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* gnu: r-annotationhub: Update to 2.14.4.•••* gnu/packages/bioinformatics.scm (r-annotationhub): Update to 2.14.4. Ricardo Wurmus2019-03-081-2/+2
* gnu: r-rhtslib: Update to 1.14.1.•••* gnu/packages/bioinformatics.scm (r-rhtslib): Update to 1.14.1. Ricardo Wurmus2019-03-081-2/+2
* gnu: r-genomicfeatures: Update to 1.34.4.•••* gnu/packages/bioinformatics.scm (r-genomicfeatures): Update to 1.34.4. Ricardo Wurmus2019-03-081-2/+2
* gnu: r-rtracklayer: Update to 1.42.2.•••* gnu/packages/bioinformatics.scm (r-rtracklayer): Update to 1.42.2. Ricardo Wurmus2019-03-081-2/+2
* gnu: r-rsamtools: Update to 1.34.1.•••* gnu/packages/bioinformatics.scm (r-rsamtools): Update to 1.34.1. Ricardo Wurmus2019-03-081-2/+2
* gnu: r-biocparallel: Update to 1.16.6.•••* gnu/packages/bioinformatics.scm (r-biocparallel): Update to 1.16.6. Ricardo Wurmus2019-03-081-2/+2
* gnu: r-variantannotation: Update to 1.28.11.•••* gnu/packages/bioinformatics.scm (r-variantannotation): Update to 1.28.11. Ricardo Wurmus2019-03-081-2/+2
* gnu: r-genomeinfodb: Update to 1.18.2.•••* gnu/packages/bioinformatics.scm (r-genomeinfodb): Update to 1.18.2. Ricardo Wurmus2019-03-081-2/+2
* gnu: r-dexseq: Update to 1.28.2.•••* gnu/packages/bioinformatics.scm (r-dexseq): Update to 1.28.2. Ricardo Wurmus2019-03-081-2/+2
* gnu: cd-hit: Support longer sequences.•••* gnu/packages/bioinformatics.scm (cd-hit)[arguments]: Pass MAX_SEQ to make flags. Ricardo Wurmus2019-03-071-1/+3
* gnu: 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 Wurmus2019-03-061-26/+0
* gnu: 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 Wurmus2019-03-061-26/+0
* gnu: 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 Wurmus2019-03-061-26/+0
* gnu: 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 Wurmus2019-03-061-26/+0
* gnu: 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 Wurmus2019-03-061-35/+0
* gnu: 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 Wurmus2019-03-061-32/+0
* gnu: 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 Wurmus2019-03-061-32/+0
* gnu: 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 Wurmus2019-03-061-32/+0
* gnu: 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 Wurmus2019-03-061-32/+0
* gnu: 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 Wurmus2019-03-061-31/+0
* gnu: 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 Wurmus2019-03-061-31/+0
* gnu: 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 Wurmus2019-03-061-31/+0
* gnu: 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 Wurmus2019-03-061-32/+0
* gnu: 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 Wurmus2019-03-061-25/+0
* gnu: 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 Wurmus2019-03-061-23/+0
* gnu: 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 Wurmus2019-03-061-14/+34
* gnu: Add r-scde.•••* gnu/packages/bioinformatics.scm (r-scde): New variable. Ricardo Wurmus2019-03-061-0/+42
* gnu: Add bowtie1.•••* gnu/packages/bioinformatics.scm (bowtie1): New variable. Ricardo Wurmus2019-03-061-0/+40
* gnu: Add genrich.•••* gnu/packages/bioinformatics.scm (genrich): New variable. Ricardo Wurmus2019-03-061-0/+32
* gnu: r-dnacopy: Remove duplicate definition.•••Reported by Christopher Baines <mail@cbaines.net>. * gnu/packages/bioinformatics.scm (r-dnacopy): Remove variable. Ricardo Wurmus2019-03-061-22/+0
* gnu: pigx-chipseq: Update to 0.0.31.•••* gnu/packages/bioinformatics.scm (pigx-chipseq): Update to 0.0.31. Ricardo Wurmus2019-03-021-2/+2
* gnu: Add velvet.•••* gnu/packages/bioinformatics.scm (velvet): New variable. Ricardo Wurmus2019-03-011-0/+58
* gnu: 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 Wurmus2019-03-011-6/+1
* gnu: flexbar: Fix reproducibility bug.•••* gnu/packages/bioinformatics.scm (flexbar)[arguments]: Add phase "do-not-tune-to-CPU". Ricardo Wurmus2019-02-271-0/+5
* gnu: pigx-chipseq: Update to 0.0.21.•••* gnu/packages/bioinformatics.scm (pigx-chipseq): Update to 0.0.21. Ricardo Wurmus2019-02-251-2/+2
* gnu: discrover: Replace "texlive" with a texlive-union.•••* 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. Ricardo Wurmus2019-02-251-19/+41
* gnu: pplacer: Remove the package, which is affected by a CVE on ocaml@4.01.•••This makes progress towards fixing <https://bugs.gnu.org/27462>. * gnu/packages/bioinformatics.scm (pplacer, pplacer-scripts): Remove variables. Andreas Enge2019-02-191-124/+0
* gnu: Remove unneeded uses of python{,2}-minimal.•••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. Marius Bakke2019-02-171-1/+1
* gnu: Add python-pyfit-sne.•••* gnu/packages/bioinformatics.scm (python-pyfit-sne): New variable. Ricardo Wurmus2019-02-151-0/+30
* gnu: python-pybedtools: Update to 0.8.0 and fix build.•••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. Maxim Cournoyer2019-02-121-47/+67
* gnu: Add cnvkit.•••* gnu/packages/bioinformatics.scm (cnvkit): New variable. Ricardo Wurmus2019-02-121-0/+36
* gnu: rcas-web: Update to 0.1.0.•••* gnu/packages/bioinformatics.scm (rcas-web): Update to 0.1.0. [inputs]: Replace guile2.2-redis with guile-redis. Ricardo Wurmus2019-02-081-3/+3
* gnu: star: Update to 2.7.0b.•••* gnu/packages/bioinformatics.scm (star): Update to 2.7.0b. [arguments]: Add "add-missing-header" build phase. Ricardo Wurmus2019-02-061-2/+9
* gnu: star: Update to 2.7.0a.•••* gnu/packages/bioinformatics.scm (star): Update to 2.7.0a. Ricardo Wurmus2019-01-301-2/+2
* gnu: r-genomicfeatures: Update to 1.34.2.•••* gnu/packages/bioinformatics.scm (r-genomicfeatures): Update to 1.34.2. Ricardo Wurmus2019-01-281-2/+2
* gnu: r-variantannotation: Update to 1.28.10.•••* gnu/packages/bioinformatics.scm (r-variantannotation): Update to 1.28.10. Ricardo Wurmus2019-01-281-2/+2
* gnu: r-qtl: Update to 1.44-9.•••* gnu/packages/bioinformatics.scm (r-qtl): Update to 1.44-9. Ricardo Wurmus2019-01-281-2/+2
* gnu: r-optparse: Update to 1.6.1.•••* gnu/packages/bioinformatics.scm (r-optparse): Update to 1.6.1. Ricardo Wurmus2019-01-281-2/+2
* gnu: Move most packages from guile.scm to new module.•••* gnu/packages/guile.scm (artanis, guildhall, guile-aspell, guile-bash, guile-8sync, guile-daemon, guile-dsv, guile-fibers, guile-syntax-highlight, guile-sjson, guile-colorized, guile-pfds, guile-aa-tree, guile-simple-zmq, jupyter-guile-kernel, guile-sparql, guile-debbugs, guile-email, guile-debbugs-next, guile-newt, guile-mastodon, guile-parted, guile-xosd, guile-dbi, guile-dbd-sqlite3, guile-config, guile-hall, guile-ics, guile-wisp, guile-sly, g-wrap, guile-miniadapton, guile-reader, guile2.2-reader, guile-ncurses, guile-ncurses/gpm, guile-lib, guile2.0-lib, guile2.2-lib, guile-minikanren, guile2.0-minikanren, guile2.2-minikanren, guile-irregex, guile2.0-irregex, guile2.2-irregex, haunt, guile2.0-haunt, guile2.2-haunt, guile-redis, guile2.0-redis, guile2.2-redis, guile-commonmark, guile2.0-commonmark, guile2.2-commonmark, mcron, mcron2): Move these variables from here... * gnu/packages/guile-xyz.scm: ...to this new file. * gnu/local.mk (GNU_SYSTEM_MODULES): Add it. * gnu/installer.scm, gnu/packages/bioinformatics.scm, gnu/packages/ci.scm, gnu/packages/gtk.scm, gnu/packages/guile.scm, gnu/packages/mail.scm, gnu/packages/package-management.scm, gnu/packages/skribilo.scm, gnu/packages/web.scm, gnu/services/mcron.scm: Update module references. Ricardo Wurmus2019-01-281-0/+1
* gnu: pepr: Use PYPI-URI.•••* gnu/packages/bioinformatics.scm (pepr)[source]: Use PYPI-URI. Ricardo Wurmus2019-01-251-2/+1
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