Commit Graph

2031 Commits

Author SHA1 Message Date
Ricardo Wurmus 8b6acb1f20
gnu: 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.
2019-03-08 23:00:07 +01:00
Ricardo Wurmus 183b6575e7
gnu: 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".
2019-03-08 09:14:01 +01:00
Ricardo Wurmus 6453d7aecc
gnu: r-gviz: Update to 1.26.5.
* gnu/packages/bioinformatics.scm (r-gviz): Update to 1.26.5.
2019-03-08 09:14:01 +01:00
Ricardo Wurmus 101dcc29d3
gnu: r-ensembldb: Update to 2.6.7.
* gnu/packages/bioinformatics.scm (r-ensembldb): Update to 2.6.7.
2019-03-08 09:14:01 +01:00
Ricardo Wurmus d3713237c5
gnu: r-annotationhub: Update to 2.14.4.
* gnu/packages/bioinformatics.scm (r-annotationhub): Update to 2.14.4.
2019-03-08 09:14:01 +01:00
Ricardo Wurmus 53e7f028ed
gnu: r-rhtslib: Update to 1.14.1.
* gnu/packages/bioinformatics.scm (r-rhtslib): Update to 1.14.1.
2019-03-08 09:14:01 +01:00
Ricardo Wurmus d86b9eca56
gnu: r-genomicfeatures: Update to 1.34.4.
* gnu/packages/bioinformatics.scm (r-genomicfeatures): Update to 1.34.4.
2019-03-08 09:14:01 +01:00
Ricardo Wurmus d493043daf
gnu: r-rtracklayer: Update to 1.42.2.
* gnu/packages/bioinformatics.scm (r-rtracklayer): Update to 1.42.2.
2019-03-08 09:14:01 +01:00
Ricardo Wurmus 57f40dc220
gnu: r-rsamtools: Update to 1.34.1.
* gnu/packages/bioinformatics.scm (r-rsamtools): Update to 1.34.1.
2019-03-08 09:14:00 +01:00
Ricardo Wurmus 58209b1e21
gnu: r-biocparallel: Update to 1.16.6.
* gnu/packages/bioinformatics.scm (r-biocparallel): Update to 1.16.6.
2019-03-08 09:14:00 +01:00
Ricardo Wurmus cd43ae3fd6
gnu: r-variantannotation: Update to 1.28.11.
* gnu/packages/bioinformatics.scm (r-variantannotation): Update to 1.28.11.
2019-03-08 09:14:00 +01:00
Ricardo Wurmus fff11bccc6
gnu: r-genomeinfodb: Update to 1.18.2.
* gnu/packages/bioinformatics.scm (r-genomeinfodb): Update to 1.18.2.
2019-03-08 09:14:00 +01:00
Ricardo Wurmus 8972989e10
gnu: r-dexseq: Update to 1.28.2.
* gnu/packages/bioinformatics.scm (r-dexseq): Update to 1.28.2.
2019-03-08 09:14:00 +01:00
Ricardo Wurmus 3b296475bf
gnu: cd-hit: Support longer sequences.
* gnu/packages/bioinformatics.scm (cd-hit)[arguments]: Pass MAX_SEQ to make
flags.
2019-03-07 13:38:01 +01:00
Ricardo Wurmus 8035819f4c
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.
2019-03-06 21:43:33 +01:00
Ricardo Wurmus d56df35a25
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.
2019-03-06 21:42:39 +01:00
Ricardo Wurmus f8780e96ff
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.
2019-03-06 21:41:48 +01:00
Ricardo Wurmus 3a08940e1a
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.
2019-03-06 21:35:20 +01:00
Ricardo Wurmus 7bc5d1b0e1
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.
2019-03-06 21:33:17 +01:00
Ricardo Wurmus 13dabd6947
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.
2019-03-06 21:31:41 +01:00
Ricardo Wurmus 0c792ffbd1
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.
2019-03-06 21:30:30 +01:00
Ricardo Wurmus b7d93cf508
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.
2019-03-06 21:29:20 +01:00
Ricardo Wurmus c3adc83054
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.
2019-03-06 21:26:54 +01:00
Ricardo Wurmus 5acb9052cf
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.
2019-03-06 21:25:18 +01:00
Ricardo Wurmus fe0b76e215
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.
