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2019-03-22gnu: Add starlong.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (starlong): New variable.
2019-03-21gnu: r-diversitree: Update to 0.9-11.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-diversitree): Update to 0.9-11.
2019-03-21gnu: r-maldiquant: Update to 1.19.2.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-maldiquant): Update to 1.19.2.
2019-03-21gnu: r-diversitree: Fix typo.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-diversitree)[propagated-inputs]: Fix typo in package labels.
2019-03-20gnu: r-annotationhub: Update to 2.14.5.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-annotationhub): Update to 2.14.5.
2019-03-20gnu: r-genomicfeatures: Update to 1.34.6.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-genomicfeatures): Update to 1.34.6.
2019-03-20gnu: r-variantannotation: Update to 1.28.13.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-variantannotation): Update to 1.28.13.
2019-03-20gnu: r-category: Update to 2.48.1.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-category): Update to 2.48.1.
2019-03-20gnu: r-dexseq: Update to 1.28.3.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-dexseq): Update to 1.28.3.
2019-03-20gnu: Add adapterremoval.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (adapterremoval): New variable.
2019-03-19gnu: nanopolish: Use python-wrapper.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (nanopolish)[inputs]: Replace "python" with "python-wrapper" as scripts require "python" executable.
2019-03-19gnu: nanopolish: Remove bundled library sources.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (nanopolish)[source]: Add snippet to remove bundled htslib sources.
2019-03-18gnu: python-biom-format: Fix build.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (python-biom-format)[source]: Remove generated C files. [arguments]: Disable second broken test.
2019-03-18gnu: Add bbmap.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (bbmap): New variable.
2019-03-18gnu: blasr: Add home page.Ricardo Wurmus
Reported by Efraim Flashner <efraim@flashner.co.il> on IRC. * gnu/packages/bioinformatics.scm (blasr)[home-page]: Add it.
2019-03-18gnu: Add arriba.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (arriba): New variable.
2019-03-18gnu: Add blasr.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (blasr): New variable.
2019-03-18gnu: Add blasr-libcpp.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (blasr-libcpp): New variable.
2019-03-18gnu: Add pbbam.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (pbbam): New variable.
2019-03-15gnu: Add bwa-meth.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (bwa-meth): New variable.
2019-03-13gnu: Add python-velocyto.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (python-velocyto): New variable.
2019-03-13gnu: python-loompy: Update to 2.0.17.Ricardo Wurmus
* 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.
2019-03-13gnu: Add tetoolkit.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (tetoolkit): New variable.
2019-03-12gnu: r-qvalue: Move to (gnu packages bioconductor).Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-qvalue): Move from here... * gnu/packages/bioconductor.scm (r-qvalue): ...to here.
2019-03-08gnu: blast+: Update to 2.7.1.Ricardo Wurmus
* 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.
2019-03-08gnu: r-mzr: Update to 2.16.2.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-mzr): Update to 2.16.2. [inputs]: Replace "boost" with "boost-for-mysql".
2019-03-08gnu: r-gviz: Update to 1.26.5.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-gviz): Update to 1.26.5.
2019-03-08gnu: r-ensembldb: Update to 2.6.7.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-ensembldb): Update to 2.6.7.
2019-03-08gnu: r-annotationhub: Update to 2.14.4.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-annotationhub): Update to 2.14.4.
2019-03-08gnu: r-rhtslib: Update to 1.14.1.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-rhtslib): Update to 1.14.1.
2019-03-08gnu: r-genomicfeatures: Update to 1.34.4.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-genomicfeatures): Update to 1.34.4.
2019-03-08gnu: r-rtracklayer: Update to 1.42.2.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-rtracklayer): Update to 1.42.2.
2019-03-08gnu: r-rsamtools: Update to 1.34.1.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-rsamtools): Update to 1.34.1.
2019-03-08gnu: r-biocparallel: Update to 1.16.6.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-biocparallel): Update to 1.16.6.
