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2018-12-20gnu: discrover: Comment on attempt of minimal texlive-union....* gnu/packages/bioinformatics.scm (discrover): Comment on attempt of minimal texlive-union. Pierre Neidhardt
2018-12-17gnu: gess: Don't hardcode python version....* gnu/packages/bioinformatics.scm (gess)[arguments]: Replace hardcoded python version with parameterized one. Efraim Flashner
2018-12-05gnu: mash: Use C++ 14....I'm looking to upgrade capnproto, and mash fails to build with 0.7. Therefore, tweak the compilation to allow it to build with 0.7. The package also builds with the current version of capnproto. I got the idea of changing the c++ version from here [1]. 1: https://github.com/marbl/Mash/issues/98 * gnu/packages/bioinformatics.scm (mash)[arguments]: Add new use-c++14 phase. Christopher Baines
2018-12-04gnu: pigx-rnaseq: Update to 0.0.5....* gnu/packages/bioinformatics.scm (pigx-rnaseq): Update to 0.0.5. [inputs]: Replace snakemake-4 with snakemake. Ricardo Wurmus
2018-11-24gnu: bless: Adjust to zlib static output....* gnu/packages/bioinformatics.scm (bless)[inputs]: Add ZLIB:STATIC. [arguments]: Adjust #:make-flags accordingly. Marius Bakke
2018-11-24gnu: mosaik: Fix FTBFS from b90289dadc8ee15848ce911a2bdcd3ae8302d58c....* gnu/packages/bioinformatics.scm (mosaik)[inputs]: Add ZLIB:STATIC. Marius Bakke
2018-11-23gnu: pigx-scrnaseq: Use latest snakemake....* gnu/packages/bioinformatics.scm (pigx-scrnaseq)[inputs]: Replace snakemake-4 with snakemake. Ricardo Wurmus
2018-11-23gnu: pigx-bsseq: Use latest snakemake....* gnu/packages/bioinformatics.scm (pigx-bsseq)[inputs]: Replace snakemake-4 with snakemake. Ricardo Wurmus
2018-11-23gnu: pigx-chipseq: Use latest snakemake....* gnu/packages/bioinformatics.scm (pigx-chipseq)[inputs]: Replace snakemake-4 with snakemake. Ricardo Wurmus
2018-11-23gnu: python-loompy: Remove python-typing....* gnu/packages/bioinformatics.scm (python-loompy)[propagated-inputs]: Remove python-typing. Ricardo Wurmus
2018-11-20Merge branch 'master' into core-updatesMarius Bakke
2018-11-19gnu: r-ensembldb: Update to 2.6.2....* gnu/packages/bioinformatics.scm (r-ensembldb): Update to 2.6.2. Roel Janssen
2018-11-19gnu: r-msnbase: Update to 2.8.1....* gnu/packages/bioinformatics.scm (r-msnbase): Update to 2.8.1. Roel Janssen
2018-11-19gnu: r-genomeinfodb: Update to 1.18.1....* gnu/packages/bioinformatics.scm (r-genomeinfodb): Update to 1.18.1. Roel Janssen
2018-11-15gnu: Add nanopolish....* gnu/packages/bioinformatics.scm (nanopolish): New variable. Signed-off-by: Ricardo Wurmus <rekado@elephly.net> pimi
2018-11-15gnu: sambamba: Update to 0.6.8....* gnu/packages/bioinformatics.scm (sambamba): Update to 0.6.8. Roel Janssen
2018-11-14gnu: bioinformatics: Return #t from all phases and snippets....* gnu/packages/bioinformatics.scm (bamtools, ribotaper, bioawk) (codingquarry, fraggenescan, minced, pplacer, star, subread, sailfish) (salmon): Return #t from all phases and snippets, use 'invoke' where appropriate, and remove vestigal plumbing. Mark H Weaver
2018-11-14gnu: Add jamm....* gnu/packages/bioinformatics.scm (jamm): New variable. Ricardo Wurmus
2018-11-13gnu: r-txdb-mmusculus-ucsc-mm10-knowngene: Update to 3.4.4....* gnu/packages/bioinformatics.scm (r-txdb-mmusculus-ucsc-mm10-knowngene): Update to 3.4.4. Ricardo Wurmus
2018-11-13gnu: r-org-mm-eg-db: Update to 3.7.0....* gnu/packages/bioinformatics.scm (r-org-mm-eg-db): Update to 3.7.0. Ricardo Wurmus
2018-11-13gnu: r-org-dm-eg-db: Update to 3.7.0....* gnu/packages/bioinformatics.scm (r-org-dm-eg-db): Update to 3.7.0. Ricardo Wurmus
2018-11-13gnu: r-org-ce-eg-db: Update to 3.7.0....* gnu/packages/bioinformatics.scm (r-org-ce-eg-db): Update to 3.7.0. Ricardo Wurmus
2018-11-13gnu: r-org-hs-eg-db: Update to 3.7.0....* gnu/packages/bioinformatics.scm (r-org-hs-eg-db): Update to 3.7.0. Ricardo Wurmus
2018-11-13gnu: r-genomationdata: Update to 1.14.0....* gnu/packages/bioinformatics.scm (r-genomationdata): Update to 1.14.0. Ricardo Wurmus
