Bumped STAR-Fusion version #6198
Merged
Conversation
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Member
micknudsen
commented
Oct 2, 2017
micknudsen
commented
- I have read the guidelines for bioconda recipes.
- This PR adds a new recipe.
- AFAIK, this recipe is directly relevant to the biological sciences (otherwise, please submit to the more general purpose conda-forge channel).
- This PR updates an existing recipe.
- This PR does something else (explain below).
|
Thank you! |
daler
added a commit
that referenced
this pull request
Oct 11, 2017
* 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 MultiQC/MultiQC#561 and MultiQC/MultiQC#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: bcbio/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)
daler
added a commit
that referenced
this pull request
Oct 11, 2017
* 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 MultiQC/MultiQC#561 and MultiQC/MultiQC#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: bcbio/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
bgruening
pushed a commit
that referenced
this pull request
Oct 27, 2017
* 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 MultiQC/MultiQC#561 and MultiQC/MultiQC#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: bcbio/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 MultiQC/MultiQC#561 and MultiQC/MultiQC#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: bcbio/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
bgruening
pushed a commit
that referenced
this pull request
Nov 17, 2017
* 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 MultiQC/MultiQC#561 and MultiQC/MultiQC#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: bcbio/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 MultiQC/MultiQC#561 and MultiQC/MultiQC#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: bcbio/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
bgruening
pushed a commit
that referenced
this pull request
Nov 22, 2017
* 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 MultiQC/MultiQC#561 and MultiQC/MultiQC#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: bcbio/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 MultiQC/MultiQC#561 and MultiQC/MultiQC#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: bcbio/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
bgruening
pushed a commit
that referenced
this pull request
Dec 19, 2017
* 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…
bgruening
added a commit
that referenced
this pull request
Dec 21, 2017
* 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.
* …
bgruening
added a commit
that referenced
this pull request
Feb 15, 2018
* 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.
* …
Colelyman
added a commit
to Colelyman/bioconda-recipes
that referenced
this pull request
Feb 28, 2018
commit 92d9eafcca7e6dc208d6163566a259318388cd20
Merge: aeb3a66bf 384354b74
Author: Cole Lyman <cole@colelyman.com>
Date: Tue Feb 27 21:13:37 2018 -0700
Merge branch 'master' of github.com:Colelyman/bioconda-recipes
commit aeb3a66bfdd03807f80a4895e0074963ea015bce
Author: Ralf Weber <RJMW@users.noreply.github.com>
Date: Wed Feb 28 00:55:39 2018 +0000
Bump version MetFrag to 2.4.2 (#8022)
commit 88497c107cdb5bec6ccc8c081f2bd6d3fd4e9055
Author: Dan Fornika <dfornika@gmail.com>
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 <wolffj@informatik.uni-freiburg.de>
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 <matthew-fogel@users.noreply.github.com>
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 <micknudsen@gmail.com>
Date: Tue Feb 27 20:14:27 2018 +0100
Bumped GATK version (#8019)
commit e7805136f0152d62f9c9e932826a43194995fd25
Author: Daniel Cooke <dcooke@well.ox.ac.uk>
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 <jk@well.ox.ac.uk>
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 <cbrisl@gmail.com>
Date: Tue Feb 27 01:26:53 2018 -0800
update BBMap (#8009)
commit 4a85ceca5b18d26821b855521efe6513fb7a62b2
Author: Andreas Sjödin <andreas.sjodin@gmail.com>
Date: Tue Feb 27 00:28:59 2018 +0100
Bump flye (#8011)
commit 58cdd6d8ac5df8b690dbaa270b61a143cb78ee13
Author: Karel Břinda <kbrinda@hsph.harvard.edu>
Date: Mon Feb 26 18:25:16 2018 -0500
SamSift 0.2.5 (#8012)
commit 9de0e8f82cca09055b361e70bd529cd10664bff9
Author: Michael T. Wolfinger <michael@wolfinger.eu>
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 <andreas.sjodin@gmail.com>
Date: Mon Feb 26 21:16:01 2018 +0100
Bump racon (#8010)
commit 125077444ac6065c86edf598ab4b360a7ccd18ca
Author: Renan Valieris <rvalieris@users.noreply.github.com>
Date: Mon Feb 26 14:59:50 2018 -0300
rebuild filtlong (#8005)
commit 5271a61515db3625a7498f3e27d5912bd0b193c5
Author: Will Rowe <will.rowe@stfc.ac.uk>
Date: Mon Feb 26 17:45:34 2018 +0000
updating groot to v0.2 (#8004)
commit f2acce2e072970d78d5186bb3d46638d31d18dd8
Author: Renan Valieris <rvalieris@users.noreply.github.com>
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 <christian@brueffer.io>
Date: Mon Feb 26 14:59:15 2018 +0100
Add bioconductor-hapfabia. (#8000)
commit 57602a6e0fe7d591872bd55118eed017e741ef51
Author: Christian Brueffer <christian@brueffer.io>
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 <bjoern@gruenings.eu>
Date: Mon Feb 26 11:44:48 2018 +0100
rebuild coreutils (#7999)
commit 17cd3140f4ac95813306ab0f1eae87c3feb26824
Author: Andreas Sjödin <andreas.sjodin@gmail.com>
Date: Mon Feb 26 00:25:32 2018 +0100
Bump sourmash (#7998)