2019-03-08gnu: r-variantannotation: Update to 1.28.11.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-variantannotation): Update to 1.28.11.
2019-03-08gnu: r-genomeinfodb: Update to 1.18.2.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-genomeinfodb): Update to 1.18.2.
2019-03-08gnu: r-dexseq: Update to 1.28.2.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-dexseq): Update to 1.28.2.
2019-03-07gnu: cd-hit: Support longer sequences.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (cd-hit)[arguments]: Pass MAX_SEQ to make flags.
2019-03-06gnu: r-org-mm-eg-db: Move to (gnu packages bioconductor).Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-org-mm-eg-db): Move from here... * gnu/packages/bioconductor.scm (r-org-mm-eg-db): ...to here.
2019-03-06gnu: r-org-hs-eg-db: Move to (gnu packages bioconductor).Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-org-hs-eg-db): Move from here... * gnu/packages/bioconductor.scm (r-org-hs-eg-db): ...to here.
2019-03-06gnu: r-org-dm-eg-db: Move to (gnu packages bioconductor).Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-org-dm-eg-db): Move from here... * gnu/packages/bioconductor.scm (r-org-dm-eg-db): ...to here.
2019-03-06gnu: r-org-ce-eg-db: Move to (gnu packages bioconductor).Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-org-ce-eg-db): Move from here... * gnu/packages/bioconductor.scm (r-org-ce-eg-db): ...to here.
2019-03-06gnu: r-txdb-mmusculus-ucsc-mm10-knowngene: Move to (gnu packages bioconductor).Ricardo Wurmus
* 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.
2019-03-06gnu: r-bsgenome-dmelanogaster-ucsc-dm3: Move to (gnu packages bioconductor).Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-bsgenome-dmelanogaster-ucsc-dm3): Move from here... * gnu/packages/bioconductor.scm (r-bsgenome-dmelanogaster-ucsc-dm3): ...to here.
2019-03-06gnu: r-bsgenome-celegans-ucsc-ce10: Move to (gnu packages bioconductor).Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-bsgenome-celegans-ucsc-ce10): Move from here... * gnu/packages/bioconductor.scm (r-bsgenome-celegans-ucsc-ce10): ...to here.
2019-03-06gnu: r-bsgenome-celegans-ucsc-ce6: Move to (gnu packages bioconductor).Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-bsgenome-celegans-ucsc-ce6): Move from here... * gnu/packages/bioconductor.scm (r-bsgenome-celegans-ucsc-ce6): ...to here.
2019-03-06gnu: r-bsgenome-mmusculus-ucsc-mm10: Move to (gnu packages bioconductor).Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-bsgenome-mmusculus-ucsc-mm10): Move from here... * gnu/packages/bioconductor.scm (r-bsgenome-mmusculus-ucsc-mm10): ...to here.
2019-03-06gnu: r-bsgenome-mmusculus-ucsc-mm9: Move to (gnu packages bioconductor).Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-bsgenome-mmusculus-ucsc-mm9): Move from here... * gnu/packages/bioconductor.scm (r-bsgenome-mmusculus-ucsc-mm9): ...to here.
2019-03-06gnu: r-bsgenome-hsapiens-ucsc-hg19: Move to (gnu packages bioconductor).Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-bsgenome-hsapiens-ucsc-hg19): Move from here... * gnu/packages/bioconductor.scm (r-bsgenome-hsapiens-ucsc-hg19): ...to here.
2019-03-06gnu: r-bsgenome-hsapiens-1000genomes-hs37d5: Move to (gnu packages ↵Ricardo Wurmus
bioconductor). * gnu/packages/bioinformatics.scm (r-bsgenome-hsapiens-1000genomes-hs37d5): Move from here... * gnu/packages/bioconductor.scm (r-bsgenome-hsapiens-1000genomes-hs37d5): ...to here.
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