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2019-03-18gnu: python-biom-format: Fix build....* gnu/packages/bioinformatics.scm (python-biom-format)[source]: Remove generated C files. [arguments]: Disable second broken test. Ricardo Wurmus
2019-03-18gnu: Add bbmap....* gnu/packages/bioinformatics.scm (bbmap): New variable. Ricardo Wurmus
2019-03-18gnu: blasr: Add home page....Reported by Efraim Flashner <efraim@flashner.co.il> on IRC. * gnu/packages/bioinformatics.scm (blasr)[home-page]: Add it. Ricardo Wurmus
2019-03-18gnu: Add arriba....* gnu/packages/bioinformatics.scm (arriba): New variable. Ricardo Wurmus
2019-03-18gnu: Add blasr....* gnu/packages/bioinformatics.scm (blasr): New variable. Ricardo Wurmus
2019-03-18gnu: Add blasr-libcpp....* gnu/packages/bioinformatics.scm (blasr-libcpp): New variable. Ricardo Wurmus
2019-03-18gnu: Add pbbam....* gnu/packages/bioinformatics.scm (pbbam): New variable. Ricardo Wurmus
2019-03-15gnu: Add bwa-meth....* gnu/packages/bioinformatics.scm (bwa-meth): New variable. Ricardo Wurmus
2019-03-13gnu: Add python-velocyto....* gnu/packages/bioinformatics.scm (python-velocyto): New variable. Ricardo Wurmus
2019-03-13gnu: python-loompy: Update to 2.0.17....* gnu/packages/bioinformatics.scm (python-loompy): Update to 2.0.17. [source]: Fetch via git. [arguments]: Enable tests, replace "check" phase. [propagated-inputs]: Add python-pandas. [native-inputs]: Add python-pytest. Ricardo Wurmus
2019-03-13gnu: Add tetoolkit....* gnu/packages/bioinformatics.scm (tetoolkit): New variable. Ricardo Wurmus
2019-03-12gnu: r-qvalue: Move to (gnu packages bioconductor)....* gnu/packages/bioinformatics.scm (r-qvalue): Move from here... * gnu/packages/bioconductor.scm (r-qvalue): ...to here. Ricardo Wurmus
2019-03-08gnu: blast+: Update to 2.7.1....* gnu/packages/bioinformatics.scm (blast+): Update to 2.7.1. [inputs]: Add lmdb. [source]: Remove obsolete patch. * gnu/package/patches/blast+-fix-makefile.patch: Remove patch. * gnu/local.mk (dist_patch_DATA): Remove it. Ricardo Wurmus
2019-03-08gnu: r-mzr: Update to 2.16.2....* gnu/packages/bioinformatics.scm (r-mzr): Update to 2.16.2. [inputs]: Replace "boost" with "boost-for-mysql". Ricardo Wurmus
2019-03-08gnu: r-gviz: Update to 1.26.5....* gnu/packages/bioinformatics.scm (r-gviz): Update to 1.26.5. Ricardo Wurmus
2019-03-08gnu: r-ensembldb: Update to 2.6.7....* gnu/packages/bioinformatics.scm (r-ensembldb): Update to 2.6.7. Ricardo Wurmus
2019-03-08gnu: r-annotationhub: Update to 2.14.4....* gnu/packages/bioinformatics.scm (r-annotationhub): Update to 2.14.4. Ricardo Wurmus
2019-03-08gnu: r-rhtslib: Update to 1.14.1....* gnu/packages/bioinformatics.scm (r-rhtslib): Update to 1.14.1. Ricardo Wurmus
2019-03-08gnu: r-genomicfeatures: Update to 1.34.4....* gnu/packages/bioinformatics.scm (r-genomicfeatures): Update to 1.34.4. Ricardo Wurmus
2019-03-08gnu: r-rtracklayer: Update to 1.42.2....* gnu/packages/bioinformatics.scm (r-rtracklayer): Update to 1.42.2. Ricardo Wurmus
