number: 1 requirements: build: @@ -27,7 +27,7 @@ requirements: - libuuid # [linux] - mysql-connector-c # [linux] - openssl # [linux] - - zlib # [linux] + - zlib {{CONDA_ZLIB}}* # [linux] run: - libgcc # [linux] @@ -35,7 +35,7 @@ requirements: - libuuid # [linux] - mysql-connector-c # [linux] - openssl # [linux] - - zlib # [linux] + - zlib {{CONDA_ZLIB}}* # [linux] test: commands: diff --git a/recipes/ucsc-hgspeciesrna/meta.yaml b/recipes/ucsc-hgspeciesrna/meta.yaml index 43dd506946bd7b..cd7bdbd3657ba8 100644 --- a/recipes/ucsc-hgspeciesrna/meta.yaml +++ b/recipes/ucsc-hgspeciesrna/meta.yaml @@ -18,7 +18,7 @@ source: fn: "{{ program }}" # [osx] build: - number: 0 + number: 1 requirements: build: @@ -27,7 +27,7 @@ requirements: - libuuid # [linux] - mysql-connector-c # [linux] - openssl # [linux] - - zlib # [linux] + - zlib {{CONDA_ZLIB}}* # [linux] run: - libgcc # [linux] @@ -35,7 +35,7 @@ requirements: - libuuid # [linux] - mysql-connector-c # [linux] - openssl # [linux] - - zlib # [linux] + - zlib {{CONDA_ZLIB}}* # [linux] test: commands: diff --git a/recipes/ucsc-hgsqldump/meta.yaml b/recipes/ucsc-hgsqldump/meta.yaml index 86a605b9dba699..016fdf9f58c685 100644 --- a/recipes/ucsc-hgsqldump/meta.yaml +++ b/recipes/ucsc-hgsqldump/meta.yaml @@ -18,7 +18,7 @@ source: fn: "{{ program }}" # [osx] build: - number: 0 + number: 1 requirements: build: @@ -27,7 +27,7 @@ requirements: - libuuid # [linux] - mysql-connector-c # [linux] - openssl # [linux] - - zlib # [linux] + - zlib {{CONDA_ZLIB}}* # [linux] run: - libgcc # [linux] @@ -35,7 +35,7 @@ requirements: - libuuid # [linux] - mysql-connector-c # [linux] - openssl # [linux] - - zlib # [linux] + - zlib {{CONDA_ZLIB}}* # [linux] test: commands: diff --git a/recipes/ucsc-hgtrackdb/meta.yaml b/recipes/ucsc-hgtrackdb/meta.yaml index 4e611a32e34ee8..ede114d9e0b7cb 100644 --- a/recipes/ucsc-hgtrackdb/meta.yaml +++ b/recipes/ucsc-hgtrackdb/meta.yaml @@ -18,7 +18,7 @@ source: fn: "{{ program }}" # [osx] build: - number: 0 + number: 1 requirements: build: @@ -27,7 +27,7 @@ requirements: - libuuid # [linux] - mysql-connector-c # [linux] - openssl # [linux] - - zlib # [linux] + - zlib {{CONDA_ZLIB}}* # [linux] run: - libgcc # [linux] @@ -35,7 +35,7 @@ requirements: - libuuid # [linux] - mysql-connector-c # [linux] - openssl # [linux] - - zlib # [linux] + - zlib {{CONDA_ZLIB}}* # [linux] test: commands: diff --git a/recipes/ucsc-htmlcheck/meta.yaml b/recipes/ucsc-htmlcheck/meta.yaml index aaa5697ebaf586..75f23195991774 100644 --- a/recipes/ucsc-htmlcheck/meta.yaml +++ b/recipes/ucsc-htmlcheck/meta.yaml @@ -18,7 +18,7 @@ source: fn: "{{ program }}" # [osx] build: - number: 0 + number: 1 requirements: build: @@ -27,7 +27,7 @@ requirements: - libuuid # [linux] - mysql-connector-c # [linux] - openssl # [linux] - - zlib # [linux] + - zlib {{CONDA_ZLIB}}* # [linux] run: - libgcc # [linux] @@ -35,7 +35,7 @@ requirements: - libuuid # [linux] - mysql-connector-c # [linux] - openssl # [linux] - - zlib # [linux] + - zlib {{CONDA_ZLIB}}* # [linux] test: commands: diff --git a/recipes/ucsc-hubcheck/meta.yaml b/recipes/ucsc-hubcheck/meta.yaml index 923ec8fe0163c9..74b2e7a6025e92 100644 --- a/recipes/ucsc-hubcheck/meta.yaml +++ b/recipes/ucsc-hubcheck/meta.yaml @@ -18,7 +18,7 @@ source: fn: "{{ program }}" # [osx] build: - number: 0 + number: 1 requirements: build: @@ -27,7 +27,7 @@ requirements: - libuuid # [linux] - mysql-connector-c # [linux] - openssl # [linux] - - zlib # [linux] + - zlib {{CONDA_ZLIB}}* # [linux] run: - libgcc # [linux] @@ -35,7 +35,7 @@ requirements: - libuuid # [linux] - mysql-connector-c # [linux] - openssl # [linux] - - zlib # [linux] + - zlib {{CONDA_ZLIB}}* # [linux] test: commands: diff --git a/recipes/ucsc-hubpubliccheck/meta.yaml b/recipes/ucsc-hubpubliccheck/meta.yaml index 34f96713789002..884f298e9014aa 100644 --- a/recipes/ucsc-hubpubliccheck/meta.yaml +++ b/recipes/ucsc-hubpubliccheck/meta.yaml @@ -27,7 +27,7 @@ requirements: - libuuid # [linux] - mysql-connector-c # [linux] - openssl # [linux] - - zlib # [linux] + - zlib {{CONDA_ZLIB}}* # [linux] run: - libgcc # [linux] @@ -35,7 +35,7 @@ requirements: - libuuid # [linux] - mysql-connector-c # [linux] - openssl # [linux] - - zlib # [linux] + - zlib {{CONDA_ZLIB}}* # [linux] test: commands: diff --git a/recipes/ucsc-ixixx/meta.yaml b/recipes/ucsc-ixixx/meta.yaml index f7fc0aa3611a6d..151b2ffc4a559e 100644 --- a/recipes/ucsc-ixixx/meta.yaml +++ b/recipes/ucsc-ixixx/meta.yaml @@ -18,7 +18,7 @@ source: fn: "{{ program }}" # [osx] build: - number: 0 + number: 1 requirements: build: @@ -27,7 +27,7 @@ requirements: - libuuid # [linux] - mysql-connector-c # [linux] - openssl # [linux] - - zlib # [linux] + - zlib {{CONDA_ZLIB}}* # [linux] run: - libgcc # [linux] @@ -35,7 +35,7 @@ requirements: - libuuid # [linux] - mysql-connector-c # [linux] - openssl # [linux] - - zlib # [linux] + - zlib {{CONDA_ZLIB}}* # [linux] test: commands: diff --git a/recipes/ucsc-lavtoaxt/meta.yaml b/recipes/ucsc-lavtoaxt/meta.yaml index 0b002f8bce7eb3..bea9e887d0a6ec 100644 --- a/recipes/ucsc-lavtoaxt/meta.yaml +++ b/recipes/ucsc-lavtoaxt/meta.yaml @@ -18,7 +18,7 @@ source: fn: "{{ program }}" # [osx] build: - number: 0 + number: 1 requirements: build: @@ -27,7 +27,7 @@ requirements: - libuuid # [linux] - mysql-connector-c # [linux] - openssl # [linux] - - zlib # [linux] + - zlib {{CONDA_ZLIB}}* # [linux] run: - libgcc # [linux] @@ -35,7 +35,7 @@ requirements: - libuuid # [linux] - mysql-connector-c # [linux] - openssl # [linux] - - zlib # [linux] + - zlib {{CONDA_ZLIB}}* # [linux] test: commands: diff --git a/recipes/ucsc-lavtopsl/meta.yaml b/recipes/ucsc-lavtopsl/meta.yaml index 48957a40ab6013..ec6b2270e25d9f 100644 --- a/recipes/ucsc-lavtopsl/meta.yaml +++ b/recipes/ucsc-lavtopsl/meta.yaml @@ -18,7 +18,7 @@ source: fn: "{{ program }}" # [osx] build: - number: 0 + number: 1 requirements: build: @@ -27,7 +27,7 @@ requirements: - libuuid # [linux] - mysql-connector-c # [linux] - openssl # [linux] - - zlib # [linux] + - zlib {{CONDA_ZLIB}}* # [linux] run: - libgcc # [linux] @@ -35,7 +35,7 @@ requirements: - libuuid # [linux] - mysql-connector-c # [linux] - openssl # [linux] - - zlib # [linux] + - zlib {{CONDA_ZLIB}}* # [linux] test: commands: diff --git a/recipes/ucsc-ldhggene/meta.yaml b/recipes/ucsc-ldhggene/meta.yaml index b1c8313dde8640..a3ca44d9ce2f22 100644 --- a/recipes/ucsc-ldhggene/meta.yaml +++ b/recipes/ucsc-ldhggene/meta.yaml @@ -18,7 +18,7 @@ source: fn: "{{ program }}" # [osx] build: - number: 0 + number: 1 requirements: build: @@ -27,7 +27,7 @@ requirements: - libuuid # [linux] - mysql-connector-c # [linux] - openssl # [linux] - - zlib # [linux] + - zlib {{CONDA_ZLIB}}* # [linux] run: - libgcc # [linux] @@ -35,7 +35,7 @@ requirements: - libuuid # [linux] - mysql-connector-c # [linux] - openssl # [linux] - - zlib # [linux] + - zlib {{CONDA_ZLIB}}* # [linux] test: commands: diff --git a/recipes/ucsc-liftover/meta.yaml b/recipes/ucsc-liftover/meta.yaml index 1c29382c172cdb..0dd5cc7dc63ed4 100644 --- a/recipes/ucsc-liftover/meta.yaml +++ b/recipes/ucsc-liftover/meta.yaml @@ -18,7 +18,7 @@ source: fn: "{{ program }}" # [osx] build: - number: 0 + number: 1 requirements: build: @@ -27,7 +27,7 @@ requirements: - libuuid # [linux] - mysql-connector-c # [linux] - openssl # [linux] - - zlib # [linux] + - zlib {{CONDA_ZLIB}}* # [linux] run: - libgcc # [linux] @@ -35,7 +35,7 @@ requirements: - libuuid # [linux] - mysql-connector-c # [linux] - openssl # [linux] - - zlib # [linux] + - zlib {{CONDA_ZLIB}}* # [linux] test: commands: diff --git a/recipes/ucsc-liftup/meta.yaml b/recipes/ucsc-liftup/meta.yaml index 7ff8535333f291..5810c4b8e80e8a 100644 --- a/recipes/ucsc-liftup/meta.yaml +++ b/recipes/ucsc-liftup/meta.yaml @@ -18,7 +18,7 @@ source: fn: "{{ program }}" # [osx] build: - number: 0 + number: 1 requirements: build: @@ -27,7 +27,7 @@ requirements: - libuuid # [linux] - mysql-connector-c # [linux] - openssl # [linux] - - zlib # [linux] + - zlib {{CONDA_ZLIB}}* # [linux] run: - libgcc # [linux] @@ -35,7 +35,7 @@ requirements: - libuuid # [linux] - mysql-connector-c # [linux] - openssl # [linux] - - zlib # [linux] + - zlib {{CONDA_ZLIB}}* # [linux] test: commands: diff --git a/recipes/ucsc-linestora/meta.yaml b/recipes/ucsc-linestora/meta.yaml index ee274b2eda961f..0c0b60e64c6f66 100644 --- a/recipes/ucsc-linestora/meta.yaml +++ b/recipes/ucsc-linestora/meta.yaml @@ -18,7 +18,7 @@ source: fn: "{{ program }}" # [osx] build: - number: 0 + number: 1 requirements: build: @@ -27,7 +27,7 @@ requirements: - libuuid # [linux] - mysql-connector-c # [linux] - openssl # [linux] - - zlib # [linux] + - zlib {{CONDA_ZLIB}}* # [linux] run: - libgcc # [linux] @@ -35,7 +35,7 @@ requirements: - libuuid # [linux] - mysql-connector-c # [linux] - openssl # [linux] - - zlib # [linux] + - zlib {{CONDA_ZLIB}}* # [linux] test: commands: diff --git a/recipes/ucsc-localtime/meta.yaml b/recipes/ucsc-localtime/meta.yaml index 7eb7833aeba9fb..652430dfc3150b 100644 --- a/recipes/ucsc-localtime/meta.yaml +++ b/recipes/ucsc-localtime/meta.yaml @@ -18,7 +18,7 @@ source: fn: "{{ program }}" # [osx] build: - number: 0 + number: 1 requirements: build: @@ -27,7 +27,7 @@ requirements: - libuuid # [linux] - mysql-connector-c # [linux] - openssl # [linux] - - zlib # [linux] + - zlib {{CONDA_ZLIB}}* # [linux] run: - libgcc # [linux] @@ -35,7 +35,7 @@ requirements: - libuuid # [linux] - mysql-connector-c # [linux] - openssl # [linux] - - zlib # [linux] + - zlib {{CONDA_ZLIB}}* # [linux] test: commands: diff --git a/recipes/ucsc-mafaddirows/meta.yaml b/recipes/ucsc-mafaddirows/meta.yaml index 6f6033f7c98b58..9deb363e063c86 100644 --- a/recipes/ucsc-mafaddirows/meta.yaml +++ b/recipes/ucsc-mafaddirows/meta.yaml @@ -18,7 +18,7 @@ source: fn: "{{ program }}" # [osx] build: - number: 0 + number: 1 requirements: build: @@ -27,7 +27,7 @@ requirements: - libuuid # [linux] - mysql-connector-c # [linux] - openssl # [linux] - - zlib # [linux] + - zlib {{CONDA_ZLIB}}* # [linux] run: - libgcc # [linux] @@ -35,7 +35,7 @@ requirements: - libuuid # [linux] - mysql-connector-c # [linux] - openssl # [linux] - - zlib # [linux] + - zlib {{CONDA_ZLIB}}* # [linux] test: commands: diff --git a/recipes/ucsc-mafaddqrows/meta.yaml b/recipes/ucsc-mafaddqrows/meta.yaml index f932b3085196cd..1acd6087091339 100644 --- a/recipes/ucsc-mafaddqrows/meta.yaml +++ b/recipes/ucsc-mafaddqrows/meta.yaml @@ -18,7 +18,7 @@ source: fn: "{{ program }}" # [osx] build: - number: 0 + number: 1 requirements: build: @@ -27,7 +27,7 @@ requirements: - libuuid # [linux] - mysql-connector-c # [linux] - openssl # [linux] - - zlib # [linux] + - zlib {{CONDA_ZLIB}}* # [linux] run: - libgcc # [linux] @@ -35,7 +35,7 @@ requirements: - libuuid # [linux] - mysql-connector-c # [linux] - openssl # [linux] - - zlib # [linux] + - zlib {{CONDA_ZLIB}}* # [linux] test: commands: diff --git a/recipes/ucsc-mafcoverage/meta.yaml b/recipes/ucsc-mafcoverage/meta.yaml index 2559f56ec3097f..fa76c5b7cc4936 100644 --- a/recipes/ucsc-mafcoverage/meta.yaml +++ b/recipes/ucsc-mafcoverage/meta.yaml @@ -18,7 +18,7 @@ source: fn: "{{ program }}" # [osx] build: - number: 0 + number: 1 requirements: build: @@ -27,7 +27,7 @@ requirements: - libuuid # [linux] - mysql-connector-c # [linux] - openssl # [linux] - - zlib # [linux] + - zlib {{CONDA_ZLIB}}* # [linux] run: - libgcc # [linux] @@ -35,7 +35,7 @@ requirements: - libuuid # [linux] - mysql-connector-c # [linux] - openssl # [linux] - - zlib # [linux] + - zlib {{CONDA_ZLIB}}* # [linux] test: commands: diff --git a/recipes/ucsc-maffetch/meta.yaml b/recipes/ucsc-maffetch/meta.yaml index 8f758086990f43..adc09174ddead0 100644 --- a/recipes/ucsc-maffetch/meta.yaml +++ b/recipes/ucsc-maffetch/meta.yaml @@ -18,7 +18,7 @@ source: fn: "{{ program }}" # [osx] build: - number: 0 + number: 1 requirements: build: @@ -27,7 +27,7 @@ requirements: - libuuid # [linux] - mysql-connector-c # [linux] - openssl # [linux] - - zlib # [linux] + - zlib {{CONDA_ZLIB}}* # [linux] run: - libgcc # [linux] diff --git a/recipes/ucsc-maffilter/meta.yaml b/recipes/ucsc-maffilter/meta.yaml index c0c883e8897500..b5319597117df4 100644 --- a/recipes/ucsc-maffilter/meta.yaml +++ b/recipes/ucsc-maffilter/meta.yaml @@ -18,7 +18,7 @@ source: fn: "{{ program }}" # [osx] build: - number: 0 + number: 1 requirements: build: @@ -27,7 +27,7 @@ requirements: - libuuid # [linux] - mysql-connector-c # [linux] - openssl # [linux] - - zlib # [linux] + - zlib {{CONDA_ZLIB}}* # [linux] run: - libgcc # [linux] @@ -35,7 +35,7 @@ requirements: - libuuid # [linux] - mysql-connector-c # [linux] - openssl # [linux] - - zlib # [linux] + - zlib {{CONDA_ZLIB}}* # [linux] test: commands: diff --git a/recipes/ucsc-maffrag/meta.yaml b/recipes/ucsc-maffrag/meta.yaml index 55e714ad59a3a9..813e7e998fd0e9 100644 --- a/recipes/ucsc-maffrag/meta.yaml +++ b/recipes/ucsc-maffrag/meta.yaml @@ -18,7 +18,7 @@ source: fn: "{{ program }}" # [osx] build: - number: 0 + number: 1 requirements: build: @@ -27,7 +27,7 @@ requirements: - libuuid # [linux] - mysql-connector-c # [linux] - openssl # [linux] - - zlib # [linux] + - zlib {{CONDA_ZLIB}}* # [linux] run: - libgcc # [linux] @@ -35,7 +35,7 @@ requirements: - libuuid # [linux] - mysql-connector-c # [linux] - openssl # [linux] - - zlib # [linux] + - zlib {{CONDA_ZLIB}}* # [linux] test: commands: diff --git a/recipes/ucsc-maffrags/meta.yaml b/recipes/ucsc-maffrags/meta.yaml index 9f0d9d5a02a885..cd31fd2f02a42a 100644 --- a/recipes/ucsc-maffrags/meta.yaml +++ b/recipes/ucsc-maffrags/meta.yaml @@ -18,7 +18,7 @@ source: fn: "{{ program }}" # [osx] build: - number: 0 + number: 1 requirements: build: @@ -27,7 +27,7 @@ requirements: - libuuid # [linux] - mysql-connector-c # [linux] - openssl # [linux] - - zlib # [linux] + - zlib {{CONDA_ZLIB}}* # [linux] run: - libgcc # [linux] @@ -35,7 +35,7 @@ requirements: - libuuid # [linux] - mysql-connector-c # [linux] - openssl # [linux] - - zlib # [linux] + - zlib {{CONDA_ZLIB}}* # [linux] test: commands: diff --git a/recipes/ucsc-mafgene/meta.yaml b/recipes/ucsc-mafgene/meta.yaml index ee46b7ae1b1f18..45454a58dee29b 100644 --- a/recipes/ucsc-mafgene/meta.yaml +++ b/recipes/ucsc-mafgene/meta.yaml @@ -18,7 +18,7 @@ source: fn: "{{ program }}" # [osx] build: - number: 0 + number: 1 requirements: build: @@ -27,7 +27,7 @@ requirements: - libuuid # [linux] - mysql-connector-c # [linux] - openssl # [linux] - - zlib # [linux] + - zlib {{CONDA_ZLIB}}* # [linux] run: - libgcc # [linux] @@ -35,7 +35,7 @@ requirements: - libuuid # [linux] - mysql-connector-c # [linux] - openssl # [linux] - - zlib # [linux] + - zlib {{CONDA_ZLIB}}* # [linux] test: commands: diff --git a/recipes/ucsc-mafmefirst/meta.yaml b/recipes/ucsc-mafmefirst/meta.yaml index a158f9d7a2704b..ef0ded0b478e85 100644 --- a/recipes/ucsc-mafmefirst/meta.yaml +++ b/recipes/ucsc-mafmefirst/meta.yaml @@ -18,7 +18,7 @@ source: fn: "{{ program }}" # [osx] build: - number: 0 + number: 1 requirements: build: @@ -27,7 +27,7 @@ requirements: - libuuid # [linux] - mysql-connector-c # [linux] - openssl # [linux] - - zlib # [linux] + - zlib {{CONDA_ZLIB}}* # [linux] run: - libgcc # [linux] @@ -35,7 +35,7 @@ requirements: - libuuid # [linux] - mysql-connector-c # [linux] - openssl # [linux] - - zlib # [linux] + - zlib {{CONDA_ZLIB}}* # [linux] test: commands: diff --git a/recipes/ucsc-maforder/meta.yaml b/recipes/ucsc-maforder/meta.yaml index 2fa3bec34464e3..e17f4240b9b558 100644 --- a/recipes/ucsc-maforder/meta.yaml +++ b/recipes/ucsc-maforder/meta.yaml @@ -18,7 +18,7 @@ source: fn: "{{ program }}" # [osx] build: - number: 0 + number: 1 requirements: build: @@ -27,7 +27,7 @@ requirements: - libuuid # [linux] - mysql-connector-c # [linux] - openssl # [linux] - - zlib # [linux] + - zlib {{CONDA_ZLIB}}* # [linux] run: - libgcc # [linux] @@ -35,7 +35,7 @@ requirements: - libuuid # [linux] - mysql-connector-c # [linux] - openssl # [linux] - - zlib # [linux] + - zlib {{CONDA_ZLIB}}* # [linux] test: commands: diff --git a/recipes/ucsc-mafranges/meta.yaml b/recipes/ucsc-mafranges/meta.yaml index f788a5097c15dc..9dfc0fc0950439 100644 --- a/recipes/ucsc-mafranges/meta.yaml +++ b/recipes/ucsc-mafranges/meta.yaml @@ -18,7 +18,7 @@ source: fn: "{{ program }}" # [osx] build: - number: 0 + number: 1 requirements: build: @@ -27,7 +27,7 @@ requirements: - libuuid # [linux] - mysql-connector-c # [linux] - openssl # [linux] - - zlib # [linux] + - zlib {{CONDA_ZLIB}}* # [linux] run: - libgcc # [linux] @@ -35,7 +35,7 @@ requirements: - libuuid # [linux] - mysql-connector-c # [linux] - openssl # [linux] - - zlib # [linux] + - zlib {{CONDA_ZLIB}}* # [linux] test: commands: diff --git a/recipes/ucsc-mafsinregion/meta.yaml b/recipes/ucsc-mafsinregion/meta.yaml index 36a0a4babd1c3c..0527d97f8abc46 100644 --- a/recipes/ucsc-mafsinregion/meta.yaml +++ b/recipes/ucsc-mafsinregion/meta.yaml @@ -18,7 +18,7 @@ source: fn: "{{ program }}" # [osx] build: - number: 0 + number: 1 requirements: build: @@ -27,7 +27,7 @@ requirements: - libuuid # [linux] - mysql-connector-c # [linux] - openssl # [linux] - - zlib # [linux] + - zlib {{CONDA_ZLIB}}* # [linux] run: - libgcc # [linux] @@ -35,7 +35,7 @@ requirements: - libuuid # [linux] - mysql-connector-c # [linux] - openssl # [linux] - - zlib # [linux] + - zlib {{CONDA_ZLIB}}* # [linux] test: commands: diff --git a/recipes/ucsc-mafspecieslist/meta.yaml b/recipes/ucsc-mafspecieslist/meta.yaml index ce41141efbb973..b392571e2a7f76 100644 --- a/recipes/ucsc-mafspecieslist/meta.yaml +++ b/recipes/ucsc-mafspecieslist/meta.yaml @@ -18,7 +18,7 @@ source: fn: "{{ program }}" # [osx] build: - number: 0 + number: 1 requirements: build: @@ -27,7 +27,7 @@ requirements: - libuuid # [linux] - mysql-connector-c # [linux] - openssl # [linux] - - zlib # [linux] + - zlib {{CONDA_ZLIB}}* # [linux] run: - libgcc # [linux] @@ -35,7 +35,7 @@ requirements: - libuuid # [linux] - mysql-connector-c # [linux] - openssl # [linux] - - zlib # [linux] + - zlib {{CONDA_ZLIB}}* # [linux] test: commands: diff --git a/recipes/ucsc-mafspeciessubset/meta.yaml b/recipes/ucsc-mafspeciessubset/meta.yaml index e3184e6359379c..9490c774241def 100644 --- a/recipes/ucsc-mafspeciessubset/meta.yaml +++ b/recipes/ucsc-mafspeciessubset/meta.yaml @@ -18,7 +18,7 @@ source: fn: "{{ program }}" # [osx] build: - number: 0 + number: 1 requirements: build: @@ -27,7 +27,7 @@ requirements: - libuuid # [linux] - mysql-connector-c # [linux] - openssl # [linux] - - zlib # [linux] + - zlib {{CONDA_ZLIB}}* # [linux] run: - libgcc # [linux] @@ -35,7 +35,7 @@ requirements: - libuuid # [linux] - mysql-connector-c # [linux] - openssl # [linux] - - zlib # [linux] + - zlib {{CONDA_ZLIB}}* # [linux] test: commands: diff --git a/recipes/ucsc-mafsplit/meta.yaml b/recipes/ucsc-mafsplit/meta.yaml index 4129dfc9a34c51..09f5488a765179 100644 --- a/recipes/ucsc-mafsplit/meta.yaml +++ b/recipes/ucsc-mafsplit/meta.yaml @@ -18,7 +18,7 @@ source: fn: "{{ program }}" # [osx] build: - number: 0 + number: 1 requirements: build: @@ -27,7 +27,7 @@ requirements: - libuuid # [linux] - mysql-connector-c # [linux] - openssl # [linux] - - zlib # [linux] + - zlib {{CONDA_ZLIB}}* # [linux] run: - libgcc # [linux] @@ -35,7 +35,7 @@ requirements: - libuuid # [linux] - mysql-connector-c # [linux] - openssl # [linux] - - zlib # [linux] + - zlib {{CONDA_ZLIB}}* # [linux] test: commands: diff --git a/recipes/ucsc-mafsplitpos/meta.yaml b/recipes/ucsc-mafsplitpos/meta.yaml index d7440c3a5d15da..8961d03fb5c9f0 100644 --- a/recipes/ucsc-mafsplitpos/meta.yaml +++ b/recipes/ucsc-mafsplitpos/meta.yaml @@ -18,7 +18,7 @@ source: fn: "{{ program }}" # [osx] build: - number: 0 + number: 1 requirements: build: @@ -27,7 +27,7 @@ requirements: - libuuid # [linux] - mysql-connector-c # [linux] - openssl # [linux] - - zlib # [linux] + - zlib {{CONDA_ZLIB}}* # [linux] run: - libgcc # [linux] @@ -35,7 +35,7 @@ requirements: - libuuid # [linux] - mysql-connector-c # [linux] - openssl # [linux] - - zlib # [linux] + - zlib {{CONDA_ZLIB}}* # [linux] test: commands: diff --git a/recipes/ucsc-maftoaxt/meta.yaml b/recipes/ucsc-maftoaxt/meta.yaml index 10678ef38942e7..c0dbd7fa2fe911 100644 --- a/recipes/ucsc-maftoaxt/meta.yaml +++ b/recipes/ucsc-maftoaxt/meta.yaml @@ -18,7 +18,7 @@ source: fn: "{{ program }}" # [osx] build: - number: 0 + number: 1 requirements: build: @@ -27,7 +27,7 @@ requirements: - libuuid # [linux] - mysql-connector-c # [linux] - openssl # [linux] - - zlib # [linux] + - zlib {{CONDA_ZLIB}}* # [linux] run: - libgcc # [linux] @@ -35,7 +35,7 @@ requirements: - libuuid # [linux] - mysql-connector-c # [linux] - openssl # [linux] - - zlib # [linux] + - zlib {{CONDA_ZLIB}}* # [linux] test: commands: diff --git a/recipes/ucsc-maftobigmaf/meta.yaml b/recipes/ucsc-maftobigmaf/meta.yaml index 1f8172b0471735..1a515461db574a 100644 --- a/recipes/ucsc-maftobigmaf/meta.yaml +++ b/recipes/ucsc-maftobigmaf/meta.yaml @@ -18,7 +18,7 @@ source: fn: "{{ program }}" # [osx] build: - number: 0 + number: 1 requirements: build: @@ -27,7 +27,7 @@ requirements: - libuuid # [linux] - mysql-connector-c # [linux] - openssl # [linux] - - zlib # [linux] + - zlib {{CONDA_ZLIB}}* # [linux] run: - libgcc # [linux] @@ -35,7 +35,7 @@ requirements: - libuuid # [linux] - mysql-connector-c # [linux] - openssl # [linux] - - zlib # [linux] + - zlib {{CONDA_ZLIB}}* # [linux] test: commands: diff --git a/recipes/ucsc-maftopsl/meta.yaml b/recipes/ucsc-maftopsl/meta.yaml index 0644a7513d6e0c..97e4f79b5777da 100644 --- a/recipes/ucsc-maftopsl/meta.yaml +++ b/recipes/ucsc-maftopsl/meta.yaml @@ -18,7 +18,7 @@ source: fn: "{{ program }}" # [osx] build: - number: 0 + number: 1 requirements: build: @@ -27,7 +27,7 @@ requirements: - libuuid # [linux] - mysql-connector-c # [linux] - openssl # [linux] - - zlib # [linux] + - zlib {{CONDA_ZLIB}}* # [linux] run: - libgcc # [linux] @@ -35,7 +35,7 @@ requirements: - libuuid # [linux] - mysql-connector-c # [linux] - openssl # [linux] - - zlib # [linux] + - zlib {{CONDA_ZLIB}}* # [linux] test: commands: diff --git a/recipes/ucsc-maftosnpbed/meta.yaml b/recipes/ucsc-maftosnpbed/meta.yaml index 9c3f12ed8cd537..21fa44489454b8 100644 --- a/recipes/ucsc-maftosnpbed/meta.yaml +++ b/recipes/ucsc-maftosnpbed/meta.yaml @@ -18,7 +18,7 @@ source: fn: "{{ program }}" # [osx] build: - number: 0 + number: 1 requirements: build: @@ -27,7 +27,7 @@ requirements: - libuuid # [linux] - mysql-connector-c # [linux] - openssl # [linux] - - zlib # [linux] + - zlib {{CONDA_ZLIB}}* # [linux] run: - libgcc # [linux] @@ -35,7 +35,7 @@ requirements: - libuuid # [linux] - mysql-connector-c # [linux] - openssl # [linux] - - zlib # [linux] + - zlib {{CONDA_ZLIB}}* # [linux] test: commands: diff --git a/recipes/ucsc-maketablelist/meta.yaml b/recipes/ucsc-maketablelist/meta.yaml index 229067db2f696c..78b686a87b71be 100644 --- a/recipes/ucsc-maketablelist/meta.yaml +++ b/recipes/ucsc-maketablelist/meta.yaml @@ -18,7 +18,7 @@ source: fn: "{{ program }}" # [osx] build: - number: 0 + number: 1 requirements: build: @@ -27,7 +27,7 @@ requirements: - libuuid # [linux] - mysql-connector-c # [linux] - openssl # [linux] - - zlib # [linux] + - zlib {{CONDA_ZLIB}}* # [linux] run: - libgcc # [linux] @@ -35,7 +35,7 @@ requirements: - libuuid # [linux] - mysql-connector-c # [linux] - openssl # [linux] - - zlib # [linux] + - zlib {{CONDA_ZLIB}}* # [linux] test: commands: diff --git a/recipes/ucsc-maskoutfa/meta.yaml b/recipes/ucsc-maskoutfa/meta.yaml index d3cede4120dc96..1aa36bf04d7732 100644 --- a/recipes/ucsc-maskoutfa/meta.yaml +++ b/recipes/ucsc-maskoutfa/meta.yaml @@ -18,7 +18,7 @@ source: fn: "{{ program }}" # [osx] build: - number: 0 + number: 1 requirements: build: @@ -27,7 +27,7 @@ requirements: - libuuid # [linux] - mysql-connector-c # [linux] - openssl # [linux] - - zlib # [linux] + - zlib {{CONDA_ZLIB}}* # [linux] run: - libgcc # [linux] @@ -35,7 +35,7 @@ requirements: - libuuid # [linux] - mysql-connector-c # [linux] - openssl # [linux] - - zlib # [linux] + - zlib {{CONDA_ZLIB}}* # [linux] test: commands: diff --git a/recipes/ucsc-mktime/meta.yaml b/recipes/ucsc-mktime/meta.yaml index b5e713cad690bb..61789efe3a6933 100644 --- a/recipes/ucsc-mktime/meta.yaml +++ b/recipes/ucsc-mktime/meta.yaml @@ -18,7 +18,7 @@ source: fn: "{{ program }}" # [osx] build: - number: 0 + number: 1 requirements: build: @@ -27,7 +27,7 @@ requirements: - libuuid # [linux] - mysql-connector-c # [linux] - openssl # [linux] - - zlib # [linux] + - zlib {{CONDA_ZLIB}}* # [linux] run: - libgcc # [linux] @@ -35,7 +35,7 @@ requirements: - libuuid # [linux] - mysql-connector-c # [linux] - openssl # [linux] - - zlib # [linux] + - zlib {{CONDA_ZLIB}}* # [linux] test: commands: diff --git a/recipes/ucsc-mrnatogene/meta.yaml b/recipes/ucsc-mrnatogene/meta.yaml index f139ae28e13ff5..b6162dccc656d7 100644 --- a/recipes/ucsc-mrnatogene/meta.yaml +++ b/recipes/ucsc-mrnatogene/meta.yaml @@ -18,7 +18,7 @@ source: fn: "{{ program }}" # [osx] build: - number: 0 + number: 1 requirements: build: @@ -27,7 +27,7 @@ requirements: - libuuid # [linux] - mysql-connector-c # [linux] - openssl # [linux] - - zlib # [linux] + - zlib {{CONDA_ZLIB}}* # [linux] run: - libgcc # [linux] @@ -35,7 +35,7 @@ requirements: - libuuid # [linux] - mysql-connector-c # [linux] - openssl # [linux] - - zlib # [linux] + - zlib {{CONDA_ZLIB}}* # [linux] test: commands: diff --git a/recipes/ucsc-netchainsubset/meta.yaml b/recipes/ucsc-netchainsubset/meta.yaml index d5aadc6ec0c122..125b5dbe3ac9f3 100644 --- a/recipes/ucsc-netchainsubset/meta.yaml +++ b/recipes/ucsc-netchainsubset/meta.yaml @@ -18,7 +18,7 @@ source: fn: "{{ program }}" # [osx] build: - number: 0 + number: 1 requirements: build: @@ -27,7 +27,7 @@ requirements: - libuuid # [linux] - mysql-connector-c # [linux] - openssl # [linux] - - zlib # [linux] + - zlib {{CONDA_ZLIB}}* # [linux] run: - libgcc # [linux] @@ -35,7 +35,7 @@ requirements: - libuuid # [linux] - mysql-connector-c # [linux] - openssl # [linux] - - zlib # [linux] + - zlib {{CONDA_ZLIB}}* # [linux] test: commands: diff --git a/recipes/ucsc-netclass/meta.yaml b/recipes/ucsc-netclass/meta.yaml index a2a77afe59fd86..dc83149f6393ab 100644 --- a/recipes/ucsc-netclass/meta.yaml +++ b/recipes/ucsc-netclass/meta.yaml @@ -18,7 +18,7 @@ source: fn: "{{ program }}" # [osx] build: - number: 0 + number: 1 requirements: build: @@ -27,7 +27,7 @@ requirements: - libuuid # [linux] - mysql-connector-c # [linux] - openssl # [linux] - - zlib # [linux] + - zlib {{CONDA_ZLIB}}* # [linux] run: - libgcc # [linux] @@ -35,7 +35,7 @@ requirements: - libuuid # [linux] - mysql-connector-c # [linux] - openssl # [linux] - - zlib # [linux] + - zlib {{CONDA_ZLIB}}* # [linux] test: commands: diff --git a/recipes/ucsc-netfilter/meta.yaml b/recipes/ucsc-netfilter/meta.yaml index 150a626f4d3455..382a2737c43106 100644 --- a/recipes/ucsc-netfilter/meta.yaml +++ b/recipes/ucsc-netfilter/meta.yaml @@ -18,7 +18,7 @@ source: fn: "{{ program }}" # [osx] build: - number: 0 + number: 1 requirements: build: @@ -27,7 +27,7 @@ requirements: - libuuid # [linux] - mysql-connector-c # [linux] - openssl # [linux] - - zlib # [linux] + - zlib {{CONDA_ZLIB}}* # [linux] run: - libgcc # [linux] @@ -35,7 +35,7 @@ requirements: - libuuid # [linux] - mysql-connector-c # [linux] - openssl # [linux] - - zlib # [linux] + - zlib {{CONDA_ZLIB}}* # [linux] test: commands: diff --git a/recipes/ucsc-netsplit/meta.yaml b/recipes/ucsc-netsplit/meta.yaml index 2a5d36eb527f7c..828b69151d80f2 100644 --- a/recipes/ucsc-netsplit/meta.yaml +++ b/recipes/ucsc-netsplit/meta.yaml @@ -18,7 +18,7 @@ source: fn: "{{ program }}" # [osx] build: - number: 0 + number: 1 requirements: build: @@ -27,7 +27,7 @@ requirements: - libuuid # [linux] - mysql-connector-c # [linux] - openssl # [linux] - - zlib # [linux] + - zlib {{CONDA_ZLIB}}* # [linux] run: - libgcc # [linux] @@ -35,7 +35,7 @@ requirements: - libuuid # [linux] - mysql-connector-c # [linux] - openssl # [linux] - - zlib # [linux] + - zlib {{CONDA_ZLIB}}* # [linux] test: commands: diff --git a/recipes/ucsc-netsyntenic/meta.yaml b/recipes/ucsc-netsyntenic/meta.yaml index 241a5a7c0a17ac..86ffa65dbb5702 100644 --- a/recipes/ucsc-netsyntenic/meta.yaml +++ b/recipes/ucsc-netsyntenic/meta.yaml @@ -18,7 +18,7 @@ source: fn: "{{ program }}" # [osx] build: - number: 0 + number: 1 # Skipping OSX because of the following error: # /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/install_name_tool: # changing install names or rpaths can't be redone for: @@ -35,7 +35,7 @@ requirements: - libuuid # [linux] - mysql-connector-c # [linux] - openssl # [linux] - - zlib # [linux] + - zlib {{CONDA_ZLIB}}* # [linux] run: - libgcc # [linux] @@ -43,7 +43,7 @@ requirements: - libuuid # [linux] - mysql-connector-c # [linux] - openssl # [linux] - - zlib # [linux] + - zlib {{CONDA_ZLIB}}* # [linux] test: commands: diff --git a/recipes/ucsc-nettoaxt/meta.yaml b/recipes/ucsc-nettoaxt/meta.yaml index 7f383ad8e38d6c..3baf2eb70899d3 100644 --- a/recipes/ucsc-nettoaxt/meta.yaml +++ b/recipes/ucsc-nettoaxt/meta.yaml @@ -18,7 +18,7 @@ source: fn: "{{ program }}" # [osx] build: - number: 0 + number: 1 requirements: build: @@ -27,7 +27,7 @@ requirements: - libuuid # [linux] - mysql-connector-c # [linux] - openssl # [linux] - - zlib # [linux] + - zlib {{CONDA_ZLIB}}* # [linux] run: - libgcc # [linux] @@ -35,7 +35,7 @@ requirements: - libuuid # [linux] - mysql-connector-c # [linux] - openssl # [linux] - - zlib # [linux] + - zlib {{CONDA_ZLIB}}* # [linux] test: commands: diff --git a/recipes/ucsc-nettobed/meta.yaml b/recipes/ucsc-nettobed/meta.yaml index 2b120170a8ed6f..b34fe93b04f8fd 100644 --- a/recipes/ucsc-nettobed/meta.yaml +++ b/recipes/ucsc-nettobed/meta.yaml @@ -18,7 +18,7 @@ source: fn: "{{ program }}" # [osx] build: - number: 0 + number: 1 requirements: build: @@ -27,7 +27,7 @@ requirements: - libuuid # [linux] - mysql-connector-c # [linux] - openssl # [linux] - - zlib # [linux] + - zlib {{CONDA_ZLIB}}* # [linux] run: - libgcc # [linux] @@ -35,7 +35,7 @@ requirements: - libuuid # [linux] - mysql-connector-c # [linux] - openssl # [linux] - - zlib # [linux] + - zlib {{CONDA_ZLIB}}* # [linux] test: commands: diff --git a/recipes/ucsc-newprog/meta.yaml b/recipes/ucsc-newprog/meta.yaml index d2954f4bd10066..74022a4d9b75dd 100644 --- a/recipes/ucsc-newprog/meta.yaml +++ b/recipes/ucsc-newprog/meta.yaml @@ -18,7 +18,7 @@ source: fn: "{{ program }}" # [osx] build: - number: 0 + number: 1 requirements: build: @@ -27,7 +27,7 @@ requirements: - libuuid # [linux] - mysql-connector-c # [linux] - openssl # [linux] - - zlib # [linux] + - zlib {{CONDA_ZLIB}}* # [linux] run: - libgcc # [linux] @@ -35,7 +35,7 @@ requirements: - libuuid # [linux] - mysql-connector-c # [linux] - openssl # [linux] - - zlib # [linux] + - zlib {{CONDA_ZLIB}}* # [linux] test: commands: diff --git a/recipes/ucsc-newpythonprog/meta.yaml b/recipes/ucsc-newpythonprog/meta.yaml index b5b81861ff7649..626d4e96be7776 100644 --- a/recipes/ucsc-newpythonprog/meta.yaml +++ b/recipes/ucsc-newpythonprog/meta.yaml @@ -18,7 +18,7 @@ source: fn: "{{ program }}" # [osx] build: - number: 0 + number: 1 requirements: build: @@ -27,7 +27,7 @@ requirements: - libuuid # [linux] - mysql-connector-c # [linux] - openssl # [linux] - - zlib # [linux] + - zlib {{CONDA_ZLIB}}* # [linux] run: - libgcc # [linux] @@ -35,7 +35,7 @@ requirements: - libuuid # [linux] - mysql-connector-c # [linux] - openssl # [linux] - - zlib # [linux] + - zlib {{CONDA_ZLIB}}* # [linux] test: commands: diff --git a/recipes/ucsc-nibfrag/meta.yaml b/recipes/ucsc-nibfrag/meta.yaml index 64c3625ab79489..c5bc9e6350a8ca 100644 --- a/recipes/ucsc-nibfrag/meta.yaml +++ b/recipes/ucsc-nibfrag/meta.yaml @@ -18,7 +18,7 @@ source: fn: "{{ program }}" # [osx] build: - number: 0 + number: 1 requirements: build: @@ -27,7 +27,7 @@ requirements: - libuuid # [linux] - mysql-connector-c # [linux] - openssl # [linux] - - zlib # [linux] + - zlib {{CONDA_ZLIB}}* # [linux] run: - libgcc # [linux] @@ -35,7 +35,7 @@ requirements: - libuuid # [linux] - mysql-connector-c # [linux] - openssl # [linux] - - zlib # [linux] + - zlib {{CONDA_ZLIB}}* # [linux] test: commands: diff --git a/recipes/ucsc-nibsize/meta.yaml b/recipes/ucsc-nibsize/meta.yaml index c7526e39a44289..004de7283ab4b7 100644 --- a/recipes/ucsc-nibsize/meta.yaml +++ b/recipes/ucsc-nibsize/meta.yaml @@ -18,7 +18,7 @@ source: fn: "{{ program }}" # [osx] build: - number: 0 + number: 1 requirements: build: @@ -27,7 +27,7 @@ requirements: - libuuid # [linux] - mysql-connector-c # [linux] - openssl # [linux] - - zlib # [linux] + - zlib {{CONDA_ZLIB}}* # [linux] run: - libgcc # [linux] @@ -35,7 +35,7 @@ requirements: - libuuid # [linux] - mysql-connector-c # [linux] - openssl # [linux] - - zlib # [linux] + - zlib {{CONDA_ZLIB}}* # [linux] test: commands: diff --git a/recipes/ucsc-oligomatch/meta.yaml b/recipes/ucsc-oligomatch/meta.yaml index 2e4e3b433e9a9b..076196f26aefe5 100644 --- a/recipes/ucsc-oligomatch/meta.yaml +++ b/recipes/ucsc-oligomatch/meta.yaml @@ -18,7 +18,7 @@ source: fn: "{{ program }}" # [osx] build: - number: 0 + number: 1 requirements: build: @@ -27,7 +27,7 @@ requirements: - libuuid # [linux] - mysql-connector-c # [linux] - openssl # [linux] - - zlib # [linux] + - zlib {{CONDA_ZLIB}}* # [linux] run: - libgcc # [linux] @@ -35,7 +35,7 @@ requirements: - libuuid # [linux] - mysql-connector-c # [linux] - openssl # [linux] - - zlib # [linux] + - zlib {{CONDA_ZLIB}}* # [linux] test: commands: diff --git a/recipes/ucsc-overlapselect/meta.yaml b/recipes/ucsc-overlapselect/meta.yaml index f9c5be5fa8ed24..edaf2a82d5d21b 100644 --- a/recipes/ucsc-overlapselect/meta.yaml +++ b/recipes/ucsc-overlapselect/meta.yaml @@ -18,7 +18,7 @@ source: fn: "{{ program }}" # [osx] build: - number: 0 + number: 1 requirements: build: @@ -27,7 +27,7 @@ requirements: - libuuid # [linux] - mysql-connector-c # [linux] - openssl # [linux] - - zlib # [linux] + - zlib {{CONDA_ZLIB}}* # [linux] run: - libgcc # [linux] @@ -35,7 +35,7 @@ requirements: - libuuid # [linux] - mysql-connector-c # [linux] - openssl # [linux] - - zlib # [linux] + - zlib {{CONDA_ZLIB}}* # [linux] test: commands: diff --git a/recipes/ucsc-parafetch/meta.yaml b/recipes/ucsc-parafetch/meta.yaml index 1da6c9f4a67a46..682759d91abccf 100644 --- a/recipes/ucsc-parafetch/meta.yaml +++ b/recipes/ucsc-parafetch/meta.yaml @@ -18,7 +18,7 @@ source: fn: "{{ program }}" # [osx] build: - number: 0 + number: 1 requirements: build: @@ -27,7 +27,7 @@ requirements: - libuuid # [linux] - mysql-connector-c # [linux] - openssl # [linux] - - zlib # [linux] + - zlib {{CONDA_ZLIB}}* # [linux] run: - libgcc # [linux] @@ -35,7 +35,7 @@ requirements: - libuuid # [linux] - mysql-connector-c # [linux] - openssl # [linux] - - zlib # [linux] + - zlib {{CONDA_ZLIB}}* # [linux] test: commands: diff --git a/recipes/ucsc-parasync/meta.yaml b/recipes/ucsc-parasync/meta.yaml index 4144db96cacfbd..b927bd6dbbfa8c 100644 --- a/recipes/ucsc-parasync/meta.yaml +++ b/recipes/ucsc-parasync/meta.yaml @@ -18,7 +18,7 @@ source: fn: "{{ program }}" # [osx] build: - number: 0 + number: 1 requirements: build: @@ -27,7 +27,7 @@ requirements: - libuuid # [linux] - mysql-connector-c # [linux] - openssl # [linux] - - zlib # [linux] + - zlib {{CONDA_ZLIB}}* # [linux] run: - libgcc # [linux] @@ -35,7 +35,7 @@ requirements: - libuuid # [linux] - mysql-connector-c # [linux] - openssl # [linux] - - zlib # [linux] + - zlib {{CONDA_ZLIB}}* # [linux] test: commands: diff --git a/recipes/ucsc-positionaltblcheck/meta.yaml b/recipes/ucsc-positionaltblcheck/meta.yaml index 3cdcd43ce45a26..86331810690278 100644 --- a/recipes/ucsc-positionaltblcheck/meta.yaml +++ b/recipes/ucsc-positionaltblcheck/meta.yaml @@ -18,7 +18,7 @@ source: fn: "{{ program }}" # [osx] build: - number: 0 + number: 1 requirements: build: @@ -27,7 +27,7 @@ requirements: - libuuid # [linux] - mysql-connector-c # [linux] - openssl # [linux] - - zlib # [linux] + - zlib {{CONDA_ZLIB}}* # [linux] run: - libgcc # [linux] @@ -35,7 +35,7 @@ requirements: - libuuid # [linux] - mysql-connector-c # [linux] - openssl # [linux] - - zlib # [linux] + - zlib {{CONDA_ZLIB}}* # [linux] test: commands: diff --git a/recipes/ucsc-pslcat/meta.yaml b/recipes/ucsc-pslcat/meta.yaml index d35ddf0d20335d..a82bc2e3233419 100644 --- a/recipes/ucsc-pslcat/meta.yaml +++ b/recipes/ucsc-pslcat/meta.yaml @@ -18,7 +18,7 @@ source: fn: "{{ program }}" # [osx] build: - number: 0 + number: 1 requirements: build: @@ -27,7 +27,7 @@ requirements: - libuuid # [linux] - mysql-connector-c # [linux] - openssl # [linux] - - zlib # [linux] + - zlib {{CONDA_ZLIB}}* # [linux] run: - libgcc # [linux] @@ -35,7 +35,7 @@ requirements: - libuuid # [linux] - mysql-connector-c # [linux] - openssl # [linux] - - zlib # [linux] + - zlib {{CONDA_ZLIB}}* # [linux] test: commands: diff --git a/recipes/ucsc-pslcdnafilter/meta.yaml b/recipes/ucsc-pslcdnafilter/meta.yaml index 26324507c25b72..46b72b9a355374 100644 --- a/recipes/ucsc-pslcdnafilter/meta.yaml +++ b/recipes/ucsc-pslcdnafilter/meta.yaml @@ -18,7 +18,7 @@ source: fn: "{{ program }}" # [osx] build: - number: 0 + number: 1 requirements: build: @@ -27,7 +27,7 @@ requirements: - libuuid # [linux] - mysql-connector-c # [linux] - openssl # [linux] - - zlib # [linux] + - zlib {{CONDA_ZLIB}}* # [linux] run: - libgcc # [linux] @@ -35,7 +35,7 @@ requirements: - libuuid # [linux] - mysql-connector-c # [linux] - openssl # [linux] - - zlib # [linux] + - zlib {{CONDA_ZLIB}}* # [linux] test: commands: diff --git a/recipes/ucsc-pslcheck/meta.yaml b/recipes/ucsc-pslcheck/meta.yaml index 9f701f0d5e40ff..00a5bf8bb48450 100644 --- a/recipes/ucsc-pslcheck/meta.yaml +++ b/recipes/ucsc-pslcheck/meta.yaml @@ -18,7 +18,7 @@ source: fn: "{{ program }}" # [osx] build: - number: 0 + number: 1 requirements: build: @@ -27,7 +27,7 @@ requirements: - libuuid # [linux] - mysql-connector-c # [linux] - openssl # [linux] - - zlib # [linux] + - zlib {{CONDA_ZLIB}}* # [linux] run: - libgcc # [linux] @@ -35,7 +35,7 @@ requirements: - libuuid # [linux] - mysql-connector-c # [linux] - openssl # [linux] - - zlib # [linux] + - zlib {{CONDA_ZLIB}}* # [linux] test: commands: diff --git a/recipes/ucsc-psldropoverlap/meta.yaml b/recipes/ucsc-psldropoverlap/meta.yaml index 913a967c090fe4..2c00db849e13f8 100644 --- a/recipes/ucsc-psldropoverlap/meta.yaml +++ b/recipes/ucsc-psldropoverlap/meta.yaml @@ -18,7 +18,7 @@ source: fn: "{{ program }}" # [osx] build: - number: 0 + number: 1 requirements: build: @@ -27,7 +27,7 @@ requirements: - libuuid # [linux] - mysql-connector-c # [linux] - openssl # [linux] - - zlib # [linux] + - zlib {{CONDA_ZLIB}}* # [linux] run: - libgcc # [linux] @@ -35,7 +35,7 @@ requirements: - libuuid # [linux] - mysql-connector-c # [linux] - openssl # [linux] - - zlib # [linux] + - zlib {{CONDA_ZLIB}}* # [linux] test: commands: diff --git a/recipes/ucsc-pslfilter/meta.yaml b/recipes/ucsc-pslfilter/meta.yaml index 1ac5af1f7f24ee..dd53aabb5ddc19 100644 --- a/recipes/ucsc-pslfilter/meta.yaml +++ b/recipes/ucsc-pslfilter/meta.yaml @@ -18,7 +18,7 @@ source: fn: "{{ program }}" # [osx] build: - number: 0 + number: 1 requirements: build: @@ -27,7 +27,7 @@ requirements: - libuuid # [linux] - mysql-connector-c # [linux] - openssl # [linux] - - zlib # [linux] + - zlib {{CONDA_ZLIB}}* # [linux] run: - libgcc # [linux] @@ -35,7 +35,7 @@ requirements: - libuuid # [linux] - mysql-connector-c # [linux] - openssl # [linux] - - zlib # [linux] + - zlib {{CONDA_ZLIB}}* # [linux] test: commands: diff --git a/recipes/ucsc-pslhisto/meta.yaml b/recipes/ucsc-pslhisto/meta.yaml index 07f9f02d186776..5ea00dc2ad60f9 100644 --- a/recipes/ucsc-pslhisto/meta.yaml +++ b/recipes/ucsc-pslhisto/meta.yaml @@ -18,7 +18,7 @@ source: fn: "{{ program }}" # [osx] build: - number: 0 + number: 1 requirements: build: diff --git a/recipes/ucsc-pslliftsubrangeblat/meta.yaml b/recipes/ucsc-pslliftsubrangeblat/meta.yaml index 918314fcc87249..fa7958b1e2d5b5 100644 --- a/recipes/ucsc-pslliftsubrangeblat/meta.yaml +++ b/recipes/ucsc-pslliftsubrangeblat/meta.yaml @@ -18,7 +18,7 @@ source: fn: "{{ program }}" # [osx] build: - number: 0 + number: 1 requirements: build: @@ -27,7 +27,7 @@ requirements: - libuuid # [linux] - mysql-connector-c # [linux] - openssl # [linux] - - zlib # [linux] + - zlib {{CONDA_ZLIB}}* # [linux] run: - libgcc # [linux] @@ -35,7 +35,7 @@ requirements: - libuuid # [linux] - mysql-connector-c # [linux] - openssl # [linux] - - zlib # [linux] + - zlib {{CONDA_ZLIB}}* # [linux] test: commands: diff --git a/recipes/ucsc-pslmap/meta.yaml b/recipes/ucsc-pslmap/meta.yaml index ef9af174449df7..a4a72291b5c755 100644 --- a/recipes/ucsc-pslmap/meta.yaml +++ b/recipes/ucsc-pslmap/meta.yaml @@ -18,7 +18,7 @@ source: fn: "{{ program }}" # [osx] build: - number: 0 + number: 1 requirements: build: @@ -27,7 +27,7 @@ requirements: - libuuid # [linux] - mysql-connector-c # [linux] - openssl # [linux] - - zlib # [linux] + - zlib {{CONDA_ZLIB}}* # [linux] run: - libgcc # [linux] @@ -35,7 +35,7 @@ requirements: - libuuid # [linux] - mysql-connector-c # [linux] - openssl # [linux] - - zlib # [linux] + - zlib {{CONDA_ZLIB}}* # [linux] test: commands: diff --git a/recipes/ucsc-pslmappostchain/meta.yaml b/recipes/ucsc-pslmappostchain/meta.yaml index 8667f18f7fbe02..678acc73e934e9 100644 --- a/recipes/ucsc-pslmappostchain/meta.yaml +++ b/recipes/ucsc-pslmappostchain/meta.yaml @@ -18,7 +18,7 @@ source: fn: "{{ program }}" # [osx] build: - number: 0 + number: 1 requirements: build: @@ -27,7 +27,7 @@ requirements: - libuuid # [linux] - mysql-connector-c # [linux] - openssl # [linux] - - zlib # [linux] + - zlib {{CONDA_ZLIB}}* # [linux] run: - libgcc # [linux] @@ -35,7 +35,7 @@ requirements: - libuuid # [linux] - mysql-connector-c # [linux] - openssl # [linux] - - zlib # [linux] + - zlib {{CONDA_ZLIB}}* # [linux] test: commands: diff --git a/recipes/ucsc-pslmrnacover/meta.yaml b/recipes/ucsc-pslmrnacover/meta.yaml index afe5b25c06e119..fb628f228738e8 100644 --- a/recipes/ucsc-pslmrnacover/meta.yaml +++ b/recipes/ucsc-pslmrnacover/meta.yaml @@ -18,7 +18,7 @@ source: fn: "{{ program }}" # [osx] build: - number: 0 + number: 1 requirements: build: @@ -27,7 +27,7 @@ requirements: - libuuid # [linux] - mysql-connector-c # [linux] - openssl # [linux] - - zlib # [linux] + - zlib {{CONDA_ZLIB}}* # [linux] run: - libgcc # [linux] @@ -35,7 +35,7 @@ requirements: - libuuid # [linux] - mysql-connector-c # [linux] - openssl # [linux] - - zlib # [linux] + - zlib {{CONDA_ZLIB}}* # [linux] test: commands: diff --git a/recipes/ucsc-pslpairs/meta.yaml b/recipes/ucsc-pslpairs/meta.yaml index bc09d7614875c5..1432e774d916ea 100644 --- a/recipes/ucsc-pslpairs/meta.yaml +++ b/recipes/ucsc-pslpairs/meta.yaml @@ -18,7 +18,7 @@ source: fn: "{{ program }}" # [osx] build: - number: 0 + number: 1 requirements: build: @@ -27,7 +27,7 @@ requirements: - libuuid # [linux] - mysql-connector-c # [linux] - openssl # [linux] - - zlib # [linux] + - zlib {{CONDA_ZLIB}}* # [linux] run: - libgcc # [linux] @@ -35,7 +35,7 @@ requirements: - libuuid # [linux] - mysql-connector-c # [linux] - openssl # [linux] - - zlib # [linux] + - zlib {{CONDA_ZLIB}}* # [linux] test: commands: diff --git a/recipes/ucsc-pslpartition/meta.yaml b/recipes/ucsc-pslpartition/meta.yaml index a02e508ac336e7..11a9434d0141a7 100644 --- a/recipes/ucsc-pslpartition/meta.yaml +++ b/recipes/ucsc-pslpartition/meta.yaml @@ -18,7 +18,7 @@ source: fn: "{{ program }}" # [osx] build: - number: 0 + number: 1 requirements: build: @@ -27,7 +27,7 @@ requirements: - libuuid # [linux] - mysql-connector-c # [linux] - openssl # [linux] - - zlib # [linux] + - zlib {{CONDA_ZLIB}}* # [linux] run: - libgcc # [linux] @@ -35,7 +35,7 @@ requirements: - libuuid # [linux] - mysql-connector-c # [linux] - openssl # [linux] - - zlib # [linux] + - zlib {{CONDA_ZLIB}}* # [linux] test: commands: diff --git a/recipes/ucsc-pslpostarget/meta.yaml b/recipes/ucsc-pslpostarget/meta.yaml index f767bcb53c55d7..4a364dccf719aa 100644 --- a/recipes/ucsc-pslpostarget/meta.yaml +++ b/recipes/ucsc-pslpostarget/meta.yaml @@ -18,7 +18,7 @@ source: fn: "{{ program }}" # [osx] build: - number: 0 + number: 1 requirements: build: @@ -27,7 +27,7 @@ requirements: - libuuid # [linux] - mysql-connector-c # [linux] - openssl # [linux] - - zlib # [linux] + - zlib {{CONDA_ZLIB}}* # [linux] run: - libgcc # [linux] @@ -35,7 +35,7 @@ requirements: - libuuid # [linux] - mysql-connector-c # [linux] - openssl # [linux] - - zlib # [linux] + - zlib {{CONDA_ZLIB}}* # [linux] test: commands: diff --git a/recipes/ucsc-pslpretty/meta.yaml b/recipes/ucsc-pslpretty/meta.yaml index 5b4cdaa1381749..1e7b367fb2f023 100644 --- a/recipes/ucsc-pslpretty/meta.yaml +++ b/recipes/ucsc-pslpretty/meta.yaml @@ -18,7 +18,7 @@ source: fn: "{{ program }}" # [osx] build: - number: 0 + number: 1 requirements: build: @@ -27,7 +27,7 @@ requirements: - libuuid # [linux] - mysql-connector-c # [linux] - openssl # [linux] - - zlib # [linux] + - zlib {{CONDA_ZLIB}}* # [linux] run: - libgcc # [linux] @@ -35,7 +35,7 @@ requirements: - libuuid # [linux] - mysql-connector-c # [linux] - openssl # [linux] - - zlib # [linux] + - zlib {{CONDA_ZLIB}}* # [linux] test: commands: diff --git a/recipes/ucsc-pslrc/meta.yaml b/recipes/ucsc-pslrc/meta.yaml index 131a8ede4ad6db..71829154466337 100644 --- a/recipes/ucsc-pslrc/meta.yaml +++ b/recipes/ucsc-pslrc/meta.yaml @@ -18,7 +18,7 @@ source: fn: "{{ program }}" # [osx] build: - number: 0 + number: 1 requirements: build: @@ -27,7 +27,7 @@ requirements: - libuuid # [linux] - mysql-connector-c # [linux] - openssl # [linux] - - zlib # [linux] + - zlib {{CONDA_ZLIB}}* # [linux] run: - libgcc # [linux] @@ -35,7 +35,7 @@ requirements: - libuuid # [linux] - mysql-connector-c # [linux] - openssl # [linux] - - zlib # [linux] + - zlib {{CONDA_ZLIB}}* # [linux] test: commands: diff --git a/recipes/ucsc-pslrecalcmatch/meta.yaml b/recipes/ucsc-pslrecalcmatch/meta.yaml index 5493552e8b6afc..92cc1f48b20b39 100644 --- a/recipes/ucsc-pslrecalcmatch/meta.yaml +++ b/recipes/ucsc-pslrecalcmatch/meta.yaml @@ -18,7 +18,7 @@ source: fn: "{{ program }}" # [osx] build: - number: 0 + number: 1 requirements: build: @@ -27,7 +27,7 @@ requirements: - libuuid # [linux] - mysql-connector-c # [linux] - openssl # [linux] - - zlib # [linux] + - zlib {{CONDA_ZLIB}}* # [linux] run: - libgcc # [linux] @@ -35,7 +35,7 @@ requirements: - libuuid # [linux] - mysql-connector-c # [linux] - openssl # [linux] - - zlib # [linux] + - zlib {{CONDA_ZLIB}}* # [linux] test: commands: diff --git a/recipes/ucsc-pslreps/meta.yaml b/recipes/ucsc-pslreps/meta.yaml index 72aa18cc76f247..6b3adda8ac1766 100644 --- a/recipes/ucsc-pslreps/meta.yaml +++ b/recipes/ucsc-pslreps/meta.yaml @@ -18,7 +18,7 @@ source: fn: "{{ program }}" # [osx] build: - number: 0 + number: 1 requirements: build: @@ -27,7 +27,7 @@ requirements: - libuuid # [linux] - mysql-connector-c # [linux] - openssl # [linux] - - zlib # [linux] + - zlib {{CONDA_ZLIB}}* # [linux] run: - libgcc # [linux] @@ -35,7 +35,7 @@ requirements: - libuuid # [linux] - mysql-connector-c # [linux] - openssl # [linux] - - zlib # [linux] + - zlib {{CONDA_ZLIB}}* # [linux] test: commands: diff --git a/recipes/ucsc-pslscore/meta.yaml b/recipes/ucsc-pslscore/meta.yaml index 9ff1cdfc9b9ecc..38fded3042b177 100644 --- a/recipes/ucsc-pslscore/meta.yaml +++ b/recipes/ucsc-pslscore/meta.yaml @@ -18,7 +18,7 @@ source: fn: "{{ program }}" # [osx] build: - number: 0 + number: 1 requirements: build: @@ -27,7 +27,7 @@ requirements: - libuuid # [linux] - mysql-connector-c # [linux] - openssl # [linux] - - zlib # [linux] + - zlib {{CONDA_ZLIB}}* # [linux] run: - libgcc # [linux] @@ -35,7 +35,7 @@ requirements: - libuuid # [linux] - mysql-connector-c # [linux] - openssl # [linux] - - zlib # [linux] + - zlib {{CONDA_ZLIB}}* # [linux] test: commands: diff --git a/recipes/ucsc-pslselect/meta.yaml b/recipes/ucsc-pslselect/meta.yaml index 04dce6eb640037..974c34d4e05953 100644 --- a/recipes/ucsc-pslselect/meta.yaml +++ b/recipes/ucsc-pslselect/meta.yaml @@ -18,7 +18,7 @@ source: fn: "{{ program }}" # [osx] build: - number: 0 + number: 1 requirements: build: @@ -27,7 +27,7 @@ requirements: - libuuid # [linux] - mysql-connector-c # [linux] - openssl # [linux] - - zlib # [linux] + - zlib {{CONDA_ZLIB}}* # [linux] run: - libgcc # [linux] @@ -35,7 +35,7 @@ requirements: - libuuid # [linux] - mysql-connector-c # [linux] - openssl # [linux] - - zlib # [linux] + - zlib {{CONDA_ZLIB}}* # [linux] test: commands: diff --git a/recipes/ucsc-pslsort/meta.yaml b/recipes/ucsc-pslsort/meta.yaml index 410594835bfba5..f753b4f59a5cfb 100644 --- a/recipes/ucsc-pslsort/meta.yaml +++ b/recipes/ucsc-pslsort/meta.yaml @@ -18,7 +18,7 @@ source: fn: "{{ program }}" # [osx] build: - number: 0 + number: 1 requirements: build: @@ -27,7 +27,7 @@ requirements: - libuuid # [linux] - mysql-connector-c # [linux] - openssl # [linux] - - zlib # [linux] + - zlib {{CONDA_ZLIB}}* # [linux] run: - libgcc # [linux] @@ -35,7 +35,7 @@ requirements: - libuuid # [linux] - mysql-connector-c # [linux] - openssl # [linux] - - zlib # [linux] + - zlib {{CONDA_ZLIB}}* # [linux] test: commands: diff --git a/recipes/ucsc-pslstats/meta.yaml b/recipes/ucsc-pslstats/meta.yaml index 537e2720e7f0fa..9ce6b84970f7c2 100644 --- a/recipes/ucsc-pslstats/meta.yaml +++ b/recipes/ucsc-pslstats/meta.yaml @@ -18,7 +18,7 @@ source: fn: "{{ program }}" # [osx] build: - number: 0 + number: 1 requirements: build: @@ -27,7 +27,7 @@ requirements: - libuuid # [linux] - mysql-connector-c # [linux] - openssl # [linux] - - zlib # [linux] + - zlib {{CONDA_ZLIB}}* # [linux] run: - libgcc # [linux] @@ -35,7 +35,7 @@ requirements: - libuuid # [linux] - mysql-connector-c # [linux] - openssl # [linux] - - zlib # [linux] + - zlib {{CONDA_ZLIB}}* # [linux] test: commands: diff --git a/recipes/ucsc-pslswap/meta.yaml b/recipes/ucsc-pslswap/meta.yaml index 7562b52727cada..a6ea4afc98a35f 100644 --- a/recipes/ucsc-pslswap/meta.yaml +++ b/recipes/ucsc-pslswap/meta.yaml @@ -18,7 +18,7 @@ source: fn: "{{ program }}" # [osx] build: - number: 0 + number: 1 requirements: build: @@ -27,7 +27,7 @@ requirements: - libuuid # [linux] - mysql-connector-c # [linux] - openssl # [linux] - - zlib # [linux] + - zlib {{CONDA_ZLIB}}* # [linux] run: - libgcc # [linux] @@ -35,7 +35,7 @@ requirements: - libuuid # [linux] - mysql-connector-c # [linux] - openssl # [linux] - - zlib # [linux] + - zlib {{CONDA_ZLIB}}* # [linux] test: commands: diff --git a/recipes/ucsc-psltobed/meta.yaml b/recipes/ucsc-psltobed/meta.yaml index 856f5b93091bd8..efd3900ac3f07c 100644 --- a/recipes/ucsc-psltobed/meta.yaml +++ b/recipes/ucsc-psltobed/meta.yaml @@ -18,7 +18,7 @@ source: fn: "{{ program }}" # [osx] build: - number: 0 + number: 1 requirements: build: @@ -27,7 +27,7 @@ requirements: - libuuid # [linux] - mysql-connector-c # [linux] - openssl # [linux] - - zlib # [linux] + - zlib {{CONDA_ZLIB}}* # [linux] run: - libgcc # [linux] @@ -35,7 +35,7 @@ requirements: - libuuid # [linux] - mysql-connector-c # [linux] - openssl # [linux] - - zlib # [linux] + - zlib {{CONDA_ZLIB}}* # [linux] test: commands: diff --git a/recipes/ucsc-psltobigpsl/meta.yaml b/recipes/ucsc-psltobigpsl/meta.yaml index c8f0d9602de113..ae24a8fc1293b3 100644 --- a/recipes/ucsc-psltobigpsl/meta.yaml +++ b/recipes/ucsc-psltobigpsl/meta.yaml @@ -18,7 +18,7 @@ source: fn: "{{ program }}" # [osx] build: - number: 0 + number: 1 requirements: build: @@ -27,7 +27,7 @@ requirements: - libuuid # [linux] - mysql-connector-c # [linux] - openssl # [linux] - - zlib # [linux] + - zlib {{CONDA_ZLIB}}* # [linux] run: - libgcc # [linux] @@ -35,7 +35,7 @@ requirements: - libuuid # [linux] - mysql-connector-c # [linux] - openssl # [linux] - - zlib # [linux] + - zlib {{CONDA_ZLIB}}* # [linux] test: commands: diff --git a/recipes/ucsc-psltochain/meta.yaml b/recipes/ucsc-psltochain/meta.yaml index 00836cdb7c992c..daa826075ab7de 100644 --- a/recipes/ucsc-psltochain/meta.yaml +++ b/recipes/ucsc-psltochain/meta.yaml @@ -18,7 +18,7 @@ source: fn: "{{ program }}" # [osx] build: - number: 0 + number: 1 requirements: build: @@ -27,7 +27,7 @@ requirements: - libuuid # [linux] - mysql-connector-c # [linux] - openssl # [linux] - - zlib # [linux] + - zlib {{CONDA_ZLIB}}* # [linux] run: - libgcc # [linux] @@ -35,7 +35,7 @@ requirements: - libuuid # [linux] - mysql-connector-c # [linux] - openssl # [linux] - - zlib # [linux] + - zlib {{CONDA_ZLIB}}* # [linux] test: commands: diff --git a/recipes/ucsc-psltopslx/meta.yaml b/recipes/ucsc-psltopslx/meta.yaml index 863bf7f41d6228..e227f607f2c4fb 100644 --- a/recipes/ucsc-psltopslx/meta.yaml +++ b/recipes/ucsc-psltopslx/meta.yaml @@ -18,7 +18,7 @@ source: fn: "{{ program }}" # [osx] build: - number: 0 + number: 1 requirements: build: @@ -27,7 +27,7 @@ requirements: - libuuid # [linux] - mysql-connector-c # [linux] - openssl # [linux] - - zlib # [linux] + - zlib {{CONDA_ZLIB}}* # [linux] run: - libgcc # [linux] @@ -35,7 +35,7 @@ requirements: - libuuid # [linux] - mysql-connector-c # [linux] - openssl # [linux] - - zlib # [linux] + - zlib {{CONDA_ZLIB}}* # [linux] test: commands: diff --git a/recipes/ucsc-pslxtofa/meta.yaml b/recipes/ucsc-pslxtofa/meta.yaml index 59bf5978acdeae..1f799bbc040682 100644 --- a/recipes/ucsc-pslxtofa/meta.yaml +++ b/recipes/ucsc-pslxtofa/meta.yaml @@ -18,7 +18,7 @@ source: fn: "{{ program }}" # [osx] build: - number: 0 + number: 1 requirements: build: @@ -27,7 +27,7 @@ requirements: - libuuid # [linux] - mysql-connector-c # [linux] - openssl # [linux] - - zlib # [linux] + - zlib {{CONDA_ZLIB}}* # [linux] run: - libgcc # [linux] @@ -35,7 +35,7 @@ requirements: - libuuid # [linux] - mysql-connector-c # [linux] - openssl # [linux] - - zlib # [linux] + - zlib {{CONDA_ZLIB}}* # [linux] test: commands: diff --git a/recipes/ucsc-qacagplift/meta.yaml b/recipes/ucsc-qacagplift/meta.yaml index 55e725088b7312..ed5ac5f5a6e2fb 100644 --- a/recipes/ucsc-qacagplift/meta.yaml +++ b/recipes/ucsc-qacagplift/meta.yaml @@ -18,7 +18,7 @@ source: fn: "{{ program }}" # [osx] build: - number: 0 + number: 1 requirements: build: @@ -27,7 +27,7 @@ requirements: - libuuid # [linux] - mysql-connector-c # [linux] - openssl # [linux] - - zlib # [linux] + - zlib {{CONDA_ZLIB}}* # [linux] run: - libgcc # [linux] @@ -35,7 +35,7 @@ requirements: - libuuid # [linux] - mysql-connector-c # [linux] - openssl # [linux] - - zlib # [linux] + - zlib {{CONDA_ZLIB}}* # [linux] test: commands: diff --git a/recipes/ucsc-qactoqa/meta.yaml b/recipes/ucsc-qactoqa/meta.yaml index 8f60ee12128f5b..b7028d0589e112 100644 --- a/recipes/ucsc-qactoqa/meta.yaml +++ b/recipes/ucsc-qactoqa/meta.yaml @@ -18,7 +18,7 @@ source: fn: "{{ program }}" # [osx] build: - number: 0 + number: 1 requirements: build: @@ -27,7 +27,7 @@ requirements: - libuuid # [linux] - mysql-connector-c # [linux] - openssl # [linux] - - zlib # [linux] + - zlib {{CONDA_ZLIB}}* # [linux] run: - libgcc # [linux] @@ -35,7 +35,7 @@ requirements: - libuuid # [linux] - mysql-connector-c # [linux] - openssl # [linux] - - zlib # [linux] + - zlib {{CONDA_ZLIB}}* # [linux] test: commands: diff --git a/recipes/ucsc-qactowig/meta.yaml b/recipes/ucsc-qactowig/meta.yaml index 17b12ea4b99fac..ae56d63447032c 100644 --- a/recipes/ucsc-qactowig/meta.yaml +++ b/recipes/ucsc-qactowig/meta.yaml @@ -18,7 +18,7 @@ source: fn: "{{ program }}" # [osx] build: - number: 0 + number: 1 requirements: build: @@ -27,7 +27,7 @@ requirements: - libuuid # [linux] - mysql-connector-c # [linux] - openssl # [linux] - - zlib # [linux] + - zlib {{CONDA_ZLIB}}* # [linux] run: - libgcc # [linux] @@ -35,7 +35,7 @@ requirements: - libuuid # [linux] - mysql-connector-c # [linux] - openssl # [linux] - - zlib # [linux] + - zlib {{CONDA_ZLIB}}* # [linux] test: commands: diff --git a/recipes/ucsc-qatoqac/meta.yaml b/recipes/ucsc-qatoqac/meta.yaml index e13de6d2545ba2..f403f77b202bd0 100644 --- a/recipes/ucsc-qatoqac/meta.yaml +++ b/recipes/ucsc-qatoqac/meta.yaml @@ -18,7 +18,7 @@ source: fn: "{{ program }}" # [osx] build: - number: 0 + number: 1 requirements: build: @@ -27,7 +27,7 @@ requirements: - libuuid # [linux] - mysql-connector-c # [linux] - openssl # [linux] - - zlib # [linux] + - zlib {{CONDA_ZLIB}}* # [linux] run: - libgcc # [linux] @@ -35,7 +35,7 @@ requirements: - libuuid # [linux] - mysql-connector-c # [linux] - openssl # [linux] - - zlib # [linux] + - zlib {{CONDA_ZLIB}}* # [linux] test: commands: diff --git a/recipes/ucsc-randomlines/meta.yaml b/recipes/ucsc-randomlines/meta.yaml index 05fcd5714d73ca..1716387c826976 100644 --- a/recipes/ucsc-randomlines/meta.yaml +++ b/recipes/ucsc-randomlines/meta.yaml @@ -18,7 +18,7 @@ source: fn: "{{ program }}" # [osx] build: - number: 0 + number: 1 requirements: build: @@ -27,7 +27,7 @@ requirements: - libuuid # [linux] - mysql-connector-c # [linux] - openssl # [linux] - - zlib # [linux] + - zlib {{CONDA_ZLIB}}* # [linux] run: - libgcc # [linux] @@ -35,7 +35,7 @@ requirements: - libuuid # [linux] - mysql-connector-c # [linux] - openssl # [linux] - - zlib # [linux] + - zlib {{CONDA_ZLIB}}* # [linux] test: commands: diff --git a/recipes/ucsc-rasqlquery/meta.yaml b/recipes/ucsc-rasqlquery/meta.yaml index 7ff4f065db5acc..0520f97a746e49 100644 --- a/recipes/ucsc-rasqlquery/meta.yaml +++ b/recipes/ucsc-rasqlquery/meta.yaml @@ -18,7 +18,7 @@ source: fn: "{{ program }}" # [osx] build: - number: 0 + number: 1 requirements: build: @@ -27,7 +27,7 @@ requirements: - libuuid # [linux] - mysql-connector-c # [linux] - openssl # [linux] - - zlib # [linux] + - zlib {{CONDA_ZLIB}}* # [linux] run: - libgcc # [linux] @@ -35,7 +35,7 @@ requirements: - libuuid # [linux] - mysql-connector-c # [linux] - openssl # [linux] - - zlib # [linux] + - zlib {{CONDA_ZLIB}}* # [linux] test: commands: diff --git a/recipes/ucsc-ratolines/meta.yaml b/recipes/ucsc-ratolines/meta.yaml index ecc093b48d9858..e3ccc309ba17cf 100644 --- a/recipes/ucsc-ratolines/meta.yaml +++ b/recipes/ucsc-ratolines/meta.yaml @@ -18,7 +18,7 @@ source: fn: "{{ program }}" # [osx] build: - number: 0 + number: 1 requirements: build: @@ -27,7 +27,7 @@ requirements: - libuuid # [linux] - mysql-connector-c # [linux] - openssl # [linux] - - zlib # [linux] + - zlib {{CONDA_ZLIB}}* # [linux] run: - libgcc # [linux] @@ -35,7 +35,7 @@ requirements: - libuuid # [linux] - mysql-connector-c # [linux] - openssl # [linux] - - zlib # [linux] + - zlib {{CONDA_ZLIB}}* # [linux] test: commands: diff --git a/recipes/ucsc-ratotab/meta.yaml b/recipes/ucsc-ratotab/meta.yaml index 7b7522ecbb576a..7673579b7c1296 100644 --- a/recipes/ucsc-ratotab/meta.yaml +++ b/recipes/ucsc-ratotab/meta.yaml @@ -18,7 +18,7 @@ source: fn: "{{ program }}" # [osx] build: - number: 0 + number: 1 requirements: build: @@ -27,7 +27,7 @@ requirements: - libuuid # [linux] - mysql-connector-c # [linux] - openssl # [linux] - - zlib # [linux] + - zlib {{CONDA_ZLIB}}* # [linux] run: - libgcc # [linux] @@ -35,7 +35,7 @@ requirements: - libuuid # [linux] - mysql-connector-c # [linux] - openssl # [linux] - - zlib # [linux] + - zlib {{CONDA_ZLIB}}* # [linux] test: commands: diff --git a/recipes/ucsc-rmfadups/meta.yaml b/recipes/ucsc-rmfadups/meta.yaml index 3412d576763acb..2410fa8b501644 100644 --- a/recipes/ucsc-rmfadups/meta.yaml +++ b/recipes/ucsc-rmfadups/meta.yaml @@ -18,7 +18,7 @@ source: fn: "{{ program }}" # [osx] build: - number: 0 + number: 1 requirements: build: @@ -27,7 +27,7 @@ requirements: - libuuid # [linux] - mysql-connector-c # [linux] - openssl # [linux] - - zlib # [linux] + - zlib {{CONDA_ZLIB}}* # [linux] run: - libgcc # [linux] @@ -35,7 +35,7 @@ requirements: - libuuid # [linux] - mysql-connector-c # [linux] - openssl # [linux] - - zlib # [linux] + - zlib {{CONDA_ZLIB}}* # [linux] test: commands: diff --git a/recipes/ucsc-rowstocols/meta.yaml b/recipes/ucsc-rowstocols/meta.yaml index a4fcc790cc9a7f..edb3d4a2e5110b 100644 --- a/recipes/ucsc-rowstocols/meta.yaml +++ b/recipes/ucsc-rowstocols/meta.yaml @@ -18,7 +18,7 @@ source: fn: "{{ program }}" # [osx] build: - number: 0 + number: 1 requirements: build: @@ -27,7 +27,7 @@ requirements: - libuuid # [linux] - mysql-connector-c # [linux] - openssl # [linux] - - zlib # [linux] + - zlib {{CONDA_ZLIB}}* # [linux] run: - libgcc # [linux] @@ -35,7 +35,7 @@ requirements: - libuuid # [linux] - mysql-connector-c # [linux] - openssl # [linux] - - zlib # [linux] + - zlib {{CONDA_ZLIB}}* # [linux] test: commands: diff --git a/recipes/ucsc-spacedtotab/meta.yaml b/recipes/ucsc-spacedtotab/meta.yaml index ed86c85a2642ce..c16f6c647cc87f 100644 --- a/recipes/ucsc-spacedtotab/meta.yaml +++ b/recipes/ucsc-spacedtotab/meta.yaml @@ -18,7 +18,7 @@ source: fn: "{{ program }}" # [osx] build: - number: 0 + number: 1 requirements: build: @@ -27,7 +27,7 @@ requirements: - libuuid # [linux] - mysql-connector-c # [linux] - openssl # [linux] - - zlib # [linux] + - zlib {{CONDA_ZLIB}}* # [linux] run: - libgcc # [linux] @@ -35,7 +35,7 @@ requirements: - libuuid # [linux] - mysql-connector-c # [linux] - openssl # [linux] - - zlib # [linux] + - zlib {{CONDA_ZLIB}}* # [linux] test: commands: diff --git a/recipes/ucsc-splitfile/meta.yaml b/recipes/ucsc-splitfile/meta.yaml index f1812fbba746a6..5add912da0a602 100644 --- a/recipes/ucsc-splitfile/meta.yaml +++ b/recipes/ucsc-splitfile/meta.yaml @@ -18,7 +18,7 @@ source: fn: "{{ program }}" # [osx] build: - number: 0 + number: 1 requirements: build: @@ -27,7 +27,7 @@ requirements: - libuuid # [linux] - mysql-connector-c # [linux] - openssl # [linux] - - zlib # [linux] + - zlib {{CONDA_ZLIB}}* # [linux] run: - libgcc # [linux] @@ -35,7 +35,7 @@ requirements: - libuuid # [linux] - mysql-connector-c # [linux] - openssl # [linux] - - zlib # [linux] + - zlib {{CONDA_ZLIB}}* # [linux] test: commands: diff --git a/recipes/ucsc-splitfilebycolumn/meta.yaml b/recipes/ucsc-splitfilebycolumn/meta.yaml index 597370af3c27a2..62234987b84421 100644 --- a/recipes/ucsc-splitfilebycolumn/meta.yaml +++ b/recipes/ucsc-splitfilebycolumn/meta.yaml @@ -18,7 +18,7 @@ source: fn: "{{ program }}" # [osx] build: - number: 0 + number: 1 requirements: build: @@ -27,7 +27,7 @@ requirements: - libuuid # [linux] - mysql-connector-c # [linux] - openssl # [linux] - - zlib # [linux] + - zlib {{CONDA_ZLIB}}* # [linux] run: - libgcc # [linux] @@ -35,7 +35,7 @@ requirements: - libuuid # [linux] - mysql-connector-c # [linux] - openssl # [linux] - - zlib # [linux] + - zlib {{CONDA_ZLIB}}* # [linux] test: commands: diff --git a/recipes/ucsc-sqltoxml/meta.yaml b/recipes/ucsc-sqltoxml/meta.yaml index e949e8b8e34571..20a3994bbe807e 100644 --- a/recipes/ucsc-sqltoxml/meta.yaml +++ b/recipes/ucsc-sqltoxml/meta.yaml @@ -18,7 +18,7 @@ source: fn: "{{ program }}" # [osx] build: - number: 0 + number: 1 requirements: build: @@ -27,7 +27,7 @@ requirements: - libuuid # [linux] - mysql-connector-c # [linux] - openssl # [linux] - - zlib # [linux] + - zlib {{CONDA_ZLIB}}* # [linux] run: - libgcc # [linux] @@ -35,7 +35,7 @@ requirements: - libuuid # [linux] - mysql-connector-c # [linux] - openssl # [linux] - - zlib # [linux] + - zlib {{CONDA_ZLIB}}* # [linux] test: commands: diff --git a/recipes/ucsc-stringify/meta.yaml b/recipes/ucsc-stringify/meta.yaml index 8a6af2f271ebd1..0091e7f2e37208 100644 --- a/recipes/ucsc-stringify/meta.yaml +++ b/recipes/ucsc-stringify/meta.yaml @@ -18,7 +18,7 @@ source: fn: "{{ program }}" # [osx] build: - number: 0 + number: 1 requirements: build: @@ -27,7 +27,7 @@ requirements: - libuuid # [linux] - mysql-connector-c # [linux] - openssl # [linux] - - zlib # [linux] + - zlib {{CONDA_ZLIB}}* # [linux] run: - libgcc # [linux] @@ -35,7 +35,7 @@ requirements: - libuuid # [linux] - mysql-connector-c # [linux] - openssl # [linux] - - zlib # [linux] + - zlib {{CONDA_ZLIB}}* # [linux] test: commands: diff --git a/recipes/ucsc-subchar/meta.yaml b/recipes/ucsc-subchar/meta.yaml index 668bcdd3d7b0d5..192a9811b16a87 100644 --- a/recipes/ucsc-subchar/meta.yaml +++ b/recipes/ucsc-subchar/meta.yaml @@ -18,7 +18,7 @@ source: fn: "{{ program }}" # [osx] build: - number: 0 + number: 1 requirements: build: @@ -27,7 +27,7 @@ requirements: - libuuid # [linux] - mysql-connector-c # [linux] - openssl # [linux] - - zlib # [linux] + - zlib {{CONDA_ZLIB}}* # [linux] run: - libgcc # [linux] @@ -35,7 +35,7 @@ requirements: - libuuid # [linux] - mysql-connector-c # [linux] - openssl # [linux] - - zlib # [linux] + - zlib {{CONDA_ZLIB}}* # [linux] test: commands: diff --git a/recipes/ucsc-subcolumn/meta.yaml b/recipes/ucsc-subcolumn/meta.yaml index b89c7726926dd5..00a147dbfc4ead 100644 --- a/recipes/ucsc-subcolumn/meta.yaml +++ b/recipes/ucsc-subcolumn/meta.yaml @@ -18,7 +18,7 @@ source: fn: "{{ program }}" # [osx] build: - number: 0 + number: 1 requirements: build: @@ -27,7 +27,7 @@ requirements: - libuuid # [linux] - mysql-connector-c # [linux] - openssl # [linux] - - zlib # [linux] + - zlib {{CONDA_ZLIB}}* # [linux] run: - libgcc # [linux] @@ -35,7 +35,7 @@ requirements: - libuuid # [linux] - mysql-connector-c # [linux] - openssl # [linux] - - zlib # [linux] + - zlib {{CONDA_ZLIB}}* # [linux] test: commands: diff --git a/recipes/ucsc-taillines/meta.yaml b/recipes/ucsc-taillines/meta.yaml index 85baf4476daa86..475872261a1193 100644 --- a/recipes/ucsc-taillines/meta.yaml +++ b/recipes/ucsc-taillines/meta.yaml @@ -18,7 +18,7 @@ source: fn: "{{ program }}" # [osx] build: - number: 0 + number: 1 requirements: build: @@ -27,7 +27,7 @@ requirements: - libuuid # [linux] - mysql-connector-c # [linux] - openssl # [linux] - - zlib # [linux] + - zlib {{CONDA_ZLIB}}* # [linux] run: - libgcc # [linux] @@ -35,7 +35,7 @@ requirements: - libuuid # [linux] - mysql-connector-c # [linux] - openssl # [linux] - - zlib # [linux] + - zlib {{CONDA_ZLIB}}* # [linux] test: commands: diff --git a/recipes/ucsc-tdbquery/meta.yaml b/recipes/ucsc-tdbquery/meta.yaml index f31668ecdf678c..12d6c28f256e8c 100644 --- a/recipes/ucsc-tdbquery/meta.yaml +++ b/recipes/ucsc-tdbquery/meta.yaml @@ -18,7 +18,7 @@ source: fn: "{{ program }}" # [osx] build: - number: 0 + number: 1 requirements: build: @@ -27,7 +27,7 @@ requirements: - libuuid # [linux] - mysql-connector-c # [linux] - openssl # [linux] - - zlib # [linux] + - zlib {{CONDA_ZLIB}}* # [linux] run: - libgcc # [linux] @@ -35,7 +35,7 @@ requirements: - libuuid # [linux] - mysql-connector-c # [linux] - openssl # [linux] - - zlib # [linux] + - zlib {{CONDA_ZLIB}}* # [linux] test: commands: diff --git a/recipes/ucsc-texthistogram/meta.yaml b/recipes/ucsc-texthistogram/meta.yaml index 739c0d115fff95..2335e3d6ee543b 100644 --- a/recipes/ucsc-texthistogram/meta.yaml +++ b/recipes/ucsc-texthistogram/meta.yaml @@ -18,7 +18,7 @@ source: fn: "{{ program }}" # [osx] build: - number: 0 + number: 1 requirements: build: @@ -27,7 +27,7 @@ requirements: - libuuid # [linux] - mysql-connector-c # [linux] - openssl # [linux] - - zlib # [linux] + - zlib {{CONDA_ZLIB}}* # [linux] run: - libgcc # [linux] @@ -35,7 +35,7 @@ requirements: - libuuid # [linux] - mysql-connector-c # [linux] - openssl # [linux] - - zlib # [linux] + - zlib {{CONDA_ZLIB}}* # [linux] test: commands: diff --git a/recipes/ucsc-ticktodate/meta.yaml b/recipes/ucsc-ticktodate/meta.yaml index 39b1d68431703a..d3ff7dbd5460a7 100644 --- a/recipes/ucsc-ticktodate/meta.yaml +++ b/recipes/ucsc-ticktodate/meta.yaml @@ -18,7 +18,7 @@ source: fn: "{{ program }}" # [osx] build: - number: 0 + number: 1 requirements: build: @@ -27,7 +27,7 @@ requirements: - libuuid # [linux] - mysql-connector-c # [linux] - openssl # [linux] - - zlib # [linux] + - zlib {{CONDA_ZLIB}}* # [linux] run: - libgcc # [linux] @@ -35,7 +35,7 @@ requirements: - libuuid # [linux] - mysql-connector-c # [linux] - openssl # [linux] - - zlib # [linux] + - zlib {{CONDA_ZLIB}}* # [linux] test: commands: diff --git a/recipes/ucsc-tolower/meta.yaml b/recipes/ucsc-tolower/meta.yaml index 87b754d68db2e5..d13b41b1f34dcf 100644 --- a/recipes/ucsc-tolower/meta.yaml +++ b/recipes/ucsc-tolower/meta.yaml @@ -18,7 +18,7 @@ source: fn: "{{ program }}" # [osx] build: - number: 0 + number: 1 requirements: build: @@ -27,7 +27,7 @@ requirements: - libuuid # [linux] - mysql-connector-c # [linux] - openssl # [linux] - - zlib # [linux] + - zlib {{CONDA_ZLIB}}* # [linux] run: - libgcc # [linux] @@ -35,7 +35,7 @@ requirements: - libuuid # [linux] - mysql-connector-c # [linux] - openssl # [linux] - - zlib # [linux] + - zlib {{CONDA_ZLIB}}* # [linux] test: commands: diff --git a/recipes/ucsc-toupper/meta.yaml b/recipes/ucsc-toupper/meta.yaml index add2ce727d75eb..7fa2881cf587b0 100644 --- a/recipes/ucsc-toupper/meta.yaml +++ b/recipes/ucsc-toupper/meta.yaml @@ -18,7 +18,7 @@ source: fn: "{{ program }}" # [osx] build: - number: 0 + number: 1 requirements: build: @@ -27,7 +27,7 @@ requirements: - libuuid # [linux] - mysql-connector-c # [linux] - openssl # [linux] - - zlib # [linux] + - zlib {{CONDA_ZLIB}}* # [linux] run: - libgcc # [linux] @@ -35,7 +35,7 @@ requirements: - libuuid # [linux] - mysql-connector-c # [linux] - openssl # [linux] - - zlib # [linux] + - zlib {{CONDA_ZLIB}}* # [linux] test: commands: diff --git a/recipes/ucsc-transmappsltogenepred/meta.yaml b/recipes/ucsc-transmappsltogenepred/meta.yaml index 7cc8cd317e5fa3..a10a10aa9d2cd6 100644 --- a/recipes/ucsc-transmappsltogenepred/meta.yaml +++ b/recipes/ucsc-transmappsltogenepred/meta.yaml @@ -18,7 +18,7 @@ source: fn: "{{ program }}" # [osx] build: - number: 0 + number: 1 requirements: build: @@ -27,7 +27,7 @@ requirements: - libuuid # [linux] - mysql-connector-c # [linux] - openssl # [linux] - - zlib # [linux] + - zlib {{CONDA_ZLIB}}* # [linux] run: - libgcc # [linux] @@ -35,7 +35,7 @@ requirements: - libuuid # [linux] - mysql-connector-c # [linux] - openssl # [linux] - - zlib # [linux] + - zlib {{CONDA_ZLIB}}* # [linux] test: commands: diff --git a/recipes/ucsc-trfbig/meta.yaml b/recipes/ucsc-trfbig/meta.yaml index d41b0a2d169059..84876f26af4737 100644 --- a/recipes/ucsc-trfbig/meta.yaml +++ b/recipes/ucsc-trfbig/meta.yaml @@ -18,7 +18,7 @@ source: fn: "{{ program }}" # [osx] build: - number: 0 + number: 1 requirements: build: @@ -27,7 +27,7 @@ requirements: - libuuid # [linux] - mysql-connector-c # [linux] - openssl # [linux] - - zlib # [linux] + - zlib {{CONDA_ZLIB}}* # [linux] run: - libgcc # [linux] @@ -35,7 +35,7 @@ requirements: - libuuid # [linux] - mysql-connector-c # [linux] - openssl # [linux] - - zlib # [linux] + - zlib {{CONDA_ZLIB}}* # [linux] test: commands: diff --git a/recipes/ucsc-twobitdup/meta.yaml b/recipes/ucsc-twobitdup/meta.yaml index c48219e7575455..3fab6ac1852bda 100644 --- a/recipes/ucsc-twobitdup/meta.yaml +++ b/recipes/ucsc-twobitdup/meta.yaml @@ -18,7 +18,7 @@ source: fn: "{{ program }}" # [osx] build: - number: 0 + number: 1 requirements: build: @@ -27,7 +27,7 @@ requirements: - libuuid # [linux] - mysql-connector-c # [linux] - openssl # [linux] - - zlib # [linux] + - zlib {{CONDA_ZLIB}}* # [linux] run: - libgcc # [linux] @@ -35,7 +35,7 @@ requirements: - libuuid # [linux] - mysql-connector-c # [linux] - openssl # [linux] - - zlib # [linux] + - zlib {{CONDA_ZLIB}}* # [linux] test: commands: diff --git a/recipes/ucsc-twobitinfo/meta.yaml b/recipes/ucsc-twobitinfo/meta.yaml index c74fe8e015e4cf..fcb032176da33e 100644 --- a/recipes/ucsc-twobitinfo/meta.yaml +++ b/recipes/ucsc-twobitinfo/meta.yaml @@ -18,7 +18,7 @@ source: fn: "{{ program }}" # [osx] build: - number: 0 + number: 1 requirements: build: @@ -27,7 +27,7 @@ requirements: - libuuid # [linux] - mysql-connector-c # [linux] - openssl # [linux] - - zlib # [linux] + - zlib {{CONDA_ZLIB}}* # [linux] run: - libgcc # [linux] @@ -35,7 +35,7 @@ requirements: - libuuid # [linux] - mysql-connector-c # [linux] - openssl # [linux] - - zlib # [linux] + - zlib {{CONDA_ZLIB}}* # [linux] test: commands: diff --git a/recipes/ucsc-twobitmask/meta.yaml b/recipes/ucsc-twobitmask/meta.yaml index ac10b52cb5b573..0c309c9933f7e1 100644 --- a/recipes/ucsc-twobitmask/meta.yaml +++ b/recipes/ucsc-twobitmask/meta.yaml @@ -18,7 +18,7 @@ source: fn: "{{ program }}" # [osx] build: - number: 0 + number: 1 requirements: build: @@ -27,7 +27,7 @@ requirements: - libuuid # [linux] - mysql-connector-c # [linux] - openssl # [linux] - - zlib # [linux] + - zlib {{CONDA_ZLIB}}* # [linux] run: - libgcc # [linux] @@ -35,7 +35,7 @@ requirements: - libuuid # [linux] - mysql-connector-c # [linux] - openssl # [linux] - - zlib # [linux] + - zlib {{CONDA_ZLIB}}* # [linux] test: commands: diff --git a/recipes/ucsc-twobittofa/meta.yaml b/recipes/ucsc-twobittofa/meta.yaml index e0088b4ec7035b..07923636d7f67c 100644 --- a/recipes/ucsc-twobittofa/meta.yaml +++ b/recipes/ucsc-twobittofa/meta.yaml @@ -18,7 +18,7 @@ source: fn: "{{ program }}" # [osx] build: - number: 0 + number: 1 requirements: build: @@ -27,7 +27,7 @@ requirements: - libuuid # [linux] - mysql-connector-c # [linux] - openssl # [linux] - - zlib # [linux] + - zlib {{CONDA_ZLIB}}* # [linux] run: - libgcc # [linux] @@ -35,7 +35,7 @@ requirements: - libuuid # [linux] - mysql-connector-c # [linux] - openssl # [linux] - - zlib # [linux] + - zlib {{CONDA_ZLIB}}* # [linux] test: commands: diff --git a/recipes/ucsc-validatefiles/meta.yaml b/recipes/ucsc-validatefiles/meta.yaml index 8d39d253a571d8..83a92608accb8e 100644 --- a/recipes/ucsc-validatefiles/meta.yaml +++ b/recipes/ucsc-validatefiles/meta.yaml @@ -18,7 +18,7 @@ source: fn: "{{ program }}" # [osx] build: - number: 0 + number: 1 requirements: build: @@ -27,7 +27,7 @@ requirements: - libuuid # [linux] - mysql-connector-c # [linux] - openssl # [linux] - - zlib # [linux] + - zlib {{CONDA_ZLIB}}* # [linux] run: - libgcc # [linux] @@ -35,7 +35,7 @@ requirements: - libuuid # [linux] - mysql-connector-c # [linux] - openssl # [linux] - - zlib # [linux] + - zlib {{CONDA_ZLIB}}* # [linux] test: commands: diff --git a/recipes/ucsc-validatemanifest/meta.yaml b/recipes/ucsc-validatemanifest/meta.yaml index 0e3b3ac169b7b3..d4e26d51a543a8 100644 --- a/recipes/ucsc-validatemanifest/meta.yaml +++ b/recipes/ucsc-validatemanifest/meta.yaml @@ -18,7 +18,7 @@ source: fn: "{{ program }}" # [osx] build: - number: 0 + number: 1 requirements: build: @@ -27,7 +27,7 @@ requirements: - libuuid # [linux] - mysql-connector-c # [linux] - openssl # [linux] - - zlib # [linux] + - zlib {{CONDA_ZLIB}}* # [linux] run: - libgcc # [linux] @@ -35,7 +35,7 @@ requirements: - libuuid # [linux] - mysql-connector-c # [linux] - openssl # [linux] - - zlib # [linux] + - zlib {{CONDA_ZLIB}}* # [linux] test: commands: diff --git a/recipes/ucsc-wigcorrelate/meta.yaml b/recipes/ucsc-wigcorrelate/meta.yaml index 9e8adb94f456e2..e961c681fa6808 100644 --- a/recipes/ucsc-wigcorrelate/meta.yaml +++ b/recipes/ucsc-wigcorrelate/meta.yaml @@ -18,7 +18,7 @@ source: fn: "{{ program }}" # [osx] build: - number: 0 + number: 1 requirements: build: @@ -27,7 +27,7 @@ requirements: - libuuid # [linux] - mysql-connector-c # [linux] - openssl # [linux] - - zlib # [linux] + - zlib {{CONDA_ZLIB}}* # [linux] run: - libgcc # [linux] @@ -35,7 +35,7 @@ requirements: - libuuid # [linux] - mysql-connector-c # [linux] - openssl # [linux] - - zlib # [linux] + - zlib {{CONDA_ZLIB}}* # [linux] test: commands: diff --git a/recipes/ucsc-wigtobigwig/meta.yaml b/recipes/ucsc-wigtobigwig/meta.yaml index 537b9051069a1f..e5e3dd299a326a 100644 --- a/recipes/ucsc-wigtobigwig/meta.yaml +++ b/recipes/ucsc-wigtobigwig/meta.yaml @@ -18,7 +18,7 @@ source: fn: "{{ program }}" # [osx] build: - number: 0 + number: 1 requirements: build: @@ -27,7 +27,7 @@ requirements: - libuuid # [linux] - mysql-connector-c # [linux] - openssl # [linux] - - zlib # [linux] + - zlib {{CONDA_ZLIB}}* # [linux] run: - libgcc # [linux] @@ -35,7 +35,7 @@ requirements: - libuuid # [linux] - mysql-connector-c # [linux] - openssl # [linux] - - zlib # [linux] + - zlib {{CONDA_ZLIB}}* # [linux] test: commands: diff --git a/recipes/ucsc-wordline/meta.yaml b/recipes/ucsc-wordline/meta.yaml index d9d06b56b56277..8be4914172a194 100644 --- a/recipes/ucsc-wordline/meta.yaml +++ b/recipes/ucsc-wordline/meta.yaml @@ -18,7 +18,7 @@ source: fn: "{{ program }}" # [osx] build: - number: 0 + number: 1 requirements: build: @@ -27,7 +27,7 @@ requirements: - libuuid # [linux] - mysql-connector-c # [linux] - openssl # [linux] - - zlib # [linux] + - zlib {{CONDA_ZLIB}}* # [linux] run: - libgcc # [linux] @@ -35,7 +35,7 @@ requirements: - libuuid # [linux] - mysql-connector-c # [linux] - openssl # [linux] - - zlib # [linux] + - zlib {{CONDA_ZLIB}}* # [linux] test: commands: diff --git a/recipes/ucsc-xmlcat/meta.yaml b/recipes/ucsc-xmlcat/meta.yaml index 0218780d0ac71f..c33e7fb8aaa19d 100644 --- a/recipes/ucsc-xmlcat/meta.yaml +++ b/recipes/ucsc-xmlcat/meta.yaml @@ -18,7 +18,7 @@ source: fn: "{{ program }}" # [osx] build: - number: 0 + number: 1 requirements: build: @@ -27,7 +27,7 @@ requirements: - libuuid # [linux] - mysql-connector-c # [linux] - openssl # [linux] - - zlib # [linux] + - zlib {{CONDA_ZLIB}}* # [linux] run: - libgcc # [linux] @@ -35,7 +35,7 @@ requirements: - libuuid # [linux] - mysql-connector-c # [linux] - openssl # [linux] - - zlib # [linux] + - zlib {{CONDA_ZLIB}}* # [linux] test: commands: diff --git a/recipes/ucsc-xmltosql/meta.yaml b/recipes/ucsc-xmltosql/meta.yaml index 74e6e93285ee53..db19e0783fb6d6 100644 --- a/recipes/ucsc-xmltosql/meta.yaml +++ b/recipes/ucsc-xmltosql/meta.yaml @@ -18,7 +18,7 @@ source: fn: "{{ program }}" # [osx] build: - number: 0 + number: 1 requirements: build: @@ -27,7 +27,7 @@ requirements: - libuuid # [linux] - mysql-connector-c # [linux] - openssl # [linux] - - zlib # [linux] + - zlib {{CONDA_ZLIB}}* # [linux] run: - libgcc # [linux] @@ -35,7 +35,7 @@ requirements: - libuuid # [linux] - mysql-connector-c # [linux] - openssl # [linux] - - zlib # [linux] + - zlib {{CONDA_ZLIB}}* # [linux] test: commands: diff --git a/recipes/variant-effect-predictor/build.sh b/recipes/variant-effect-predictor/build.sh index cb2ab7f3b63e80..f7e04f1be3aeb1 100644 --- a/recipes/variant-effect-predictor/build.sh +++ b/recipes/variant-effect-predictor/build.sh @@ -31,10 +31,11 @@ perl vep_install.pl -a a --NO_HTSLIB --CURL # Remove test data rm -rf t/ # Install plugins -wget --no-check-certificate https://raw.githubusercontent.com/Ensembl/VEP_plugins/release/87/CADD.pm -wget --no-check-certificate https://raw.githubusercontent.com/Ensembl/VEP_plugins/release/87/dbNSFP.pm -wget --no-check-certificate https://raw.githubusercontent.com/Ensembl/VEP_plugins/release/87/MaxEntScan.pm -wget --no-check-certificate https://raw.githubusercontent.com/Ensembl/VEP_plugins/release/87/GeneSplicer.pm -wget --no-check-certificate https://raw.githubusercontent.com/Ensembl/VEP_plugins/release/87/dbscSNV.pm -wget --no-check-certificate https://raw.githubusercontent.com/konradjk/loftee/master/LoF.pm -wget --no-check-certificate https://raw.githubusercontent.com/konradjk/loftee/master/splice_module.pl +WGET="wget --ca-certificate=$PREFIX/ssl/cert.pem" +$WGET https://raw.githubusercontent.com/Ensembl/VEP_plugins/release/87/CADD.pm +$WGET https://raw.githubusercontent.com/Ensembl/VEP_plugins/release/87/dbNSFP.pm +$WGET https://raw.githubusercontent.com/Ensembl/VEP_plugins/release/87/MaxEntScan.pm +$WGET https://raw.githubusercontent.com/Ensembl/VEP_plugins/release/87/GeneSplicer.pm +$WGET https://raw.githubusercontent.com/Ensembl/VEP_plugins/release/87/dbscSNV.pm +$WGET https://raw.githubusercontent.com/konradjk/loftee/v0.3-beta/LoF.pm +$WGET https://raw.githubusercontent.com/konradjk/loftee/v0.3-beta/splice_module.pl diff --git a/recipes/variant-effect-predictor/meta.yaml b/recipes/variant-effect-predictor/meta.yaml index 1a5f1ca8d2fd99..33cea4229e87d5 100644 --- a/recipes/variant-effect-predictor/meta.yaml +++ b/recipes/variant-effect-predictor/meta.yaml @@ -5,26 +5,27 @@ package: source: fn: vep-87.zip url: https://github.com/Ensembl/ensembl-tools/archive/release/87.zip + sha256: e0675f21e102335e973fc3641b946adb5c9082d833fe22c7e1515326b3a08cfb build: - number: 0 + number: 1 skip: True # [osx] requirements: build: - gnu-wget - gcc - - perl-threaded + - perl - perl-file-copy-recursive - perl-archive-extract - perl-archive-zip - perl-lwp-simple - perl-lwp-protocol-https - - zlib - - htslib + - zlib {{CONDA_ZLIB}}* + - htslib {{ CONDA_HTSLIB }}* - unzip run: - - perl-threaded + - perl - perl-bioperl ==1.6.924 4 - perl-bio-db-hts - perl-encode-locale @@ -43,8 +44,8 @@ requirements: - perl-lwp-protocol-https - perl-statistics-descriptive - perl-time-hires - - zlib - - htslib + - zlib {{CONDA_ZLIB}}* + - htslib {{ CONDA_HTSLIB }}* test: commands: diff --git a/recipes/variantbam/meta.yaml b/recipes/variantbam/meta.yaml index f473a1b2c6282b..34548e36d497b7 100644 --- a/recipes/variantbam/meta.yaml +++ b/recipes/variantbam/meta.yaml @@ -5,7 +5,7 @@ package: version: {{ version }} build: - number: 1 + number: 2 skip: True # [osx] source: @@ -20,14 +20,14 @@ source: requirements: build: - gcc # [not osx] - - xz - - bzip2 - - zlib + - xz {{CONDA_XZ}}* + - bzip2 {{CONDA_BZIP2}}* + - zlib {{CONDA_ZLIB}}* run: - libgcc # [not osx] - - xz - - bzip2 - - zlib + - xz {{CONDA_XZ}}* + - bzip2 {{CONDA_BZIP2}}* + - zlib {{CONDA_ZLIB}}* test: commands: diff --git a/recipes/vcf2maf/meta.yaml b/recipes/vcf2maf/meta.yaml index cf0b24c7cae11d..11f256f2c0c550 100644 --- a/recipes/vcf2maf/meta.yaml +++ b/recipes/vcf2maf/meta.yaml @@ -1,9 +1,9 @@ {% set name = "vcf2maf" %} {% set version = "1.6.15" %} -{% set sha256hash = "44cce0c2f13fea615f31ecf52a2b968d0dd151f9246d6123723fc1cfef7e216f" %} +{% set sha256hash = "9464dd6a190570018904fc63deeec0b95f3377c0bf9bf60fb70d621fcdd84c7b" %} build: - number: 0 + number: 1 skip: True # [osx] since variant-effect-predictor is not there yet package: diff --git a/recipes/vcflib/meta.yaml b/recipes/vcflib/meta.yaml index f266f8c96107f7..fdbbc0fcbd3015 100644 --- a/recipes/vcflib/meta.yaml +++ b/recipes/vcflib/meta.yaml @@ -7,16 +7,16 @@ source: git_rev: 3e03c7a10098b3888aaa258d4e339ddcdbf3b951 build: - number: 0 + number: 1 skip: True # [osx] requirements: build: - gcc # [linux] - llvm # [osx] - - zlib + - zlib {{CONDA_ZLIB}}* run: - - zlib + - zlib {{CONDA_ZLIB}}* - libgcc # [linux] test: diff --git a/recipes/vcftools/0.1.10/meta.yaml b/recipes/vcftools/0.1.10/meta.yaml index 78b1a087329622..4b12a33bc03460 100644 --- a/recipes/vcftools/0.1.10/meta.yaml +++ b/recipes/vcftools/0.1.10/meta.yaml @@ -8,19 +8,19 @@ source: sha256: 0680dd38dc41a9fdbb5ddb22d79e0314009e5e464a5bb7b6da4845cce0181a23 build: - number: 0 + number: 1 requirements: build: - gcc # [not osx] - llvm # [osx] - perl - - zlib + - zlib {{CONDA_ZLIB}}* - perl-vcftools-vcf ==0.797 run: - libgcc # [not osx] - - zlib + - zlib {{CONDA_ZLIB}}* - perl-vcftools-vcf ==0.797 test: diff --git a/recipes/vcftools/0.1.11/meta.yaml b/recipes/vcftools/0.1.11/meta.yaml index 80b044edb41e51..eaa3622171d742 100644 --- a/recipes/vcftools/0.1.11/meta.yaml +++ b/recipes/vcftools/0.1.11/meta.yaml @@ -8,16 +8,16 @@ source: sha256: 81b98c8bc93e366e2f0b14eb78e2736ae1c790176939eef88dbf0546ab952aab build: - number: 1 + number: 2 requirements: build: - - zlib + - zlib {{CONDA_ZLIB}}* - perl - perl-vcftools-vcf ==0.840 run: - - zlib + - zlib {{CONDA_ZLIB}}* - perl-vcftools-vcf ==0.840 test: diff --git a/recipes/vcftools/meta.yaml b/recipes/vcftools/meta.yaml index 5e8d90526761a7..b494e7ea25760b 100644 --- a/recipes/vcftools/meta.yaml +++ b/recipes/vcftools/meta.yaml @@ -12,7 +12,7 @@ source: sha256: {{ sha256 }} build: - number: 0 + number: 1 requirements: build: diff --git a/recipes/vdjer/meta.yaml b/recipes/vdjer/meta.yaml index c0c1dd0433bb0c..00d853f361cc6d 100644 --- a/recipes/vdjer/meta.yaml +++ b/recipes/vdjer/meta.yaml @@ -9,18 +9,18 @@ source: build: - number: 0 + number: 1 skip: True # [osx] requirements: build: - gcc # [not osx] - - zlib + - zlib {{CONDA_ZLIB}}* run: - libgcc # [not osx] - - zlib + - zlib {{CONDA_ZLIB}}* test: diff --git a/recipes/verifybamid/meta.yaml b/recipes/verifybamid/meta.yaml index 43dd5fbc1917a4..57ed5a3cf03ad2 100644 --- a/recipes/verifybamid/meta.yaml +++ b/recipes/verifybamid/meta.yaml @@ -7,7 +7,7 @@ package: version: {{ version }} build: - number: 0 + number: 1 source: fn: {{ name }}LibStatGen.{{ version }}.tgz @@ -18,11 +18,11 @@ requirements: build: - gcc # [not osx] - llvm # [osx] - - zlib + - zlib {{CONDA_ZLIB}}* run: - libgcc # [not osx] - - zlib + - zlib {{CONDA_ZLIB}}* test: commands: diff --git a/recipes/verse/meta.yaml b/recipes/verse/meta.yaml index 7694f1fee43066..5fcdcef7e41c8d 100644 --- a/recipes/verse/meta.yaml +++ b/recipes/verse/meta.yaml @@ -7,17 +7,17 @@ source: git_rev: e390069b3d1c44340c086c52f5a9c977c8ab0216 build: - number: 0 + number: 1 requirements: build: - gcc # [not osx] - llvm # [osx] - - zlib + - zlib {{CONDA_ZLIB}}* run: - libgcc # [not osx] - - zlib + - zlib {{CONDA_ZLIB}}* test: commands: diff --git a/recipes/vphaser2/meta.yaml b/recipes/vphaser2/meta.yaml index 2c8564533b8dd4..a0669abb2c73ba 100644 --- a/recipes/vphaser2/meta.yaml +++ b/recipes/vphaser2/meta.yaml @@ -3,25 +3,30 @@ about: license: 'single user license for academic non-commercial research purposes only' license_file: 'V-Phaser-2.0/license/V_Phaser_2_License_v20130317.pdf' summary: 'V-Phaser 2 is a tool to call variants in genetically heterogeneous populations from ultra-deep sequence data' + package: name: "vphaser2" version: '2.0' + source: url: https://github.com/broadinstitute/v-phaser2/archive/6b5483a8e1a9bf24061a0aa211fee18e6b845668.tar.gz #[osx or linux64] md5: fd22b1c4403903576e62defb51b6ae32 - #git_url: https://github.com/broadinstitute/v-phaser2.git #[osx or linux64] + build: - number: 4 + number: 6 rpaths: - "$PREFIX/opt/$PKG_NAME-$PKG_VERSION" - lib/ + string: bamtools{{CONDA_BAMTOOLS}}_{{PKG_BUILDNUM}} + requirements: build: - - bamtools - - zlib + - bamtools {{ CONDA_BAMTOOLS }}* + - zlib {{ CONDA_ZLIB }}* run: - - bamtools - - zlib + - bamtools {{ CONDA_BAMTOOLS }}* + - zlib {{ CONDA_ZLIB }}* + test: commands: - 'vphaser2 | grep "BAM file"' diff --git a/recipes/vsearch/meta.yaml b/recipes/vsearch/meta.yaml index e4c7196c743bdd..981dfdcc28894a 100644 --- a/recipes/vsearch/meta.yaml +++ b/recipes/vsearch/meta.yaml @@ -1,6 +1,6 @@ {% set name = "vsearch" %} -{% set version = "2.6.0" %} -{% set hash = "d9fa6907aa0535bff8578a6a38d948569e13cdcd7db270c604bccfa6f77df466" %} +{% set version = "2.7.0" %} +{% set hash = "a50577ee89d3f663b40f5f6749c54801666faa0bb54c40bd0286bb823b5a4314" %} package: name: {{ name|lower }} @@ -12,7 +12,7 @@ source: sha256: {{ hash }} build: - number: 0 + number: 1 requirements: build: diff --git a/recipes/vt/meta.yaml b/recipes/vt/meta.yaml index 87f410f316395c..d07362b2389c2a 100644 --- a/recipes/vt/meta.yaml +++ b/recipes/vt/meta.yaml @@ -5,16 +5,20 @@ package: source: fn: vt-15f90de5.tar.gz url: https://github.com/atks/vt/archive/15f90de5.tar.gz + sha256: a135be9a9b3094e21e92e915633e114a794d197172093fcab4c0999b97fa7e87 build: - number: 1 + number: 2 skip: True # [osx] requirements: build: - - zlib + - gcc # [not osx] + - llvm # [osx] + - zlib {{CONDA_ZLIB}}* run: - - zlib + - libgcc # [not osx] + - zlib {{CONDA_ZLIB}}* test: commands: diff --git a/recipes/watchdog-wms/meta.yaml b/recipes/watchdog-wms/meta.yaml index 0a7f4ac377530c..a32be3a72acd99 100644 --- a/recipes/watchdog-wms/meta.yaml +++ b/recipes/watchdog-wms/meta.yaml @@ -1,5 +1,5 @@ {% set name = "watchdog-wms" %} -{% set version = "1.2.5" %} +{% set version = "1.2.6" %} about: home: https://www.bio.ifi.lmu.de/watchdog @@ -23,12 +23,12 @@ package: version: {{ version }} build: - number: 1 + number: 0 source: fn: {{ name }}-{{ version }}.tar.gz url: https://github.com/klugem/watchdog/archive/v{{ version }}.tar.gz - sha256: f2141432dee56be6af1edbde9600409e85bdca2bb42fd830edfd9320b41e63c9 + sha256: 14ecc514f889fac471fc404b76b5f11fb06b201ee969a5ad0b23cde3cbe107ec requirements: build: diff --git a/recipes/wgsim/meta.yaml b/recipes/wgsim/meta.yaml index 92ec47070f665e..a7c79f24da5e58 100644 --- a/recipes/wgsim/meta.yaml +++ b/recipes/wgsim/meta.yaml @@ -12,11 +12,11 @@ requirements: - gcc # [not osx] - llvm # [osx] - libgcc # [not osx] - - zlib + - zlib {{CONDA_ZLIB}}* run: - libgcc # [not osx] - - zlib + - zlib {{CONDA_ZLIB}}* test: commands: diff --git a/recipes/wiggletools/meta.yaml b/recipes/wiggletools/meta.yaml index c86ed5dc3d5b73..da579c25ed5862 100644 --- a/recipes/wiggletools/meta.yaml +++ b/recipes/wiggletools/meta.yaml @@ -6,7 +6,7 @@ package: version: {{ version }} build: - number: 0 + number: 1 source: fn: wiggletools-{{ version }}.tar.gz diff --git a/recipes/xtandem/meta.yaml b/recipes/xtandem/meta.yaml index 2d30d6b4cb0ad0..ed1bb78b05273d 100644 --- a/recipes/xtandem/meta.yaml +++ b/recipes/xtandem/meta.yaml @@ -8,12 +8,12 @@ package: version: 15.12.15.2 build: - number: 0 + number: 1 skip: False source: fn: tandem-linux-15-12-15-2.zip - url: ftp://ftp.thegpm.org/projects/tandem/source/tandem-linux-15-12-15-2.zip + url: https://depot.galaxyproject.org/software/xtandem/xtandem_15.12.15.2_src_all.zip md5: 40058cd84fc3f56d671d32ff393f7aa3 patches: - makefile.patch @@ -21,11 +21,11 @@ source: requirements: build: - gcc - - zlib + - zlib {{CONDA_ZLIB}}* - expat run: - libgcc - - zlib + - zlib {{CONDA_ZLIB}}* - expat test: diff --git a/scripts/env_matrix.yml b/scripts/env_matrix.yml index 9dcb4e90595887..17a60f08109422 100644 --- a/scripts/env_matrix.yml +++ b/scripts/env_matrix.yml @@ -2,7 +2,7 @@ CONDA_PY: - 27 - 35 - 36 -CONDA_HTSLIB: "1.6" +CONDA_HTSLIB: "1.7" CONDA_BOOST: "1.64" CONDA_R: "3.4.1" CONDA_PERL: "5.22.0" @@ -12,6 +12,7 @@ CONDA_GSL: "1.16" CONDA_GMP: "5.1" CONDA_HDF5: "1.8.17" MACOSX_DEPLOYMENT_TARGET: "10.9" -CONDA_ZLIB: "1.2.8" +CONDA_ZLIB: "1.2.11" CONDA_BZIP2: "1.0" CONDA_XZ: "5.2" +CONDA_BAMTOOLS: "2.4.1" diff --git a/scripts/ucsc/template-meta.yaml b/scripts/ucsc/template-meta.yaml index d7bcc30b8b7c63..428a866b8bfa45 100644 --- a/scripts/ucsc/template-meta.yaml +++ b/scripts/ucsc/template-meta.yaml @@ -27,7 +27,7 @@ requirements: - libuuid # [linux] - mysql-connector-c # [linux] - openssl # [linux] - - zlib # [linux] + - zlib {{CONDA_ZLIB}}* # [linux] run: - libgcc # [linux] @@ -35,7 +35,7 @@ requirements: - libuuid # [linux] - mysql-connector-c # [linux] - openssl # [linux] - - zlib # [linux] + - zlib {{CONDA_ZLIB}}* # [linux] test: commands: