Update bcftools to v1.6 #6221

nsoranzo · 2017-10-04T15:36:59Z

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).

@daler

* 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

* 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

@daler

* 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

@daler

* 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

@daler

* 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

* 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…

* 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. * …

Update bcftools to v1.6

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nsoranzo added the enhancement label Oct 4, 2017

nsoranzo merged commit 5d7a817 into bioconda:master Oct 4, 2017

nsoranzo deleted the bcftools_1.6 branch October 4, 2017 16:15

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Update bcftools to v1.6 #6221

Update bcftools to v1.6 #6221

nsoranzo commented Oct 4, 2017 •

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Update bcftools to v1.6 #6221

Update bcftools to v1.6 #6221

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nsoranzo commented Oct 4, 2017 • edited

nsoranzo commented Oct 4, 2017 •

edited