commit f3f09ef56fd0a43a6181f2412bf0090f8f276165
Author: Andreas Sjödin <andreas.sjodin@gmail.com>
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 <jdblischak@gmail.com>
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 <lh3@me.com>
Date: Sun Feb 25 10:23:07 2018 -0500
Updated minimap2 and mappy to v2.9 (#7996)
commit f9d194d5d051c8933293cda36fd262ba21da6659
Author: Brad Chapman <chapmanb@fastmail.com>
Date: Sun Feb 25 05:11:01 2018 -0500
Update fastp 0.12.3 with polyG improvements (#7995)
commit ade4a2b3d53de77e2f9f6b0b4b8a5ed7082d97cc
Author: rspreafico <rspreafico@users.noreply.github.com>
Date: Fri Feb 23 22:01:35 2018 -0800
update shortstack (#7994)
commit 00ee08eb57545fa90b4a12df06ef58eeb3b01e53
Author: Yasset Perez-Riverol <ypriverol@gmail.com>
Date: Sat Feb 24 01:57:11 2018 +0000
identifiers added to the abyss container (#7940)
commit 2d8243356ad528334e7b0731639de9624f8ca9ad
Author: Slugger70 <slugger70@gmail.com>
Date: Sat Feb 24 08:35:38 2018 +1100
chewBBACA version bump to 2.0.6 (#7982)
commit 0affd3550e5d08079bc14f55c35d527eabdef987
Author: Renan Valieris <rvalieris@users.noreply.github.com>
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 <krthornt@uci.edu>
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 <eclarke@users.noreply.github.com>
Date: Fri Feb 23 12:57:06 2018 -0500
new rbt release (#7990)
commit 62ff725b6a4712d36e8f5f3f4a11ca21ca06b56c
Author: Christian Brueffer <christian@brueffer.io>
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 <davide.chicco@gmail.com>
Date: Fri Feb 23 11:50:51 2018 -0500
behst2.9 (#7988)
commit 4880c5feb15a0dbf550b02b9d76f94662d48ae4b
Author: David Laehnemann <david.laehnemann@hhu.de>
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 <christian@brueffer.io>
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 <chapmanb@fastmail.com>
Date: Fri Feb 23 06:50:06 2018 -0500
Update: bcbio with effects/trim CWL support (#7980)
commit 5462f14636dcc660915d6537124d392e4b293c1b
Author: Davide Chicco <davide.chicco@gmail.com>
Date: Thu Feb 22 18:32:42 2018 -0500
behst2.8 (#7977)
commit 6918532f77613c5f9b172237f15904c71f90743f
Author: Andreas Sjödin <andreas.sjodin@gmail.com>
Date: Thu Feb 22 22:40:30 2018 +0100
Bump swga (#7976)
commit a56e2c7d52e886140c30ca3596df07f5e2236d0d
Author: zachcp <zachcp@users.noreply.github.com>
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 <davide.chicco@gmail.com>
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 <p.j.a.cock@googlemail.com>
Date: Thu Feb 22 18:34:33 2018 +0000
kodoja v0.0.3 (#7970)
commit 1e519214eb78d06b8e6289a5f2ad348c0cfcd489
Author: Michael T. Wolfinger <michael@wolfinger.eu>
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 <andreas.sjodin@gmail.com>
Date: Thu Feb 22 17:19:08 2018 +0100
Bump racon to 1.0.0 (#7969)
commit e37eb5ae15378e3a34c9949d8b9d9b1894dc5e5b
Author: Gildas Le Corguillé <lecorguille@users.noreply.github.com>
Date: Thu Feb 22 13:43:46 2018 +0100
add r-asics (#7953)
commit c7223a272e58798bfed4f0709fbddad2f151ac32
Author: Michael Kluge <klugem@users.noreply.github.com>
Date: Thu Feb 22 13:25:13 2018 +0100
new watchdog release 1.2.6 (#7966)
commit c2656db73dfea609d70e584817e5dc3a1b470240
Author: Will Rowe <will.rowe@stfc.ac.uk>
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 <shenwei356@gmail.com>
Date: Thu Feb 22 16:18:17 2018 +0800
update csvtk to v0.13.0 (#7964)
commit 6a5b6781441426c3a209fbe2515c70fcfc4c49d0
Author: Jens Preußner <jenzopr@users.noreply.github.com>
Date: Thu Feb 22 08:39:14 2018 +0100
Bumped comb-p version to 0.48 (#7958)
commit 4602ca450dc4d8f14afe00a543eeb1a18a03610f
Author: Michael T. Wolfinger <michael@wolfinger.eu>
Date: Wed Feb 21 21:59:38 2018 +0100
added tests to bio-perl-viennangs(#7961)
commit 081cd7437bd2871de85b37ee88164e80417bbdbf
Author: Michael T. Wolfinger <michael@wolfinger.eu>
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 <mail@marcelm.net>
Date: Wed Feb 21 18:23:37 2018 +0100
Cutadapt 1.16 (#7957)
commit 1b963b5d872c56bdebb568e4898c210cff0f3c61
Author: Karl Nordström <karl.nordstrom@gmail.com>
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 <michael@wolfinger.eu>
Date: Wed Feb 21 17:39:57 2018 +0100
add recipe for perl-file-share (#7959)
commit c6f951bb16cafd902ee77954ebddfd38741dfab0
Author: Johannes Köster <johannes.koester@tu-dortmund.de>
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 <michael@wolfinger.eu>
Date: Tue Feb 20 22:44:35 2018 +0100
add recipe for perl-ipc-cmd (#7951)
commit 9185d701d3256ac16fc1738ee8ccf9c42e944a27
Author: David Laehnemann <david.laehnemann@hhu.de>
Date: Tue Feb 20 21:27:55 2018 +0100
prosolo: update to version 0.4.0 (#7948)
commit 1d4480049a8d83a7dc8352e1e71c7186fa1028e1
Author: Florian Eggenhofer <egg@informatik.uni-freiburg.de>
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 <michael@wolfinger.eu>
Date: Tue Feb 20 20:06:29 2018 +0100
add perl-module-load-conditional 0.68 (#7946)
commit 811a844ae0b2b4f4b3ffd33500bce4cc54e6ab0c
Author: Davide Chicco <davide.chicco@gmail.com>
Date: Tue Feb 20 13:11:59 2018 -0500
behst2.6 (#7945)
commit 8bc76775fdec2f68aabbf15003ddb92a7fb7fbcc
Author: Michael T. Wolfinger <michael@wolfinger.eu>
Date: Tue Feb 20 18:53:46 2018 +0100
add recipe for perl-module-corelist (#7944)
commit f4c57db142c9521d551eee2c3114badf40bcde76
Author: Philippe Bordron <pbordron@users.noreply.github.com>
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 <michael@wolfinger.eu>
Date: Tue Feb 20 18:20:46 2018 +0100
add recipe for perl-test-file-contents (#7943)