2019-03-08gnu: r-rsamtools: Update to 1.34.1....* gnu/packages/bioinformatics.scm (r-rsamtools): Update to 1.34.1. Ricardo Wurmus
2019-03-08gnu: r-biocparallel: Update to 1.16.6....* gnu/packages/bioinformatics.scm (r-biocparallel): Update to 1.16.6. Ricardo Wurmus
2019-03-08gnu: r-variantannotation: Update to 1.28.11....* gnu/packages/bioinformatics.scm (r-variantannotation): Update to 1.28.11. Ricardo Wurmus
2019-03-08gnu: r-genomeinfodb: Update to 1.18.2....* gnu/packages/bioinformatics.scm (r-genomeinfodb): Update to 1.18.2. Ricardo Wurmus
2019-03-08gnu: r-dexseq: Update to 1.28.2....* gnu/packages/bioinformatics.scm (r-dexseq): Update to 1.28.2. Ricardo Wurmus
2019-03-07gnu: cd-hit: Support longer sequences....* gnu/packages/bioinformatics.scm (cd-hit)[arguments]: Pass MAX_SEQ to make flags. Ricardo Wurmus
2019-03-06gnu: r-org-mm-eg-db: Move to (gnu packages bioconductor)....* gnu/packages/bioinformatics.scm (r-org-mm-eg-db): Move from here... * gnu/packages/bioconductor.scm (r-org-mm-eg-db): ...to here. Ricardo Wurmus
2019-03-06gnu: r-org-hs-eg-db: Move to (gnu packages bioconductor)....* gnu/packages/bioinformatics.scm (r-org-hs-eg-db): Move from here... * gnu/packages/bioconductor.scm (r-org-hs-eg-db): ...to here. Ricardo Wurmus
2019-03-06gnu: r-org-dm-eg-db: Move to (gnu packages bioconductor)....* gnu/packages/bioinformatics.scm (r-org-dm-eg-db): Move from here... * gnu/packages/bioconductor.scm (r-org-dm-eg-db): ...to here. Ricardo Wurmus
2019-03-06gnu: r-org-ce-eg-db: Move to (gnu packages bioconductor)....* gnu/packages/bioinformatics.scm (r-org-ce-eg-db): Move from here... * gnu/packages/bioconductor.scm (r-org-ce-eg-db): ...to here. Ricardo Wurmus
2019-03-06gnu: r-txdb-mmusculus-ucsc-mm10-knowngene: Move to (gnu packages bioconductor)....* gnu/packages/bioinformatics.scm (r-txdb-mmusculus-ucsc-mm10-knowngene): Move from here... * gnu/packages/bioconductor.scm (r-txdb-mmusculus-ucsc-mm10-knowngene): ...to here. Ricardo Wurmus
2019-03-06gnu: r-bsgenome-dmelanogaster-ucsc-dm3: Move to (gnu packages bioconductor)....* gnu/packages/bioinformatics.scm (r-bsgenome-dmelanogaster-ucsc-dm3): Move from here... * gnu/packages/bioconductor.scm (r-bsgenome-dmelanogaster-ucsc-dm3): ...to here. Ricardo Wurmus
2019-03-06gnu: r-bsgenome-celegans-ucsc-ce10: Move to (gnu packages bioconductor)....* gnu/packages/bioinformatics.scm (r-bsgenome-celegans-ucsc-ce10): Move from here... * gnu/packages/bioconductor.scm (r-bsgenome-celegans-ucsc-ce10): ...to here. Ricardo Wurmus
2019-03-06gnu: r-bsgenome-celegans-ucsc-ce6: Move to (gnu packages bioconductor)....* gnu/packages/bioinformatics.scm (r-bsgenome-celegans-ucsc-ce6): Move from here... * gnu/packages/bioconductor.scm (r-bsgenome-celegans-ucsc-ce6): ...to here. Ricardo Wurmus
2019-03-06gnu: r-bsgenome-mmusculus-ucsc-mm10: Move to (gnu packages bioconductor)....* gnu/packages/bioinformatics.scm (r-bsgenome-mmusculus-ucsc-mm10): Move from here... * gnu/packages/bioconductor.scm (r-bsgenome-mmusculus-ucsc-mm10): ...to here. Ricardo Wurmus