2019-03-06 21:23:42 +01:00
Ricardo Wurmus 40a6505711
gnu: r-bsgenome-hsapiens-1000genomes-hs37d5: Move to (gnu packages bioconductor).
* gnu/packages/bioinformatics.scm (r-bsgenome-hsapiens-1000genomes-hs37d5):
Move from here...
* gnu/packages/bioconductor.scm (r-bsgenome-hsapiens-1000genomes-hs37d5):
...to here.
2019-03-06 21:23:20 +01:00
Ricardo Wurmus 66e35ce63b
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.
2019-03-06 21:16:33 +01:00
Ricardo Wurmus bfb93b4889
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.
2019-03-06 21:13:38 +01:00
Ricardo Wurmus 3d13b448e5
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.
2019-03-06 21:07:49 +01:00
Ricardo Wurmus 38502a7d13
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.
2019-03-06 16:26:23 +01:00
Ricardo Wurmus cb66fb101f
gnu: Add r-scde.
* gnu/packages/bioinformatics.scm (r-scde): New variable.
2019-03-06 15:55:54 +01:00
Ricardo Wurmus afeb10a056
gnu: Add bowtie1.
* gnu/packages/bioinformatics.scm (bowtie1): New variable.
2019-03-06 15:32:45 +01:00
Ricardo Wurmus 4fc9b5b1dd
gnu: Add genrich.
* gnu/packages/bioinformatics.scm (genrich): New variable.
2019-03-06 13:28:45 +01:00
Ricardo Wurmus 1fe9a36173
gnu: r-dnacopy: Remove duplicate definition.
Reported by Christopher Baines <mail@cbaines.net>.

* gnu/packages/bioinformatics.scm (r-dnacopy): Remove variable.
2019-03-06 10:39:28 +01:00
Ricardo Wurmus c335df433f
gnu: pigx-chipseq: Update to 0.0.31.
* gnu/packages/bioinformatics.scm (pigx-chipseq): Update to 0.0.31.
2019-03-02 22:05:30 +01:00
Ricardo Wurmus a27ca96f10
gnu: Add velvet.
* gnu/packages/bioinformatics.scm (velvet): New variable.
2019-03-01 12:55:35 +01:00
Ricardo Wurmus 0ce256dc79
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.
2019-03-01 12:55:35 +01:00
Ricardo Wurmus 8aa1ca85ac
gnu: flexbar: Fix reproducibility bug.
* gnu/packages/bioinformatics.scm (flexbar)[arguments]: Add phase
"do-not-tune-to-CPU".
2019-02-27 15:40:46 +01:00
Ricardo Wurmus cc842b58af
gnu: pigx-chipseq: Update to 0.0.21.
* gnu/packages/bioinformatics.scm (pigx-chipseq): Update to 0.0.21.
2019-02-25 15:40:12 +01:00
Ricardo Wurmus 3ca1d917b6
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.
2019-02-25 15:05:35 +01:00
Andreas Enge 2e125ece09
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.
2019-02-19 22:37:02 +01:00
Marius Bakke 61506fe551
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.
2019-02-17 18:44:18 +01:00
Ricardo Wurmus 9846ec0bea
gnu: Add python-pyfit-sne.
* gnu/packages/bioinformatics.scm (python-pyfit-sne): New variable.
2019-02-15 11:03:26 +01:00
Maxim Cournoyer 155194d97d
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.
2019-02-12 17:16:05 +01:00
Ricardo Wurmus 385d7546e1
gnu: Add cnvkit.
* gnu/packages/bioinformatics.scm (cnvkit): New variable.
2019-02-12 15:41:02 +01:00
Ricardo Wurmus 307182d4f7
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.
2019-02-08 22:45:12 +01:00
Ricardo Wurmus 6df215f8c8
gnu: star: Update to 2.7.0b.
* gnu/packages/bioinformatics.scm (star): Update to 2.7.0b.
[arguments]: Add "add-missing-header" build phase.
2019-02-06 21:32:16 +01:00
Ricardo Wurmus ba123b6dda
gnu: star: Update to 2.7.0a.
* gnu/packages/bioinformatics.scm (star): Update to 2.7.0a.
2019-01-30 15:44:47 +01:00
Ricardo Wurmus 1d1e3676ba
gnu: r-genomicfeatures: Update to 1.34.2.
* gnu/packages/bioinformatics.scm (r-genomicfeatures): Update to 1.34.2.