commit 0f8cb2039fcdc26780a7f3ee00b18fcc341be44b
Author: Karl Nordström <karl.nordstrom@gmail.com>
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 <davide.chicco@gmail.com>
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 <christian@brueffer.io>
Date: Tue Feb 20 15:27:07 2018 +0100
Add bioconductor-flowq. (#7936)
commit 9ea7be364e28ce29d217225d3dd418b820d95c44
Author: Christian Brueffer <christian@brueffer.io>
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 <christian@brueffer.io>
Date: Tue Feb 20 14:06:10 2018 +0100
Update Picard to 2.17.10. (#7934)
commit 43fcd91ab60028c3b366f7d0612e4f3e47d26436
Author: Brad Chapman <chapmanb@fastmail.com>
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 <RJMW@users.noreply.github.com>
Date: Tue Feb 20 11:16:06 2018 +0000
Bump version dimspy (#7932)
commit 368ffd42acbabd16ad5e6d2467d6145d24e6e94d
Author: Michael T. Wolfinger <michael@wolfinger.eu>
Date: Tue Feb 20 11:52:54 2018 +0100
add perl-test-prereq (#7931)
commit 8fa27a8fac754d07e2152fa2f64f8c082082bf91
Author: Michael T. Wolfinger <michael@wolfinger.eu>
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 <michael@wolfinger.eu>
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 <michael@wolfinger.eu>
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 <michael@wolfinger.eu>
Date: Tue Feb 20 08:11:30 2018 +0100
add perl-class-xsaccessor (#7925)
commit ca62523f8b3dc86a88dd6c989bbeed7d1c544ee5
Author: Christian Brueffer <christian@brueffer.io>
Date: Tue Feb 20 00:59:57 2018 +0100
Add r-tidygenomics. (#7929)
commit 831566d4f04e7e6dd079eb4d88c24af275ed3d43
Author: ArneKr <arnekratz@hotmail.de>
Date: Mon Feb 19 21:34:12 2018 +0100
Added recipe for cisPath (#7875)
commit 68ea9b79d9ff32098aee0dd5dffc374d0315480a
Author: ArneKr <arnekratz@hotmail.de>
Date: Mon Feb 19 21:33:46 2018 +0100
Added recipe for ClassifyR (#7874)
commit 40d1c2e175e20ba8a8691aaef165f166d9901ffb
Author: ArneKr <arnekratz@hotmail.de>
Date: Mon Feb 19 21:33:33 2018 +0100
Added recipe for CINdex (#7876)
commit a0168ce576775bb4a5ed6c0ba267a6ece8de8324
Author: ArneKr <arnekratz@hotmail.de>
Date: Mon Feb 19 21:33:19 2018 +0100
Added recipe for chromstaR (#7877)
commit 94080b4a78ede7f03a4c18a2227e40415acad25b
Author: ArneKr <arnekratz@hotmail.de>
Date: Mon Feb 19 21:33:03 2018 +0100
Added recipe for ChromHeatMap (#7878)
commit 38b8497d04efadbfc3d186413b6aa9832613664b
Author: ArneKr <arnekratz@hotmail.de>
Date: Mon Feb 19 21:32:29 2018 +0100
Added recipe for chopsticks (#7879)
commit 395d53cd6dc5f56809c5446e7f1a67c3ae4982b6
Author: ArneKr <arnekratz@hotmail.de>
Date: Mon Feb 19 21:31:56 2018 +0100
Added recipe for CGHnormaliter (#7882)
commit 4944fedba12247cd6c62a443ae39e88a9b0a8167
Author: ArneKr <arnekratz@hotmail.de>
Date: Mon Feb 19 21:30:47 2018 +0100
Added recipe for iCOBRA (#7883)
commit b37ab5be03b7eeb5366d01ddaa03982461eab05a
Author: ArneKr <arnekratz@hotmail.de>
Date: Mon Feb 19 21:30:33 2018 +0100
Added recipe for iChip (#7884)
commit 8680b5e53fc79b8a08dcd05421154802112029b1
Author: ArneKr <arnekratz@hotmail.de>
Date: Mon Feb 19 21:15:39 2018 +0100
Added recipe for cleanUpdTSeq (#7873)
commit 41dd406278999ac768d15ffc47ece1a99b360598
Author: ArneKr <arnekratz@hotmail.de>
Date: Mon Feb 19 21:15:17 2018 +0100
Added recipe for clonotypeR (#7872)
commit d22bed87ef04a16dc6ffa46978425f743e863b43
Author: ArneKr <arnekratz@hotmail.de>
Date: Mon Feb 19 21:14:57 2018 +0100
Added recipe for clstutils (#7871)
commit 19d5661362a63a572ce51b254e073b5a5fd2d4b5
Author: ArneKr <arnekratz@hotmail.de>
Date: Mon Feb 19 21:14:36 2018 +0100
Added recipe for ibh (#7885)
commit d9087168d9ed8bdb480f9df2668ed879b8e91708
Author: ArneKr <arnekratz@hotmail.de>
Date: Mon Feb 19 21:14:12 2018 +0100
Added recipe for iASeq (#7886)
commit 873f4af0e3aad26a7839fe80b144b4ab92a91765
Author: ArneKr <arnekratz@hotmail.de>
Date: Mon Feb 19 21:12:50 2018 +0100
Added recipe for CancerInSilico (#7887)
commit 649b44ce2edd2aa702f7ff6d1bcf17e5bf28b87e
Author: ArneKr <arnekratz@hotmail.de>
Date: Mon Feb 19 21:12:37 2018 +0100
Added recipe for BUS (#7888)
commit 60aaee4246659bd07a3dba3373fec18868f5d9a5
Author: ArneKr <arnekratz@hotmail.de>
Date: Mon Feb 19 21:12:26 2018 +0100
Added recipe for BufferedMatrixMethods (#7889)
commit 63270220ff728ba221cc6d68f662d48fc98ccd67
Author: ArneKr <arnekratz@hotmail.de>
Date: Mon Feb 19 21:11:47 2018 +0100
Added recipe for BrowserVizDemo (#7890)
commit 0dd4f6cc5a10a85ff0f8924ffe28420cf838d3a5
Author: ArneKr <arnekratz@hotmail.de>
Date: Mon Feb 19 21:11:30 2018 +0100
Added recipe for bridge (#7891)
commit 1732cad70dda834e7d08fa50da8a5707e5332617
Author: ArneKr <arnekratz@hotmail.de>
Date: Mon Feb 19 21:10:52 2018 +0100
Added recipe for BrainStars (#7892)
commit 1521cde047f286dca20457ee0abd28ae6ba286df
Author: ArneKr <arnekratz@hotmail.de>
Date: Mon Feb 19 21:10:41 2018 +0100
Added recipe for BiRewire (#7893)
commit e56203461322252832f436a95948c7f2cb6dd03a
Author: ArneKr <arnekratz@hotmail.de>
Date: Mon Feb 19 21:10:21 2018 +0100
Added recipe for BioQC (#7895)
commit bb6791a311a4e258bb514e0c40ef6355197fd701
Author: ArneKr <arnekratz@hotmail.de>
Date: Mon Feb 19 20:09:52 2018 +0100
Added recipe for biosvd (#7894)
commit 7487c126415414581bd5cdbdb00ac455e7602c6c
Author: ArneKr <arnekratz@hotmail.de>
Date: Mon Feb 19 20:09:40 2018 +0100
Added recipe for hopach (#7901)
commit 56792d451e88c3acc7658cccaed54395f540a6f8
Author: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
Date: Mon Feb 19 20:06:32 2018 +0100
nextflow 0.27.6 (#7864)