2019-03-06gnu: r-bsgenome-mmusculus-ucsc-mm9: Move to (gnu packages bioconductor)....* gnu/packages/bioinformatics.scm (r-bsgenome-mmusculus-ucsc-mm9): Move from here... * gnu/packages/bioconductor.scm (r-bsgenome-mmusculus-ucsc-mm9): ...to here. Ricardo Wurmus
2019-03-06gnu: r-bsgenome-hsapiens-ucsc-hg19: Move to (gnu packages bioconductor)....* gnu/packages/bioinformatics.scm (r-bsgenome-hsapiens-ucsc-hg19): Move from here... * gnu/packages/bioconductor.scm (r-bsgenome-hsapiens-ucsc-hg19): ...to here. Ricardo Wurmus
2019-03-06gnu: r-bsgenome-hsapiens-1000genomes-hs37d5: Move to (gnu packages bioconduct......* gnu/packages/bioinformatics.scm (r-bsgenome-hsapiens-1000genomes-hs37d5): Move from here... * gnu/packages/bioconductor.scm (r-bsgenome-hsapiens-1000genomes-hs37d5): ...to here. Ricardo Wurmus
2019-03-06gnu: r-txdb-hsapiens-ucsc-hg19-knowngene: Move to (gnu packages bioconductor)....* gnu/packages/bioinformatics.scm (r-txdb-hsapiens-ucsc-hg19-knowngene): Move from here... * gnu/packages/bioconductor.scm (r-txdb-hsapiens-ucsc-hg19-knowngene): ...to here. Ricardo Wurmus
2019-03-06gnu: r-geneplotter: Move to (gnu packages bioconductor)....* gnu/packages/bioinformatics.scm (r-geneplotter): Move from here... * gnu/packages/bioconductor.scm (r-geneplotter): ...to here. Ricardo Wurmus
2019-03-06gnu: r-copynumber: Move to (gnu packages bioconductor)....* gnu/packages/bioinformatics.scm (r-copynumber): Move from here... * gnu/packages/bioconductor.scm (r-copynumber): ...to here. Ricardo Wurmus
2019-03-06gnu: bismark: Update to 0.20.1....* gnu/packages/bioinformatics.scm (bismark): Update to 0.20.1. [source]: Remove obsolete snippet. [arguments]: Add build phase "replace-plotly.js" and add requried modules; adjust "install" phase. [inputs]: Add perl-carp and perl-getopt-long. [native-inputs]: Add plotly.js and uglify-js. Ricardo Wurmus
2019-03-06gnu: Add r-scde....* gnu/packages/bioinformatics.scm (r-scde): New variable. Ricardo Wurmus
2019-03-06gnu: Add bowtie1....* gnu/packages/bioinformatics.scm (bowtie1): New variable. Ricardo Wurmus
2019-03-06gnu: Add genrich....* gnu/packages/bioinformatics.scm (genrich): New variable. Ricardo Wurmus
2019-03-06gnu: r-dnacopy: Remove duplicate definition....Reported by Christopher Baines <mail@cbaines.net>. * gnu/packages/bioinformatics.scm (r-dnacopy): Remove variable. Ricardo Wurmus
2019-03-02gnu: pigx-chipseq: Update to 0.0.31....* gnu/packages/bioinformatics.scm (pigx-chipseq): Update to 0.0.31. Ricardo Wurmus
2019-03-01gnu: Add velvet....* gnu/packages/bioinformatics.scm (velvet): New variable. Ricardo Wurmus
2019-03-01gnu: discrover: Remove indirect TexLive dependencies....* gnu/packages/bioinformatics.scm (discrover)[native-inputs]: Remove texlive-generic-ifxetex, texlive-latex-oberdiek, texlive-latex-url, and texlive-latex-xcolor from texlive-union. Ricardo Wurmus
2019-02-27gnu: flexbar: Fix reproducibility bug....* gnu/packages/bioinformatics.scm (flexbar)[arguments]: Add phase "do-not-tune-to-CPU". Ricardo Wurmus
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