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2019-03-29gnu: Add python-bbknn.•••* gnu/packages/bioinformatics.scm (python-bbknn): New variable. Ricardo Wurmus
2019-03-27gnu: trim-galore: Add pigz.•••* gnu/packages/bioinformatics.scm (trim-galore)[inputs]: Add pigz. [arguments]: Embed reference to pigz. Ricardo Wurmus
2019-03-27gnu: trim-galore: Fix test for Python.•••* gnu/packages/bioinformatics.scm (trim-galore)[arguments]: Replace "configure" phase to skip ill-advised test for Python. Ricardo Wurmus
2019-03-27gnu: r-rhdf5lib: Update to 1.4.3.•••* gnu/packages/bioinformatics.scm (r-rhdf5lib): Update to 1.4.3. Ricardo Wurmus
2019-03-27gnu: r-genomicfeatures: Update to 1.34.7.•••* gnu/packages/bioinformatics.scm (r-genomicfeatures): Update to 1.34.7. Ricardo Wurmus
2019-03-26gnu: python-scanpy: Update to 1.4.•••* gnu/packages/bioinformatics.scm (python-scanpy): Update to 1.4. [source]: Fetch from git. [arguments]: Disable broken tests. [native-inputs]: Add python-pytest. [home-page]: Use HTTPS. Ricardo Wurmus
2019-03-26gnu: trim-galore: Update to 0.6.1.•••* gnu/packages/bioinformatics.scm (trim-galore): Update to 0.6.1. [arguments]: Adjust patching. Ricardo Wurmus
2019-03-26gnu: cutadapt: Update to 2.1.•••* gnu/packages/bioinformatics.scm (cutadapt): Update to 2.1. [source]: Fetch from pypi. [native-inputs]: Add python-setuptools-scm. Ricardo Wurmus
2019-03-25gnu: r-gkmsvm: Move to (gnu packages bioconductor).•••* gnu/packages/bioinformatics.scm (r-gkmsvm): Move from here... * gnu/packages/bioconductor.scm (r-gkmsvm): ...to here. Ricardo Wurmus
2019-03-25gnu: r-wgcna: Move to (gnu packages cran).•••* gnu/packages/bioinformatics.scm (r-wgcna): Move from here... * gnu/packages/cran.scm (r-wgcna): ...to here. Ricardo Wurmus
2019-03-25gnu: r-optparse: Move to (gnu packages cran).•••* gnu/packages/bioinformatics.scm (r-optparse): Move from here... * gnu/packages/cran.scm (r-optparse): ...to here. Ricardo Wurmus
2019-03-25gnu: r-bookdown: Move to (gnu packages cran).•••* gnu/packages/bioinformatics.scm (r-bookdown): Move from here... * gnu/packages/cran.scm (r-bookdown): ...to here. Ricardo Wurmus
2019-03-25gnu: r-sparql: Move to (gnu packages cran).•••* gnu/packages/bioinformatics.scm (r-sparql): Move from here... * gnu/packages/cran.scm (r-sparql): ...to here. Ricardo Wurmus
2019-03-24gnu: r-seqinr: Move to (gnu packages cran).•••* gnu/packages/bioinformatics.scm (r-seqinr): Move from here... * gnu/packages/cran.scm (r-seqinr): ...to here. Ricardo Wurmus
2019-03-24gnu: r-acsnminer: Move to (gnu packages cran).•••* gnu/packages/bioinformatics.scm (r-acsnminer): Move from here... * gnu/packages/cran.scm (r-acsnminer): ...to here. Ricardo Wurmus
2019-03-24gnu: r-phangorn: Update to 2.5.3.•••* gnu/packages/bioinformatics.scm (r-phangorn): Update to 2.5.3. Ricardo Wurmus
2019-03-24gnu: r-gqtlstats: Update to 1.14.1.•••* gnu/packages/bioinformatics.scm (r-gqtlstats): Update to 1.14.1. Ricardo Wurmus
2019-03-24gnu: r-rbgl: Update to 1.58.2.•••* gnu/packages/bioinformatics.scm (r-rbgl): Update to 1.58.2. Ricardo Wurmus
2019-03-22gnu: Add starlong.•••* gnu/packages/bioinformatics.scm (starlong): New variable. Ricardo Wurmus
2019-03-21gnu: r-diversitree: Update to 0.9-11.•••* gnu/packages/bioinformatics.scm (r-diversitree): Update to 0.9-11. Ricardo Wurmus
2019-03-21gnu: r-maldiquant: Update to 1.19.2.•••* gnu/packages/bioinformatics.scm (r-maldiquant): Update to 1.19.2. Ricardo Wurmus
2019-03-21gnu: r-diversitree: Fix typo.•••* gnu/packages/bioinformatics.scm (r-diversitree)[propagated-inputs]: Fix typo in package labels. Ricardo Wurmus
2019-03-20gnu: r-annotationhub: Update to 2.14.5.•••* gnu/packages/bioinformatics.scm (r-annotationhub): Update to 2.14.5. Ricardo Wurmus
2019-03-20gnu: r-genomicfeatures: Update to 1.34.6.•••* gnu/packages/bioinformatics.scm (r-genomicfeatures): Update to 1.34.6. Ricardo Wurmus
2019-03-20gnu: r-variantannotation: Update to 1.28.13.•••* gnu/packages/bioinformatics.scm (r-variantannotation): Update to 1.28.13. Ricardo Wurmus
2019-03-20gnu: r-category: Update to 2.48.1.•••* gnu/packages/bioinformatics.scm (r-category): Update to 2.48.1. Ricardo Wurmus
2019-03-20gnu: r-dexseq: Update to 1.28.3.•••* gnu/packages/bioinformatics.scm (r-dexseq): Update to 1.28.3. Ricardo Wurmus
2019-03-20gnu: Add adapterremoval.•••* gnu/packages/bioinformatics.scm (adapterremoval): New variable. Ricardo Wurmus
2019-03-19gnu: nanopolish: Use python-wrapper.•••* gnu/packages/bioinformatics.scm (nanopolish)[inputs]: Replace "python" with "python-wrapper" as scripts require "python" executable. Ricardo Wurmus
2019-03-19gnu: nanopolish: Remove bundled library sources.•••* gnu/packages/bioinformatics.scm (nanopolish)[source]: Add snippet to remove bundled htslib sources. Ricardo Wurmus
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
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