commit 78cacc91edf17111c69c6b344bffa35fc8181ead
Author: ArneKr <arnekratz@hotmail.de>
Date: Mon Feb 19 20:06:04 2018 +0100
Added recipe for BioMVCClass (#7896)
commit 356f46fd181495bae0f2f82a11258f82c8e2e7ac
Author: ArneKr <arnekratz@hotmail.de>
Date: Mon Feb 19 20:02:45 2018 +0100
Added recipe for hyperdraw (#7897)
commit b8c3bff0cee1efa1318be8fade5b3b2bf73ba2a5
Author: ArneKr <arnekratz@hotmail.de>
Date: Mon Feb 19 20:02:28 2018 +0100
Added recipe for HybridMTest (#7898)
commit f7e5b8d6dbb18e037096f6e91e4f8007295c9c5b
Author: ArneKr <arnekratz@hotmail.de>
Date: Mon Feb 19 20:01:19 2018 +0100
Added recipe for htSeqTools (#7899)
commit 398d27b46aac58e54e6cafe2ad1ee633835f3330
Author: ArneKr <arnekratz@hotmail.de>
Date: Mon Feb 19 19:35:18 2018 +0100
Added recipe for HTqPCR (#7900)
commit 5184537aed24cccae1aaa08713e2ba1428c0f662
Author: ArneKr <arnekratz@hotmail.de>
Date: Mon Feb 19 19:18:35 2018 +0100
Added recipe for HiTC (#7902)
commit 3f120a09032cc9b532707e2ced9e9ecdfe48b0a7
Author: ArneKr <arnekratz@hotmail.de>
Date: Mon Feb 19 19:00:00 2018 +0100
Added recipe for HIBAG (#7903)
commit 35832be06334043ac08fa26a01090a254acf5f28
Author: ArneKr <arnekratz@hotmail.de>
Date: Mon Feb 19 18:59:42 2018 +0100
Added recipe for HEM (#7904)
commit 3c04f152889dca8e904d054e840c0660084fe956
Author: ArneKr <arnekratz@hotmail.de>
Date: Mon Feb 19 18:54:30 2018 +0100
Added recipe for HELP (#7905)
commit eb95f49690655bf720ae3cfe935d918d71df0ecf
Author: ArneKr <arnekratz@hotmail.de>
Date: Mon Feb 19 18:50:23 2018 +0100
Added recipe for Harshlight (#7906)
commit af0f2dc6022a851b0d15beed4b19f8f9acb59c7e
Author: ArneKr <arnekratz@hotmail.de>
Date: Mon Feb 19 18:50:10 2018 +0100
Added recipe for Harman (#7907)
commit 4103c4fe56eb97192a4f61abcb10fc5276dfe683
Author: ArneKr <arnekratz@hotmail.de>
Date: Mon Feb 19 18:43:49 2018 +0100
Added recipe for GSRI (#7908)
commit bc5e0e08552b6369a456d5b11794e756fe1272d4
Author: ArneKr <arnekratz@hotmail.de>
Date: Mon Feb 19 18:29:29 2018 +0100
Added recipe for GSReg (#7909)
commit 4fa732f24cddd558b74fc1d3d1f1e5d9c3bfa3e6
Author: Michael T. Wolfinger <michael@wolfinger.eu>
Date: Mon Feb 19 18:23:53 2018 +0100
add perl-test-object (#7921)
commit 07a60076e50b30e0da8031d33e978db3202c6d26
Author: ArneKr <arnekratz@hotmail.de>
Date: Mon Feb 19 18:22:58 2018 +0100
Added recipe for GSEAlm (#7910)
commit 6aa3f9f7f823a928825ea7bc4b5fa445b15003de
Author: ArneKr <arnekratz@hotmail.de>
Date: Mon Feb 19 18:22:35 2018 +0100
Added recipe for GSCA (#7911)
commit 35a903d706f7f663992feaa379b80229eb8efdb9
Author: ArneKr <arnekratz@hotmail.de>
Date: Mon Feb 19 18:22:11 2018 +0100
Added recipe for GSALightning (#7912)
commit f87e8f0babd75b4dccc7b7a8304375545e991579
Author: ArneKr <arnekratz@hotmail.de>
Date: Mon Feb 19 18:21:52 2018 +0100
Added recipe for GRmetrics (#7913)
commit 73c58dfa5144ffa6f0de07d1624d96d1755206eb
Author: ArneKr <arnekratz@hotmail.de>
Date: Mon Feb 19 18:21:35 2018 +0100
Added recipe for GraphAT (#7914)
commit 0487b213def927148ad5a582b988ce88a3a74332
Author: ArneKr <arnekratz@hotmail.de>
Date: Mon Feb 19 18:12:41 2018 +0100
Added recipe for ChIPXpress (#7880)
commit f47f67dd55dc8804814ee9080cded9a5eb692897
Author: ArneKr <arnekratz@hotmail.de>
Date: Mon Feb 19 18:12:21 2018 +0100
Added recipe for ChIPsim (#7881)
commit 459c7e7a8596b0d0a1d0287cc1ad6b450c86d611
Author: Michael T. Wolfinger <michael@wolfinger.eu>
Date: Mon Feb 19 18:11:44 2018 +0100
add perl-file-remove (#7870)
commit 615430729e9a4f7c8fd6ee57f3b8e4a7d6a2a538
Author: ArneKr <arnekratz@hotmail.de>
Date: Mon Feb 19 18:11:25 2018 +0100
Added recipe for gpls (#7915)
commit 15145ca5ec4438347789bccc8ad1673681bebfae
Author: ArneKr <arnekratz@hotmail.de>
Date: Mon Feb 19 18:02:19 2018 +0100
Added recipe for goTools (#7916)
commit 7898f493a8e3c3769a673f02c4df3e180ea3b74f
Author: ArneKr <arnekratz@hotmail.de>
Date: Mon Feb 19 17:56:35 2018 +0100
Added recipe for wateRmelon (#7917)
commit d712bb15af4eeda235286174e4747dc2cf3792f4
Author: ArneKr <arnekratz@hotmail.de>
Date: Mon Feb 19 17:31:33 2018 +0100
Added recipe for waveTiling (#7918)
commit 68f0f068375f130fc5f9ebc3c2718f4a44adfceb
Author: Jim Johnson <jj@umn.edu>
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 <rvalieris@users.noreply.github.com>
Date: Mon Feb 19 10:16:00 2018 -0300
fix metavelvet recipe (#7813)
* fix metavelvet recipe
commit 109b6f10c5703fcc65a219ee255d3d1bdaeaba1c
Author: Michael T. Wolfinger <michael@wolfinger.eu>
Date: Mon Feb 19 11:30:06 2018 +0100
add perl-hook-lexwrap (#7863)
commit 51eed1481db69a43c7b86e85dbba5ee86987907a
Author: Michael T. Wolfinger <michael@wolfinger.eu>
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 <berenice.batut@gmail.com>
Date: Mon Feb 19 00:12:27 2018 +0100
Add metaphlan2 2.7.5 (#7861)
commit d6615c2316649d551ef30c622b5f6263f00ccb09
Author: ArneKr <arnekratz@hotmail.de>
Date: Sun Feb 18 17:39:08 2018 +0100
Added recipe for interactiveDisplay (#7852)
commit 99b99f7d53f8b0173053b6d8b8d9277a8c3c84b5
Author: ArneKr <arnekratz@hotmail.de>
Date: Sun Feb 18 17:38:55 2018 +0100
Added recipe for inveRsion (#7851)
commit 681dcc590e065cd0a3a8f5b6f75fc456cb97d07a
Author: ArneKr <arnekratz@hotmail.de>
Date: Sun Feb 18 17:38:45 2018 +0100
Added recipe for IPPD (#7850)
commit d8d5dc508d22460bc9e802d56d3f442ab736fa5b
Author: ArneKr <arnekratz@hotmail.de>
Date: Sun Feb 18 17:38:34 2018 +0100
Added recipe for iSeq (#7849)
commit e2a9db68cb6f05d9c8992f7eac1c448839bdadd4
Author: ArneKr <arnekratz@hotmail.de>
Date: Sun Feb 18 17:38:25 2018 +0100
