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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.
2019-03-06gnu: r-txdb-hsapiens-ucsc-hg19-knowngene: Move to (gnu packages bioconductor).Ricardo Wurmus
* 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.
2019-03-06gnu: r-geneplotter: Move to (gnu packages bioconductor).Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-geneplotter): Move from here... * gnu/packages/bioconductor.scm (r-geneplotter): ...to here.
2019-03-06gnu: r-copynumber: Move to (gnu packages bioconductor).Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-copynumber): Move from here... * gnu/packages/bioconductor.scm (r-copynumber): ...to here.
2019-03-06gnu: bismark: Update to 0.20.1.Ricardo Wurmus
* 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.
2019-03-06gnu: Add r-scde.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-scde): New variable.
2019-03-06gnu: Add bowtie1.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (bowtie1): New variable.
2019-03-06gnu: Add genrich.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (genrich): New variable.
2019-03-06gnu: r-dnacopy: Remove duplicate definition.Ricardo Wurmus
Reported by Christopher Baines <mail@cbaines.net>. * gnu/packages/bioinformatics.scm (r-dnacopy): Remove variable.
2019-03-02gnu: pigx-chipseq: Update to 0.0.31.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (pigx-chipseq): Update to 0.0.31.
2019-03-01gnu: Add velvet.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (velvet): New variable.
2019-03-01gnu: discrover: Remove indirect TexLive dependencies.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (discrover)[native-inputs]: Remove texlive-generic-ifxetex, texlive-latex-oberdiek, texlive-latex-url, and texlive-latex-xcolor from texlive-union.
2019-02-27gnu: flexbar: Fix reproducibility bug.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (flexbar)[arguments]: Add phase "do-not-tune-to-CPU".
2019-02-25gnu: pigx-chipseq: Update to 0.0.21.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (pigx-chipseq): Update to 0.0.21.
2019-02-25gnu: discrover: Replace "texlive" with a texlive-union.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (discrover)[arguments]: Add build phase "fix-latex-errors"; add build phase "setenv-HOME". [inputs]: Add rmath-standalone. [native-inputs]: Replace "texlive" with a texlive-union consisting of texlive-fonts-cm, texlive-fonts-amsfonts, texlive-generic-ifxetex, texlive-latex-doi, texlive-latex-examplep, texlive-latex-hyperref, texlive-latex-ms, texlive-latex-natbib, texlive-bibtex, texlive-latex-oberdiek, texlive-latex-pgf, texlive-latex-url, texlive-latex-verbatimbox, and texlive-latex-xcolor.
2019-02-19gnu: pplacer: Remove the package, which is affected by a CVE on ocaml@4.01.Andreas Enge
This makes progress towards fixing <https://bugs.gnu.org/27462>. * gnu/packages/bioinformatics.scm (pplacer, pplacer-scripts): Remove variables.
2019-02-17gnu: Remove unneeded uses of python{,2}-minimal.Marius Bakke
The "python-minimal" package exists mostly to resolve a dependency cycle. To reduce duplication, packages should prefer the regular Python variants. * gnu/packages/admin.scm (htop)[native-inputs]: Change PYTHON-MINIMAL-WRAPPER to PYTHON-WRAPPER. * gnu/packages/crypto.scm (botan)[native-inputs]: Likewise. * gnu/packages/bioinformatics.scm (sambamba)[native-inputs]: Change PYTHON-MINIMAL to PYTHON. * gnu/packages/dictionaries.scm (apertium)[native-inputs]: Likewise. * gnu/packages/databases.scm (mongodb)[native-inputs]: Change PYTHON2-MINIMAL to PYTHON2. * gnu/packages/games.scm (openttd-opensfx, openttd-openmsx)[native-inputs]: Likewise. * gnu/packages/gnome.scm (deja-dup)[native-inputs]: Likewise.
2019-02-15gnu: Add python-pyfit-sne.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (python-pyfit-sne): New variable.
2019-02-12gnu: python-pybedtools: Update to 0.8.0 and fix build.Maxim Cournoyer
From 40db2b4eae5ca61a3134cdaf7b156ed1ae9f7415 Mon Sep 17 00:00:00 2001 From: Maxim Cournoyer <maxim.cournoyer@gmail.com> Date: Sun, 10 Feb 2019 23:39:25 -0500 Subject: [PATCH] gnu: python-pybedtools: Update to 0.8.0 and fix build. * gnu/packages/bioinformatics.scm (python-pybedtools): Update to 0.8.0. [phases]{disable-broken-tests}: Do not disable "test_issue_157" and "test_to_dataframe" tests. Disable the "test_getting_example_beds". {remove-cython-generated-files}: Add phase. {generate-cython-extensions}: Add phase. {check}: Move from python2-pybedtools to here. Add a scripts subdirectory of the build directory to the PATH, so that the tests can call them. Invoke pytest rather than nosetests. [modules]: Move from python2-pybedtools to here. [propagated-inputs]: Depend on the current BEDTOOLS rather than version 1.26. [native-inputs]: Replace python-nose by python-pytest and add python-psutil.
2019-02-12gnu: Add cnvkit.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (cnvkit): New variable.
2019-02-08gnu: rcas-web: Update to 0.1.0.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (rcas-web): Update to 0.1.0. [inputs]: Replace guile2.2-redis with guile-redis.
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