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2019-01-12gnu: r-singlecellexperiment: Update to 1.4.1....* gnu/packages/bioinformatics.scm (r-singlecellexperiment): Update to 1.4.1. Ricardo Wurmus
2019-01-12gnu: r-rhdf5lib: Update to 1.4.2....* gnu/packages/bioinformatics.scm (r-rhdf5lib): Update to 1.4.2. Ricardo Wurmus
2019-01-12gnu: r-hdf5array: Update to 1.10.1....* gnu/packages/bioinformatics.scm (r-hdf5array): Update to 1.10.1. Ricardo Wurmus
2019-01-12gnu: r-qvalue: Update to 2.14.1....* gnu/packages/bioinformatics.scm (r-qvalue): Update to 2.14.1. Ricardo Wurmus
2019-01-12gnu: r-gviz: Update to 1.26.4....* gnu/packages/bioinformatics.scm (r-gviz): Update to 1.26.4. Ricardo Wurmus
2019-01-12gnu: r-biovizbase: Update to 1.30.1....* gnu/packages/bioinformatics.scm (r-biovizbase): Update to 1.30.1. Ricardo Wurmus
2019-01-12gnu: r-ensembldb: Update to 2.6.3....* gnu/packages/bioinformatics.scm (r-ensembldb): Update to 2.6.3. Ricardo Wurmus
2019-01-12gnu: r-dirichletmultinomial: Update to 1.24.1....* gnu/packages/bioinformatics.scm (r-dirichletmultinomial): Update to 1.24.1. Ricardo Wurmus
2019-01-12gnu: r-gage: Update to 2.32.1....* gnu/packages/bioinformatics.scm (r-gage): Update to 2.32.1. Ricardo Wurmus
2019-01-12gnu: r-annotationhub: Update to 2.14.2....* gnu/packages/bioinformatics.scm (r-annotationhub): Update to 2.14.2. Ricardo Wurmus
2019-01-12gnu: r-edaseq: Update to 2.16.3....* gnu/packages/bioinformatics.scm (r-edaseq): Update to 2.16.3. [propagated-inputs]: Add r-biocmanager. Ricardo Wurmus
2019-01-12gnu: r-deseq: Update to 1.34.1....* gnu/packages/bioinformatics.scm (r-deseq): Update to 1.34.1. Ricardo Wurmus
2019-01-12gnu: r-msnid: Update to 1.16.1....* gnu/packages/bioinformatics.scm (r-msnid): Update to 1.16.1. Ricardo Wurmus
2019-01-12gnu: r-msnbase: Update to 2.8.3....* gnu/packages/bioinformatics.scm (r-msnbase): Update to 2.8.3. Ricardo Wurmus
2019-01-12gnu: r-mzid: Update to 1.20.1....* gnu/packages/bioinformatics.scm (r-mzid): Update to 1.20.1. Ricardo Wurmus
2019-01-12gnu: r-mzr: Update to 2.16.1....* gnu/packages/bioinformatics.scm (r-mzr): Update to 2.16.1. Ricardo Wurmus
2019-01-12gnu: r-sva: Update to 3.30.1....* gnu/packages/bioinformatics.scm (r-sva): Update to 3.30.1. Ricardo Wurmus
2019-01-12gnu: r-methylkit: Update to 1.8.1....* gnu/packages/bioinformatics.scm (r-methylkit): Update to 1.8.1. Ricardo Wurmus
2019-01-12gnu: r-copywriter: Update to 2.14.1....* gnu/packages/bioinformatics.scm (r-copywriter): Update to 2.14.1. Ricardo Wurmus
2019-01-12gnu: r-rhdf5: Update to 2.26.2....* gnu/packages/bioinformatics.scm (r-rhdf5): Update to 2.26.2. Ricardo Wurmus
2019-01-12gnu: r-tximport: Update to 1.10.1....* gnu/packages/bioinformatics.scm (r-tximport): Update to 1.10.1. Ricardo Wurmus
2019-01-12gnu: r-genomicalignments: Update to 1.18.1....* gnu/packages/bioinformatics.scm (r-genomicalignments): Update to 1.18.1. Ricardo Wurmus
2019-01-12gnu: r-biostrings: Update to 2.50.2....* gnu/packages/bioinformatics.scm (r-biostrings): Update to 2.50.2. Ricardo Wurmus
2019-01-12gnu: r-biocparallel: Update to 1.16.5....* gnu/packages/bioinformatics.scm (r-biocparallel): Update to 1.16.5. Ricardo Wurmus
2019-01-12gnu: r-limma: Update to 3.38.3....* gnu/packages/bioinformatics.scm (r-limma): Update to 3.38.3. Ricardo Wurmus
2019-01-12gnu: r-variantannotation: Update to 1.28.8....* gnu/packages/bioinformatics.scm (r-variantannotation): Update to 1.28.8. Ricardo Wurmus
2019-01-12gnu: r-edger: Update to 3.24.3....* gnu/packages/bioinformatics.scm (r-edger): Update to 3.24.3. Ricardo Wurmus
2019-01-12gnu: r-biocviews: Update to 1.50.10....* gnu/packages/bioinformatics.scm (r-biocviews): Update to 1.50.10. Ricardo Wurmus
2019-01-12gnu: r-systempiper: Update to 1.16.1....* gnu/packages/bioinformatics.scm (r-systempiper): Update to 1.16.1. Ricardo Wurmus
2019-01-12gnu: r-rbgl: Update to 1.58.1....* gnu/packages/bioinformatics.scm (r-rbgl): Update to 1.58.1. Ricardo Wurmus
2019-01-12gnu: r-dexseq: Update to 1.28.1....* gnu/packages/bioinformatics.scm (r-dexseq): Update to 1.28.1. Ricardo Wurmus
2019-01-12gnu: r-deseq2: Update to 1.22.2....* gnu/packages/bioinformatics.scm (r-deseq2): Update to 1.22.2. Ricardo Wurmus
2019-01-12gnu: r-scran: Update to 1.10.2....* gnu/packages/bioinformatics.scm (r-scran): Update to 1.10.2. Ricardo Wurmus
2019-01-12gnu: r-seqminer: Update to 7.1....* gnu/packages/bioinformatics.scm (r-seqminer): Update to 7.1. Ricardo Wurmus
2019-01-12gnu: r-bookdown: Update to 0.9....* gnu/packages/bioinformatics.scm (r-bookdown): Update to 0.9. Ricardo Wurmus
2019-01-12gnu: Move Java compression packages to new module....* gnu/packages/compression.scm (bitshuffle-for-snappy): Export variable. (java-snappy, java-snappy-1, java-iq80-snappy, java-jbzip2, java-tukaani-xz): Move these variables from here... * gnu/packages/java-compression.scm: ...to this new file. * gnu/local.mk (GNU_SYSTEM_MODULES): Add it. * gnu/packages/java.scm, gnu/packages/bioinformatics.scm: Adjust module references. Ricardo Wurmus
2019-01-11gnu: jamm: Remove broken "build" phase....* gnu/packages/bioinformatics.scm (jamm)[arguments]: Remove "build" phase. Ricardo Wurmus
2019-01-07gnu: mantis: Limit to x86_64-linux....* gnu/packages/bioinformatics.scm (mantis)[supported-systems]: New field. Efraim Flashner
2019-01-07gnu: Add mantis....* gnu/packages/bioinformatics.scm (mantis): New variable. Ricardo Wurmus
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
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