Added recipe for ISoLDE (#7848)
commit cda3242dcdb7d80c75794b678d09286b67477c34
Author: ArneKr <arnekratz@hotmail.de>
Date: Sun Feb 18 17:37:41 2018 +0100
Added recipe for iterativeBMA (#7847)
commit de2d757122bb1d33721899384814a065194c680c
Author: ArneKr <arnekratz@hotmail.de>
Date: Sun Feb 18 17:37:34 2018 +0100
Added recipe for iterativeBMAsurv (#7846)
commit 21ae3249cef94cc7a4c1687efb956a2932380edb
Author: ArneKr <arnekratz@hotmail.de>
Date: Sun Feb 18 17:37:26 2018 +0100
Added recipe for MCRestimate (#7845)
commit 3ccf0050d80b1116ab6b3bde2c0024021a8813b1
Author: ArneKr <arnekratz@hotmail.de>
Date: Sun Feb 18 17:37:19 2018 +0100
Added recipe for KEGGlincs (#7844)
commit 024eaa8c1dda5b132bb03cbdbf0cf5803f68af36
Author: ArneKr <arnekratz@hotmail.de>
Date: Sun Feb 18 17:37:09 2018 +0100
Added recipe for keggorthology (#7843)
commit 5affeb1b850762a47c58c26025635b14e1027964
Author: ArneKr <arnekratz@hotmail.de>
Date: Sun Feb 18 17:34:42 2018 +0100
Added recipe for kimod (#7842)
commit 9b6c93d4ff5ddebedf80b79598c92fb44d93ba86
Author: ArneKr <arnekratz@hotmail.de>
Date: Sun Feb 18 17:34:37 2018 +0100
Added recipe for LBE (#7841)
commit 4b4355a6f07420ae0aa4a6c5e2ba5b4a414881dc
Author: ArneKr <arnekratz@hotmail.de>
Date: Sun Feb 18 17:34:27 2018 +0100
Added recipe for les (#7840)
commit 85a2a0519e9005e66ead5210e35fe508ea896395
Author: ArneKr <arnekratz@hotmail.de>
Date: Sun Feb 18 17:34:17 2018 +0100
Added recipe for lfa (#7839)
commit 9d277158aef743e7da90fde7e576ac42d6403ae9
Author: ArneKr <arnekratz@hotmail.de>
Date: Sun Feb 18 17:34:00 2018 +0100
Added recipe for LINC (#7838)
commit 462294a6902625cefc3f4431f7eaf02d39304478
Author: ArneKr <arnekratz@hotmail.de>
Date: Sun Feb 18 17:33:53 2018 +0100
Added recipe for CMA (#7837)
commit 5a7f50c07eb8bfb36f2bb15e135e4adb06888603
Author: ArneKr <arnekratz@hotmail.de>
Date: Sun Feb 18 17:33:48 2018 +0100
Added recipe for cn.farms (#7836)
commit d4b20632ef941d7643c0baba80aa7bcc431a5c45
Author: ArneKr <arnekratz@hotmail.de>
Date: Sun Feb 18 17:33:41 2018 +0100
Added recipe for LiquidAssociation (#7835)
commit 296f0c1f6461036563778bcc695369bf812ac4f3
Author: ArneKr <arnekratz@hotmail.de>
Date: Sun Feb 18 17:33:33 2018 +0100
Added recipe for lmdme (#7833)
commit ab586c21abf0e5f88a3e2f13d3edf199674803bb
Author: ArneKr <arnekratz@hotmail.de>
Date: Sun Feb 18 17:33:26 2018 +0100
Added recipe for CNVPanelizer (#7832)
commit 87c5376fa5932039e1f3a9a7433477b7f2d664c9
Author: ArneKr <arnekratz@hotmail.de>
Date: Sun Feb 18 17:33:12 2018 +0100
Added recipe for LOBSTAHS (#7831)
commit 1fe51b48e40a5988ebb6476d32ca573571a366cf
Author: ArneKr <arnekratz@hotmail.de>
Date: Sun Feb 18 17:32:44 2018 +0100
Added recipe for CNVtools (#7830)
commit 65c567fcc7485a1654777b79ef5bb3377434ae02
Author: ArneKr <arnekratz@hotmail.de>
Date: Sun Feb 18 17:32:19 2018 +0100
Added recipe for INSPEcT (#7853)
commit ff51b3819da54ce8d4544a5ec559586247cb8b65
Author: ArneKr <arnekratz@hotmail.de>
Date: Sun Feb 18 17:29:20 2018 +0100
Added recipe for INPower (#7854)
commit ba0d7d5f734c5765021f18aaf800149db2321dae
Author: ArneKr <arnekratz@hotmail.de>
Date: Sun Feb 18 17:28:54 2018 +0100
Added recipe for ImpulseDE (#7855)
commit a2a0bbf2dece573dc4a4d67e3084552ddc08ab5c
Author: ArneKr <arnekratz@hotmail.de>
Date: Sun Feb 18 17:25:42 2018 +0100
Added recipe for clusterStab (#7856)
commit 064df095e36aae59a61d2567a245717d42b11087
Author: ArneKr <arnekratz@hotmail.de>
Date: Sun Feb 18 17:25:29 2018 +0100
Added recipe for ClusterSignificance (#7857)
commit 2c61e34eac4d92b1e50e52ce7d224e18f59eaeac
Author: ArneKr <arnekratz@hotmail.de>
Date: Sun Feb 18 17:23:32 2018 +0100
Added recipe for CNORfuzzy (#7834)
commit bdcdb57634855dff1a9f64abc71c8bb6c4f0b38e
Author: ArneKr <arnekratz@hotmail.de>
Date: Sun Feb 18 17:22:09 2018 +0100
Added recipe for clustComp (#7858)
commit e6826bb5adadd0250b0e47702554e3b7ad5e530d
Author: ArneKr <arnekratz@hotmail.de>
Date: Sun Feb 18 17:16:20 2018 +0100
Added recipe for lol (#7829)
commit b9cf497976ba3c82de862a17fb43bb5255c0221c
Author: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
Date: Sun Feb 18 17:14:58 2018 +0100
nextflow 0.27.5 (#7817)
commit 189b08ff36423d21de413a2f45c2ec7331e832fb
Author: Michael T. Wolfinger <michael@wolfinger.eu>
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 <michael@wolfinger.eu>
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 <egg@informatik.uni-freiburg.de>
Date: Sat Feb 17 23:46:51 2018 +0100
Updated to version 2.1.3 (#7828)
commit df2937f2ffa5e40091d6602cf919031cbcad5dc0
Author: Christian Brueffer <christian@brueffer.io>
Date: Sat Feb 17 23:12:28 2018 +0100
Add bioconductor-ffpe. (#7388)
commit 1b4d77cd6605853746d3bfb9f20c3c5e11cd9cae
Author: Björn Grüning <bjoern@gruenings.eu>
Date: Sat Feb 17 18:29:28 2018 +0100
Update meta.yaml (#7825)
commit d7a7d03c969e4379ff00218a8bb1012a0e0f5c82
Author: Michael T. Wolfinger <michael@wolfinger.eu>
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 <michael@wolfinger.eu>
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 <johannes.koester@tu-dortmund.de>
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 <dfornika@gmail.com>
Date: Fri Feb 16 17:54:02 2018 -0800
Update MentaliST to v0.2.1 (#7824)
commit 68e8b620728059ebb75bf1366e225dd41df3902d
Author: Dan Fornika <dfornika@gmail.com>
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 <ptbrooks@ucdavis.edu>
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 <module>
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 <mbargull@users.noreply.github.com>
