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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.
2019-02-06gnu: star: Update to 2.7.0b.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (star): Update to 2.7.0b. [arguments]: Add "add-missing-header" build phase.
2019-01-30gnu: star: Update to 2.7.0a.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (star): Update to 2.7.0a.
2019-01-28gnu: r-genomicfeatures: Update to 1.34.2.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-genomicfeatures): Update to 1.34.2.
2019-01-28gnu: r-variantannotation: Update to 1.28.10.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-variantannotation): Update to 1.28.10.
2019-01-28gnu: r-qtl: Update to 1.44-9.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-qtl): Update to 1.44-9.
2019-01-28gnu: r-optparse: Update to 1.6.1.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-optparse): Update to 1.6.1.
2019-01-28gnu: Move most packages from guile.scm to new module.Ricardo Wurmus
* 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.
2019-01-25gnu: pepr: Use PYPI-URI.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (pepr)[source]: Use PYPI-URI.
2019-01-25gnu: python2-warpedlmm: Use PYPI-URI.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (python2-warpedlmm)[source]: Use PYPI-URI.
2019-01-15gnu: Move Python compression packages to new module.Ricardo Wurmus
* gnu/packages/compression.scm (python-lzo, python2-lzo, python-lz4, python2-lz4, python-lzstring, python2-lzstring, bitshuffle, bitshuffle-for-snappy): Move variables from here... * gnu/packages/python-compression.scm: ...to this new module. * gnu/local.mk (GNU_SYSTEM_MODULES): Add it. * gnu/packages/bioinformatics.scm, gnu/packages/java-compression.scm, gnu/packages/xorg.scm: Adjust module references.
2019-01-15gnu: Separate Python core packages from the rest.Ricardo Wurmus
* gnu/packages/python.scm: Move hundreds of package definitions from here... * gnu/packages/python-xyz.scm: ...to this new module. * gnu/local.mk (GNU_SYSTEM_MODULES): Add it. * gnu/packages/ada.scm, gnu/packages/admin.scm, gnu/packages/android.scm, gnu/packages/audio.scm, gnu/packages/backup.scm, gnu/packages/benchmark.scm, gnu/packages/bioinformatics.scm, gnu/packages/bittorrent.scm, gnu/packages/calendar.scm, gnu/packages/check.scm, gnu/packages/chemistry.scm, gnu/packages/cluster.scm, gnu/packages/compression.scm, gnu/packages/connman.scm, gnu/packages/crypto.scm, gnu/packages/cups.scm, gnu/packages/databases.scm, gnu/packages/dav.scm, gnu/packages/direct-connect.scm, gnu/packages/disk.scm, gnu/packages/django.scm, gnu/packages/dlang.scm, gnu/packages/docker.scm, gnu/packages/ebook.scm, gnu/packages/elf.scm, gnu/packages/emacs.scm, gnu/packages/emulators.scm, gnu/packages/engineering.scm, gnu/packages/enlightenment.scm, gnu/packages/finance.scm, gnu/packages/fltk.scm, gnu/packages/fontutils.scm, gnu/packages/freedesktop.scm, gnu/packages/game-development.scm, gnu/packages/games.scm, gnu/packages/geo.scm, gnu/packages/gl.scm, gnu/packages/glib.scm, gnu/packages/gnome.scm, gnu/packages/gnupg.scm, gnu/packages/gnuzilla.scm, gnu/packages/graph.scm, gnu/packages/graphics.scm, gnu/packages/graphviz.scm, gnu/packages/gtk.scm, gnu/packages/ham-radio.scm, gnu/packages/image-processing.scm, gnu/packages/image-viewers.scm, gnu/packages/image.scm, gnu/packages/irc.scm, gnu/packages/jrnl.scm, gnu/packages/julia.scm, gnu/packages/kde-frameworks.scm, gnu/packages/key-mon.scm, gnu/packages/libffi.scm, gnu/packages/libreoffice.scm, gnu/packages/libusb.scm, gnu/packages/lirc.scm, gnu/packages/logging.scm, gnu/packages/machine-learning.scm, gnu/packages/mail.scm, gnu/packages/mate.scm, gnu/packages/maths.scm, gnu/packages/medical.scm, gnu/packages/messaging.scm, gnu/packages/monitoring.scm, gnu/packages/mp3.scm, gnu/packages/mpd.scm, gnu/packages/music.scm, gnu/packages/networking.scm, gnu/packages/nutrition.scm, gnu/packages/openldap.scm, gnu/packages/openstack.scm, gnu/packages/package-management.scm, gnu/packages/password-utils.scm, gnu/packages/patchutils.scm, gnu/packages/pdf.scm, gnu/packages/photo.scm, gnu/packages/polkit.scm, gnu/packages/protobuf.scm, gnu/packages/python-crypto.scm, gnu/packages/python-web.scm, gnu/packages/qt.scm, gnu/packages/rdf.scm, gnu/packages/ruby.scm, gnu/packages/search.scm, gnu/packages/selinux.scm, gnu/packages/serialization.scm, gnu/packages/shells.scm, gnu/packages/simulation.scm, gnu/packages/ssh.scm, gnu/packages/statistics.scm, gnu/packages/storage.scm, gnu/packages/sync.scm, gnu/packages/terminals.scm, gnu/packages/textutils.scm, gnu/packages/time.scm, gnu/packages/tls.scm, gnu/packages/tor.scm, gnu/packages/tryton.scm, gnu/packages/version-control.scm, gnu/packages/video.scm, gnu/packages/virtualization.scm, gnu/packages/vpn.scm, gnu/packages/web-browsers.scm, gnu/packages/web.scm, gnu/packages/wicd.scm, gnu/packages/xdisorg.scm, gnu/packages/xorg.scm: Update module references.