2019-01-28 16:27:35 +01:00
Ricardo Wurmus ea0eaf537a
gnu: r-variantannotation: Update to 1.28.10.
* gnu/packages/bioinformatics.scm (r-variantannotation): Update to 1.28.10.
2019-01-28 16:27:35 +01:00
Ricardo Wurmus 5d9b140b29
gnu: r-qtl: Update to 1.44-9.
* gnu/packages/bioinformatics.scm (r-qtl): Update to 1.44-9.
2019-01-28 16:27:34 +01:00
Ricardo Wurmus 439d821a3b
gnu: r-optparse: Update to 1.6.1.
* gnu/packages/bioinformatics.scm (r-optparse): Update to 1.6.1.
2019-01-28 16:27:33 +01:00
Ricardo Wurmus 0791437f97
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.
2019-01-28 14:57:10 +01:00
Ricardo Wurmus fdb0b40b0e
gnu: pepr: Use PYPI-URI.
* gnu/packages/bioinformatics.scm (pepr)[source]: Use PYPI-URI.
2019-01-25 23:27:25 +01:00
Ricardo Wurmus 4cd7c58cf1
gnu: python2-warpedlmm: Use PYPI-URI.
* gnu/packages/bioinformatics.scm (python2-warpedlmm)[source]: Use PYPI-URI.
2019-01-25 23:26:50 +01:00
Ricardo Wurmus 4fec042b54
gnu: Move Python compression packages to new module.
* 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.
2019-01-15 17:45:33 +01:00
Ricardo Wurmus 44d10b1f72
gnu: Separate Python core packages from the rest.
* 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.
2019-01-15 14:46:44 +01:00
Ricardo Wurmus 14bba460ab
gnu: r-biocgenerics: Move to bioconductor.
* gnu/packages/bioinformatics.scm (r-biocgenerics): Move from here...
* gnu/packages/bioconductor.scm (r-biocgenerics): ...to here.
2019-01-13 13:04:18 +01:00
Ricardo Wurmus 7097c7009d
gnu: r-annotate: Move to bioconductor.
* gnu/packages/bioinformatics.scm (r-annotate): Move from here...
* gnu/packages/bioconductor.scm (r-annotate): ...to here.
2019-01-13 13:04:18 +01:00
Ricardo Wurmus c80fb90f4a
gnu: r-vegan: Move from bioinformatics to cran.
* gnu/packages/bioinformatics.scm (r-vegan): Move from here...
* gnu/packages/cran.scm (r-vegan): ...to here.
2019-01-13 13:04:18 +01:00
Ricardo Wurmus c476edc2cd
gnu: r-rtracklayer: Update to 1.42.1.
* gnu/packages/bioinformatics.scm (r-rtracklayer): Update to 1.42.1.
2019-01-12 23:35:18 +01:00
Ricardo Wurmus 1e107b0960
gnu: r-scater: Update to 1.10.1.
* gnu/packages/bioinformatics.scm (r-scater): Update to 1.10.1.
2019-01-12 23:35:18 +01:00
Ricardo Wurmus 0f268bb275
gnu: r-singlecellexperiment: Update to 1.4.1.
* gnu/packages/bioinformatics.scm (r-singlecellexperiment): Update to 1.4.1.
2019-01-12 23:35:18 +01:00
Ricardo Wurmus a0224bd4f6
gnu: r-rhdf5lib: Update to 1.4.2.
* gnu/packages/bioinformatics.scm (r-rhdf5lib): Update to 1.4.2.
2019-01-12 23:35:18 +01:00
Ricardo Wurmus 40561d0249
gnu: r-hdf5array: Update to 1.10.1.
* gnu/packages/bioinformatics.scm (r-hdf5array): Update to 1.10.1.
2019-01-12 23:35:18 +01:00
Ricardo Wurmus ad10b3979d
gnu: r-qvalue: Update to 2.14.1.
* gnu/packages/bioinformatics.scm (r-qvalue): Update to 2.14.1.
2019-01-12 23:35:18 +01:00
Ricardo Wurmus 19cacb5a2d
gnu: r-gviz: Update to 1.26.4.
* gnu/packages/bioinformatics.scm (r-gviz): Update to 1.26.4.
2019-01-12 23:35:18 +01:00
Ricardo Wurmus c80595935d
gnu: r-biovizbase: Update to 1.30.1.