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 <chapmanb@fastmail.com>
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 <mbargull@users.noreply.github.com>
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 <arnekratz@hotmail.de>
Date: Fri Feb 16 15:41:00 2018 +0100
Added recipe for codelink (#7811)
commit 3d023871794a16247d84b35ebd5e0d1ad2e1fd4c
Author: ArneKr <arnekratz@hotmail.de>
Date: Fri Feb 16 15:40:49 2018 +0100
Added recipe for cogena (#7810)
commit 2c5257e3145e029654647e5edb93c11456d18919
Author: ArneKr <arnekratz@hotmail.de>
Date: Fri Feb 16 15:40:38 2018 +0100
Added recipe for coGPS (#7809)
commit 20e13504ec0a461e452514c39e480d19fd47d392
Author: ArneKr <arnekratz@hotmail.de>
Date: Fri Feb 16 15:40:25 2018 +0100
Added recipe for COHCAP (#7808)
commit 73c8558079f53606535b02b9798332575163ea4b
Author: ArneKr <arnekratz@hotmail.de>
Date: Fri Feb 16 15:40:16 2018 +0100
Added recipe for COMPASS (#7807)
commit 76f193a8f3af37792dde863b141331b832f57239
Author: ArneKr <arnekratz@hotmail.de>
Date: Fri Feb 16 15:40:03 2018 +0100
Added recipe for consensusSeekeR (#7806)
commit bd17cf50b63b169de2d5d5489fea3684a1e47197
Author: ArneKr <arnekratz@hotmail.de>
Date: Fri Feb 16 15:39:53 2018 +0100
Added recipe for contiBAIT (#7805)
commit 2a3284fa555463f820b96c6e509d1b454c226208
Author: ArneKr <arnekratz@hotmail.de>
Date: Fri Feb 16 15:39:39 2018 +0100
Added recipe for CopywriteR (#7804)
commit 9a4c23a346831361d0facdcbc7a7b840ec662a18
Author: ArneKr <arnekratz@hotmail.de>
Date: Fri Feb 16 15:39:29 2018 +0100
Added recipe for Cormotif (#7803)
commit 474da29ecdb802dc17702324a159e0d6d0d4b504
Author: ArneKr <arnekratz@hotmail.de>
Date: Fri Feb 16 15:39:16 2018 +0100
Added recipe for CORREP (#7802)
commit af2846bf3a15239256647935f6af16c2f676db2f
Author: ArneKr <arnekratz@hotmail.de>
Date: Fri Feb 16 12:13:20 2018 +0100
Added recipe for cosmiq (#7800)
commit d1d74e7aca1d1fe8f8c11f5f20fdaab0e8a93a8e
Author: ArneKr <arnekratz@hotmail.de>
Date: Fri Feb 16 12:13:05 2018 +0100
Added recipe for LPEadj (#7799)
commit d55cdbcee9910ee38da2ba47870dd963a6e51ba5
Author: ArneKr <arnekratz@hotmail.de>
Date: Fri Feb 16 12:12:40 2018 +0100
Added recipe for lpNet (#7798)
commit ca39a394931046ca0dc3daea8dad0792c40fc244
Author: ArneKr <arnekratz@hotmail.de>
Date: Fri Feb 16 11:02:45 2018 +0100
Added recipe for LVSmiRNA (#7797)
commit 6f1fd7162a2f40054ea88d1f39d6f2e08ff4b840
Author: ArneKr <arnekratz@hotmail.de>
Date: Fri Feb 16 11:02:35 2018 +0100
Added recipe for M3D (#7796)
commit 4f36b1dcfff1ad38fb09afd152a98dc9080e075e
Author: ArneKr <arnekratz@hotmail.de>
Date: Fri Feb 16 11:02:26 2018 +0100
Added recipe for MADSEQ (#7795)
commit b8710ea15aec03fd7d5423b5dfa489f1abf795ac
Author: ArneKr <arnekratz@hotmail.de>
Date: Fri Feb 16 11:02:16 2018 +0100
Added recipe for maigesPack (#7794)
commit af45c76c859307f3e4089b1c637acc2b9aad36ce
Author: ArneKr <arnekratz@hotmail.de>
Date: Fri Feb 16 11:02:05 2018 +0100
Added recipe for maPredictDSC (#7793)
commit f43643c4eb2615af584d092ee9c608d8f72ddab4
Author: ArneKr <arnekratz@hotmail.de>
Date: Fri Feb 16 11:01:54 2018 +0100
Added recipe for maskBAD (#7792)
commit be2288e92449d99222ba6c3f8c1adb7a9df4bb9b
Author: ArneKr <arnekratz@hotmail.de>
Date: Fri Feb 16 11:01:43 2018 +0100
Added recipe for MeasurementError.cor (#7791)
commit 97447fd7cc2afc4a3f8d0835379e562e4b12eafc
Author: ArneKr <arnekratz@hotmail.de>
Date: Fri Feb 16 11:01:32 2018 +0100
Added recipe for covRNA (#7790)
commit 2c7b1db449e2a5dc6eefddff5b5bb3711c8d4bdf
Author: ArneKr <arnekratz@hotmail.de>
Date: Fri Feb 16 11:01:19 2018 +0100
Added recipe for cpvSNP (#7789)
commit 4a9e9315bd53b336affea2295da513e443cc66c6
Author: ArneKr <arnekratz@hotmail.de>
Date: Fri Feb 16 11:01:08 2018 +0100
Added recipe for CRImage (#7788)
commit 28c271a65e128054fc2448a1f82ca1364f400b8c
Author: ArneKr <arnekratz@hotmail.de>
Date: Fri Feb 16 11:00:57 2018 +0100
Added recipe for crisprseekplus (#7787)
commit eb9a61579fc6b7939b4fec3adafeba3d710a963e
Author: ArneKr <arnekratz@hotmail.de>
Date: Fri Feb 16 11:00:48 2018 +0100
Added recipe for CrispRVariants (#7786)
commit 7c00edec35ea441323e24b6bfaa6e55cd74b9aff
Author: ArneKr <arnekratz@hotmail.de>
Date: Fri Feb 16 11:00:38 2018 +0100
Added recipe for ctsGE (#7785)
commit 7fd3290d20079942141270dd3046f99c0c9f9542
Author: ArneKr <arnekratz@hotmail.de>
Date: Fri Feb 16 11:00:27 2018 +0100
Added recipe for CVE (#7784)
commit 701554008788f1acf6e6e5ae269b9ebaa2a18873
Author: ArneKr <arnekratz@hotmail.de>
Date: Fri Feb 16 10:59:27 2018 +0100
Added recipe for daMA (#7783)
commit ecbe68afb9621d2bfef8f7343665dd53e1bc7ece
Author: ArneKr <arnekratz@hotmail.de>
Date: Fri Feb 16 10:59:17 2018 +0100
Added recipe for DBChIP (#7782)
commit 5a81b3668bc43104528cee7c172fa48d3a663f2f
Author: ArneKr <arnekratz@hotmail.de>
Date: Fri Feb 16 10:59:07 2018 +0100
Added recipe for dcGSA (#7781)
commit e04cfa5106e4d9cbeaccd3fb703d8d2eeb7a6717
Author: ArneKr <arnekratz@hotmail.de>
Date: Fri Feb 16 10:58:57 2018 +0100
Added recipe for DChIPRep (#7780)
commit 0dbfaa94ef87e9015c489a21f68097b5f1008474
Author: ArneKr <arnekratz@hotmail.de>
Date: Fri Feb 16 10:58:46 2018 +0100
Added recipe for MEDME (#7779)
commit 91e133ff7e435af4167c0ecd6d850aa21a83c723
Author: ArneKr <arnekratz@hotmail.de>
Date: Fri Feb 16 10:58:36 2018 +0100
Added recipe for MEIGOR (#7778)
commit 7539cb1f7b176c457d03cce0fb6b819056a93ac8
Author: ArneKr <arnekratz@hotmail.de>
Date: Fri Feb 16 10:58:27 2018 +0100
Added recipe for ddCt (#7777)
commit fa1db5afa6e7c8d11a27848ea41a2ad0c2b4cb37