2019-01-13gnu: r-biocgenerics: Move to bioconductor.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-biocgenerics): Move from here... * gnu/packages/bioconductor.scm (r-biocgenerics): ...to here.
2019-01-13gnu: r-annotate: Move to bioconductor.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-annotate): Move from here... * gnu/packages/bioconductor.scm (r-annotate): ...to here.
2019-01-13gnu: r-vegan: Move from bioinformatics to cran.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-vegan): Move from here... * gnu/packages/cran.scm (r-vegan): ...to here.
2019-01-12gnu: r-rtracklayer: Update to 1.42.1.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-rtracklayer): Update to 1.42.1.
2019-01-12gnu: r-scater: Update to 1.10.1.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-scater): Update to 1.10.1.
2019-01-12gnu: r-singlecellexperiment: Update to 1.4.1.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-singlecellexperiment): Update to 1.4.1.
2019-01-12gnu: r-rhdf5lib: Update to 1.4.2.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-rhdf5lib): Update to 1.4.2.
2019-01-12gnu: r-hdf5array: Update to 1.10.1.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-hdf5array): Update to 1.10.1.
2019-01-12gnu: r-qvalue: Update to 2.14.1.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-qvalue): Update to 2.14.1.
2019-01-12gnu: r-gviz: Update to 1.26.4.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-gviz): Update to 1.26.4.
2019-01-12gnu: r-biovizbase: Update to 1.30.1.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-biovizbase): Update to 1.30.1.
2019-01-12gnu: r-ensembldb: Update to 2.6.3.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-ensembldb): Update to 2.6.3.
2019-01-12gnu: r-dirichletmultinomial: Update to 1.24.1.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-dirichletmultinomial): Update to 1.24.1.
2019-01-12gnu: r-gage: Update to 2.32.1.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-gage): Update to 2.32.1.
2019-01-12gnu: r-annotationhub: Update to 2.14.2.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-annotationhub): Update to 2.14.2.
2019-01-12gnu: r-edaseq: Update to 2.16.3.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-edaseq): Update to 2.16.3. [propagated-inputs]: Add r-biocmanager.
2019-01-12gnu: r-deseq: Update to 1.34.1.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-deseq): Update to 1.34.1.
2019-01-12gnu: r-msnid: Update to 1.16.1.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-msnid): Update to 1.16.1.
2019-01-12gnu: r-msnbase: Update to 2.8.3.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-msnbase): Update to 2.8.3.
2019-01-12gnu: r-mzid: Update to 1.20.1.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-mzid): Update to 1.20.1.
2019-01-12gnu: r-mzr: Update to 2.16.1.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-mzr): Update to 2.16.1.
2019-01-12gnu: r-sva: Update to 3.30.1.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-sva): Update to 3.30.1.
2019-01-12gnu: r-methylkit: Update to 1.8.1.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-methylkit): Update to 1.8.1.
2019-01-12gnu: r-copywriter: Update to 2.14.1.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-copywriter): Update to 2.14.1.
2019-01-12gnu: r-rhdf5: Update to 2.26.2.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-rhdf5): Update to 2.26.2.
2019-01-12gnu: r-tximport: Update to 1.10.1.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-tximport): Update to 1.10.1.
2019-01-12gnu: r-genomicalignments: Update to 1.18.1.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-genomicalignments): Update to 1.18.1.
2019-01-12gnu: r-biostrings: Update to 2.50.2.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-biostrings): Update to 2.50.2.
2019-01-12gnu: r-biocparallel: Update to 1.16.5.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-biocparallel): Update to 1.16.5.
2019-01-12gnu: r-limma: Update to 3.38.3.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-limma): Update to 3.38.3.
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