2018-11-13gnu: r-go-db: Update to 3.7.0....* gnu/packages/bioinformatics.scm (r-go-db): Update to 3.7.0. Ricardo Wurmus
2018-11-13gnu: r-genomeinfodbdata: Update to 1.2.0....* gnu/packages/bioinformatics.scm (r-genomeinfodbdata): Update to 1.2.0. Ricardo Wurmus
2018-11-11gnu: r-s4vectors: Update to 0.20.1....* gnu/packages/bioinformatics.scm (r-s4vectors): Update to 0.20.1. Ricardo Wurmus
2018-11-09gnu: r-ensembldb: Update to 2.6.1....* gnu/packages/bioinformatics.scm (r-ensembldb): Update to 2.6.1. Ricardo Wurmus
2018-11-09gnu: r-biostrings: Update to 2.50.1....* gnu/packages/bioinformatics.scm (r-biostrings): Update to 2.50.1. Ricardo Wurmus
2018-11-09gnu: r-biocviews: Update to 1.50.5....* gnu/packages/bioinformatics.scm (r-biocviews): Update to 1.50.5. Ricardo Wurmus
2018-11-08gnu: pplacer-scripts: Use INVOKE....* gnu/packages/bioinformatics.scm (pplacer-scripts)[arguments]: Use INVOKE and return #T unconditionally. Ricardo Wurmus
2018-11-08gnu: roary: Use INVOKE....* gnu/packages/bioinformatics.scm (roary)[arguments]: Use INVOKE and return #T unconditionally. Ricardo Wurmus
2018-11-08gnu: seek: Use INVOKE....* gnu/packages/bioinformatics.scm (seek)[arguments]: Use INVOKE and return #T unconditionally; patch "gen_tools_am" shebang in "bootstrap" phase. Ricardo Wurmus
2018-11-08gnu: sailfish: Use INVOKE....* gnu/packages/bioinformatics.scm (sailfish)[arguments]: Use INVOKE instead of SYSTEM*. Ricardo Wurmus
2018-11-08gnu: vsearch: Update to 2.9.1....* gnu/packages/bioinformatics.scm (vsearch): Update to 2.9.1. * gnu/packages/patches/vsearch-unbundle-cityhash.patch: Update. Ricardo Wurmus
2018-11-08gnu: sra-tools: Update to 2.9.3....* gnu/packages/bioinformatics.scm (sra-tools): Update to 2.9.3. [arguments]: Remove build phase patch-away-glibc-conflict. Ricardo Wurmus
2018-11-08gnu: plink-ng: Fetch sources from git....* gnu/packages/bioinformatics.scm (plink-ng)[source]: Fetch from git. Ricardo Wurmus
2018-11-08gnu: ncbi-vdb: Update to 2.9.3....* gnu/packages/bioinformatics.scm (ncbi-vdb): Update to 2.9.3. Ricardo Wurmus
2018-11-08gnu: ngs-sdk: Update to 2.9.3....* gnu/packages/bioinformatics.scm (ngs-sdk): Update to 2.9.3. Ricardo Wurmus
2018-11-08gnu: ngs-sdk: Use INVOKE....* gnu/packages/bioinformatics.scm (ngs-sdk)[arguments]: Use INVOKE and return #T unconditionally. Ricardo Wurmus
2018-11-08gnu: emboss: Use INVOKE....* gnu/packages/bioinformatics.scm (emboss)[arguments]: Use INVOKE and return #T unconditionally. Ricardo Wurmus
2018-11-08gnu: taxtastic: Use INVOKE....* gnu/packages/bioinformatics.scm (taxtastic)[arguments]: Use INVOKE and return #T unconditionally. Ricardo Wurmus
2018-11-08gnu: sra-tools: Use INVOKE....* gnu/packages/bioinformatics.scm (sra-tools)[arguments]: Use INVOKE and return #T unconditionally. Ricardo Wurmus
2018-11-08gnu: muscle: Use INVOKE....* gnu/packages/bioinformatics.scm (muscle)[arguments]: Use INVOKE and return #T unconditionally. Ricardo Wurmus
2018-11-08gnu: newick-utils: Remove custom autoconf phase....* gnu/packages/bioinformatics.scm (newick-utils)[arguments]: Remove. Ricardo Wurmus
2018-11-08gnu: mash: Remove custom autoconf phase....* gnu/packages/bioinformatics.scm (mash)[arguments]: Remove autoconf phase. Ricardo Wurmus
2018-11-08gnu: vsearch: Remove custom autogen phase....* gnu/packages/bioinformatics.scm (vsearch)[arguments]: Remove. Ricardo Wurmus
2018-11-08gnu: java-picard-1.113: Use INVOKE....* gnu/packages/bioinformatics.scm (java-picard-1.113)[arguments]: Use INVOKE and return #T unconditionally. Ricardo Wurmus
2018-11-08gnu: fraggenescan: Use INVOKE....* gnu/packages/bioinformatics.scm (fraggenescan)[arguments]: Use INVOKE in build phases and return #T unconditionally. Ricardo Wurmus
2018-11-08gnu: sailfish: Fetch sources from git....* gnu/packages/bioinformatics.scm (sailfish)[source]: Fetch from git. Ricardo Wurmus
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