Author: ArneKr <arnekratz@hotmail.de>
Date: Fri Feb 16 10:58:17 2018 +0100
Added recipe for meshes (#7776)
commit 48596f67f7bf9fc7d7334391dc7b56df9bd14d55
Author: ArneKr <arnekratz@hotmail.de>
Date: Fri Feb 16 10:58:06 2018 +0100
Added recipe for Metab (#7775)
commit 1eee769d731a4db9104ba6d40d756d90aaadc378
Author: ArneKr <arnekratz@hotmail.de>
Date: Fri Feb 16 10:57:56 2018 +0100
Added recipe for MetaboSignal (#7774)
commit 7213e2202b5ac6e41b9f0c5bc13cadd0c97a6fa9
Author: ArneKr <arnekratz@hotmail.de>
Date: Fri Feb 16 10:57:46 2018 +0100
Added recipe for methyAnalysis (#7773)
commit bc0ae5f97c05f209b453c88038d1bcb5ce65a616
Author: ArneKr <arnekratz@hotmail.de>
Date: Fri Feb 16 10:57:34 2018 +0100
Added recipe for DEDS (#7772)
commit ee795343e7981a097f7c8f4e9cf70e8dacbfe890
Author: ArneKr <arnekratz@hotmail.de>
Date: Fri Feb 16 10:52:04 2018 +0100
Added recipe for DNABarcodes (#7771)
commit 192652e2e11f1e02cc3a9a38b29c4f73eb00723c
Author: ArneKr <arnekratz@hotmail.de>
Date: Fri Feb 16 10:51:54 2018 +0100
Added recipe for DOQTL (#7770)
commit 9c1cee43f363004080d03b2506638bcb4880947d
Author: ArneKr <arnekratz@hotmail.de>
Date: Fri Feb 16 10:51:44 2018 +0100
Added recipe for DrugVsDisease (#7769)
commit a1d85fcdd34576fbd2b6aa5f2fff50a2ae200ced
Author: ArneKr <arnekratz@hotmail.de>
Date: Fri Feb 16 10:51:34 2018 +0100
Added recipe for DeepBlueR (#7768)
commit 23dc220d680c9b1da32715aff3f25bd0d78cabc7
Author: ArneKr <arnekratz@hotmail.de>
Date: Fri Feb 16 10:51:25 2018 +0100
Added recipe for DEFormats (#7767)
commit f2dfd95625f94356d3da230f054f213fa7393fe8
Author: ArneKr <arnekratz@hotmail.de>
Date: Fri Feb 16 10:51:15 2018 +0100
Added recipe for DEGraph (#7766)
commit 9773eca6b4061621c3a8cb4ee767edaf78078caa
Author: ArneKr <arnekratz@hotmail.de>
Date: Fri Feb 16 10:51:06 2018 +0100
Added recipe for DeMAND (#7765)
commit 083d18eaab39c67a0792432f432734daa826e308
Author: ArneKr <arnekratz@hotmail.de>
Date: Fri Feb 16 10:50:57 2018 +0100
Added recipe for MineICA (#7764)
commit 5724e1a14927500a2577c62d8a71406ba1897e0e
Author: ArneKr <arnekratz@hotmail.de>
Date: Fri Feb 16 10:50:47 2018 +0100
Added recipe for MinimumDistance (#7763)
commit ca5c4cf85d04c2c26abc65b7cd6a92dd439c034e
Author: ArneKr <arnekratz@hotmail.de>
Date: Fri Feb 16 10:50:37 2018 +0100
Added recipe for mirIntegrator (#7762)
commit 77848f99a6a2faff12e66bef93b5271cbf0ccb68
Author: ArneKr <arnekratz@hotmail.de>
Date: Fri Feb 16 10:50:27 2018 +0100
Added recipe for miRNAmeConverter (#7761)
commit ef45abfdf51b61745b86d0ff21de952c06cba394
Author: ArneKr <arnekratz@hotmail.de>
Date: Fri Feb 16 10:50:17 2018 +0100
Added recipe for dexus (#7760)
commit 7429059fb12426ebec87d69f5363d920cb7e91bd
Author: ArneKr <arnekratz@hotmail.de>
Date: Fri Feb 16 10:50:07 2018 +0100
Added recipe for DFP (#7759)
commit a34957866e222039370226ced200fd693d4bb01b
Author: ArneKr <arnekratz@hotmail.de>
Date: Fri Feb 16 10:49:57 2018 +0100
Added recipe for diffGeneAnalysis (#7758)
commit 7c28f72c284b123548bcd20a3c01ca6c0272ddcf
Author: ArneKr <arnekratz@hotmail.de>
Date: Fri Feb 16 10:49:47 2018 +0100
Added recipe for diffloop (#7757)
commit 06bbc6382d7e91c2b0fb93cd2ae8e991d907f523
Author: ArneKr <arnekratz@hotmail.de>
Date: Fri Feb 16 10:49:39 2018 +0100
Added recipe for Director (#7756)
commit 4cfe24096a9253201744279dcd1d61119516ecbe
Author: ArneKr <arnekratz@hotmail.de>
Date: Fri Feb 16 10:48:03 2018 +0100
Added recipe for easyRNASeq (#7755)
commit 8e462b47e429f8a832e2c549a0881b7e945f6a1d
Author: ArneKr <arnekratz@hotmail.de>
Date: Fri Feb 16 10:47:52 2018 +0100
Added recipe for missMethyl (#7754)
commit bbe4aa297b1e235f5a6202dfe10f62e45a5a0b93
Author: ArneKr <arnekratz@hotmail.de>
Date: Fri Feb 16 10:47:39 2018 +0100
Added recipe for mQTL.NMR (#7753)
commit 6e2949b5636bccadf429dff385b4da1fc54ca2dd
Author: ArneKr <arnekratz@hotmail.de>
Date: Fri Feb 16 10:47:28 2018 +0100
Added recipe for EDDA (#7752)
commit 4da3d9a235745fb635728d826fb2e9b6113d6b76
Author: ArneKr <arnekratz@hotmail.de>
Date: Fri Feb 16 10:47:15 2018 +0100
Added recipe for MSnID (#7751)
commit cfb9dfda7c14d6e3ff3d1bb34da6eb0da67ee27d
Author: ArneKr <arnekratz@hotmail.de>
Date: Fri Feb 16 10:47:04 2018 +0100
Added recipe for EmpiricalBrownsMethod (#7750)
commit d038257fa5ab7d07780eec0f094b83dfa722baff
Author: ArneKr <arnekratz@hotmail.de>
Date: Fri Feb 16 10:46:50 2018 +0100
Added recipe for ENCODExplorer (#7749)
commit 49dfeba173c068c00d77c8f90242ce6c924f2af9
Author: ArneKr <arnekratz@hotmail.de>
Date: Fri Feb 16 10:46:38 2018 +0100
Added recipe for EnrichmentBrowser (#7748)
commit f3d9beceb7b0a140f01b768f877e00ba3655f469
Author: ArneKr <arnekratz@hotmail.de>
Date: Fri Feb 16 10:46:27 2018 +0100
Added recipe for epigenomix (#7747)
commit bada3577172e6996275aa096ee424b563a40d24c
Author: ArneKr <arnekratz@hotmail.de>
Date: Fri Feb 16 10:46:13 2018 +0100
Added recipe for MultiAssayExperiment (#7746)
commit b59ea711067ca0c5d0688d0b3f620268d41859a0
Author: ArneKr <arnekratz@hotmail.de>
Date: Fri Feb 16 10:46:05 2018 +0100
Added recipe for multiClust (#7745)
commit d7299a87a53a0c7fb7a491740493e7e06b3ae23f
Author: ArneKr <arnekratz@hotmail.de>
Date: Fri Feb 16 10:45:54 2018 +0100
Added recipe for epivizrStandalone (#7744)
commit f5598f5bce28e88046598c632bd53a5adec4716a
Author: ArneKr <arnekratz@hotmail.de>
Date: Fri Feb 16 10:45:43 2018 +0100
Added recipe for esetVis (#7743)
commit 939d4b3244e6de4abe8b004c26c2a35edb836f5f
Author: ArneKr <arnekratz@hotmail.de>
Date: Fri Feb 16 10:45:32 2018 +0100
Added recipe for eudysbiome (#7742)
commit c3e7457e7707f5dfc6056e6d35acdee4eab59dc0
Author: ArneKr <arnekratz@hotmail.de>
Date: Fri Feb 16 10:45:21 2018 +0100
Added recipe for ExiMiR (#7741)
commit e863f1e38728a851c3a06a26959b5ac8ae51cce8
Author: ArneKr <arnekratz@hotmail.de>
Date: Fri Feb 16 10:45:10 2018 +0100
Added recipe for exomePeak (#7740)
commit 18f13941934f6beddd776ce9ab6de8ac7fcc660b
Author: ArneKr <arnekratz@hotmail.de>
Date: Fri Feb 16 10:28:10 2018 +0100
Added recipe for FindMyFriends (#7739)
commit c7c6fa93cd6adeeac57c2360de0731f6a5eff5cb
Author: ArneKr <arnekratz@hotmail.de>
Date: Fri Feb 16 10:27:53 2018 +0100
Added recipe for flowMatch (#7738)
commit cfe965bbb3c1dee53cf06ce06d63a5e67c9f5a95
Author: ArneKr <arnekratz@hotmail.de>
Date: Fri Feb 16 10:27:33 2018 +0100
Added recipe for geneRxCluster (#7737)
commit c1ceebd1cf909f4bc3d2658fabb1b217d2a6d7cc
Author: ArneKr <arnekratz@hotmail.de>
Date: Fri Feb 16 10:27:23 2018 +0100
Added recipe for GeneSelector (#7736)
commit 31be69de6867c9952edb589c8e976fd5912a2832
Author: ArneKr <arnekratz@hotmail.de>
Date: Fri Feb 16 10:27:09 2018 +0100
Added recipe for PathoStat (#7735)
commit 5a3d7d941fc0f173719ac5d995c3fbcd08755dc8
Author: ArneKr <arnekratz@hotmail.de>
Date: Fri Feb 16 10:27:00 2018 +0100
Added recipe for pathRender (#7734)
commit 61a797ba8838f2862bbfc5f2bc83c12b32ad7744
Author: ArneKr <arnekratz@hotmail.de>
Date: Fri Feb 16 10:26:50 2018 +0100
Added recipe for pathVar (#7733)
commit f5814e77455759c32eaaf24f1c4dd406d3cc36ab
Author: ArneKr <arnekratz@hotmail.de>
Date: Fri Feb 16 10:26:40 2018 +0100
Added recipe for Pbase (#7732)
commit 9ba28aeed3682c88e5a1f4f79693e80806d62709
Author: ArneKr <arnekratz@hotmail.de>
Date: Fri Feb 16 10:26:30 2018 +0100
Added recipe for geNetClassifier (#7731)
commit 4c46c37026adbb87133008ad716529a35de3b2b2
Author: ArneKr <arnekratz@hotmail.de>
Date: Fri Feb 16 10:26:19 2018 +0100
Added recipe for GeneticsDesign (#7730)
commit 407f986496282d408e818210f21bc101c36ad8b3
Author: ArneKr <arnekratz@hotmail.de>
Date: Fri Feb 16 10:23:56 2018 +0100
Added recipe for pcaGoPromoter (#7729)
commit 13df0553bb2f8bb3e82c5102c87f3bfe84178047
Author: ArneKr <arnekratz@hotmail.de>
Date: Fri Feb 16 10:23:45 2018 +0100
Added recipe for GenoGAM (#7728)
commit 6119e849fbea7b9ca345a5d27ff305e9c91d6159
Author: ArneKr <arnekratz@hotmail.de>
Date: Fri Feb 16 10:23:27 2018 +0100
Added recipe for PCpheno (#7727)
commit e57e477c6eedb1cc7d697d97df9f5e070f8d8858
Author: ArneKr <arnekratz@hotmail.de>
Date: Fri Feb 16 10:23:16 2018 +0100
Added recipe for GenRank (#7726)
commit bd3ef4ed0b15dc65fb49a12a3edd258152558a11
Author: ArneKr <arnekratz@hotmail.de>
Date: Fri Feb 16 10:23:06 2018 +0100
Added recipe for GEOsubmission (#7725)
commit da7fb2f1725c48f4f361b047ae6707d3335d986a
Author: ArneKr <arnekratz@hotmail.de>
Date: Fri Feb 16 10:09:30 2018 +0100
Added recipe for pRolocGUI (#7724)
commit 5bae735a184bff94a9c742dcc43a52cea5c6bcdf
Author: ArneKr <arnekratz@hotmail.de>
Date: Fri Feb 16 10:09:15 2018 +0100
Added recipe for qsea (#7723)
commit a135a47526d87777436f70d745398649e7f946b0
Author: ArneKr <arnekratz@hotmail.de>
Date: Fri Feb 16 10:08:47 2018 +0100
Added recipe for QuartPAC (#7722)
commit 03ae80f0640245a3d27c76658979e72b99e26bda
Author: ArneKr <arnekratz@hotmail.de>
Date: Fri Feb 16 10:08:35 2018 +0100
Added recipe for QuaternaryProd (#7721)
commit 11aba2ddd2d3d6a2d7d57f57a3698afcbcf62f78
Author: ArneKr <arnekratz@hotmail.de>
Date: Fri Feb 16 10:08:22 2018 +0100
Added recipe for RareVariantVis (#7720)
commit 5483ac702389de27b7cb39524baa947dbb1d6b65
Author: ArneKr <arnekratz@hotmail.de>
Date: Fri Feb 16 10:08:11 2018 +0100
Added recipe for Rariant (#7719)
commit 91704c72c8320901e2dcc4c58897d116cc0b8a9a
Author: ArneKr <arnekratz@hotmail.de>
Date: Fri Feb 16 10:07:46 2018 +0100
Added recipe for GAprediction (#7718)
commit 74732d92c5e1c919b235a84a634be4f91de1ea58
Author: ArneKr <arnekratz@hotmail.de>
Date: Fri Feb 16 10:07:00 2018 +0100
Added recipe for gcatest (#7716)
commit 4fe7bdb4d7ed42e68fcb199d3659321762eaff81
Author: Philip Reiner Kensche <vinjana@users.noreply.github.com>
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 <michael@wolfinger.eu>
Date: Fri Feb 16 10:00:52 2018 +0100
add recipe fore perl-filedirutil (#7715)
commit 01f6c50c11266729b6e9f7d3f97792f7fc7460fd
Author: Michael T. Wolfinger <michael@wolfinger.eu>
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 <andreas.sjodin@gmail.com>
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 <bjoern@gruenings.eu>
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 t…
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
Add this suggestion to a batch that can be applied as a single commit.
This suggestion is invalid because no changes were made to the code.
Suggestions cannot be applied while the pull request is closed.
Suggestions cannot be applied while viewing a subset of changes.
Only one suggestion per line can be applied in a batch.
Add this suggestion to a batch that can be applied as a single commit.
Applying suggestions on deleted lines is not supported.
You must change the existing code in this line in order to create a valid suggestion.
Outdated suggestions cannot be applied.
This suggestion has been applied or marked resolved.
Suggestions cannot be applied from pending reviews.
Suggestions cannot be applied on multi-line comments.
Suggestions cannot be applied while the pull request is queued to merge.
Suggestion cannot be applied right now. Please check back later.