* gnu/packages/bioinformatics.scm (r-biovizbase): Update to 1.30.1.
2019-01-12 23:35:18 +01:00
Ricardo Wurmus 27194effd7
gnu: r-ensembldb: Update to 2.6.3.
* gnu/packages/bioinformatics.scm (r-ensembldb): Update to 2.6.3.
2019-01-12 23:35:18 +01:00
Ricardo Wurmus 43931ff72f
gnu: r-dirichletmultinomial: Update to 1.24.1.
* gnu/packages/bioinformatics.scm (r-dirichletmultinomial): Update to 1.24.1.
2019-01-12 23:35:18 +01:00
Ricardo Wurmus 15d89fe9f8
gnu: r-gage: Update to 2.32.1.
* gnu/packages/bioinformatics.scm (r-gage): Update to 2.32.1.
2019-01-12 23:35:18 +01:00
Ricardo Wurmus 4615cf9f1a
gnu: r-annotationhub: Update to 2.14.2.
* gnu/packages/bioinformatics.scm (r-annotationhub): Update to 2.14.2.
2019-01-12 23:35:18 +01:00
Ricardo Wurmus ab4a862ab8
gnu: r-edaseq: Update to 2.16.3.
* gnu/packages/bioinformatics.scm (r-edaseq): Update to 2.16.3.
[propagated-inputs]: Add r-biocmanager.
2019-01-12 23:35:18 +01:00
Ricardo Wurmus 3bdc41b352
gnu: r-deseq: Update to 1.34.1.
* gnu/packages/bioinformatics.scm (r-deseq): Update to 1.34.1.
2019-01-12 23:35:18 +01:00
Ricardo Wurmus 9abf344f8b
gnu: r-msnid: Update to 1.16.1.
* gnu/packages/bioinformatics.scm (r-msnid): Update to 1.16.1.
2019-01-12 23:35:17 +01:00
Ricardo Wurmus 880ed11e9f
gnu: r-msnbase: Update to 2.8.3.
* gnu/packages/bioinformatics.scm (r-msnbase): Update to 2.8.3.
2019-01-12 23:35:17 +01:00
Ricardo Wurmus 6451af78e1
gnu: r-mzid: Update to 1.20.1.
* gnu/packages/bioinformatics.scm (r-mzid): Update to 1.20.1.
2019-01-12 23:35:17 +01:00
Ricardo Wurmus a4f038dc97
gnu: r-mzr: Update to 2.16.1.
* gnu/packages/bioinformatics.scm (r-mzr): Update to 2.16.1.
2019-01-12 23:35:17 +01:00
Ricardo Wurmus 46508c3a92
gnu: r-sva: Update to 3.30.1.
* gnu/packages/bioinformatics.scm (r-sva): Update to 3.30.1.
2019-01-12 23:35:17 +01:00
Ricardo Wurmus c20426ec5c
gnu: r-methylkit: Update to 1.8.1.
* gnu/packages/bioinformatics.scm (r-methylkit): Update to 1.8.1.
2019-01-12 23:35:17 +01:00
Ricardo Wurmus 5c72ebafeb
gnu: r-copywriter: Update to 2.14.1.
* gnu/packages/bioinformatics.scm (r-copywriter): Update to 2.14.1.
2019-01-12 23:35:17 +01:00
Ricardo Wurmus 86162c767e
gnu: r-rhdf5: Update to 2.26.2.
* gnu/packages/bioinformatics.scm (r-rhdf5): Update to 2.26.2.
2019-01-12 23:35:17 +01:00
Ricardo Wurmus 4c7b9222dd
gnu: r-tximport: Update to 1.10.1.
* gnu/packages/bioinformatics.scm (r-tximport): Update to 1.10.1.
2019-01-12 23:35:17 +01:00
Ricardo Wurmus 4bfde52178
gnu: r-genomicalignments: Update to 1.18.1.
* gnu/packages/bioinformatics.scm (r-genomicalignments): Update to 1.18.1.
2019-01-12 23:35:17 +01:00
Ricardo Wurmus 1fa12b2f06
gnu: r-biostrings: Update to 2.50.2.
* gnu/packages/bioinformatics.scm (r-biostrings): Update to 2.50.2.
2019-01-12 23:35:17 +01:00
Ricardo Wurmus d4fc834cf7
gnu: r-biocparallel: Update to 1.16.5.
* gnu/packages/bioinformatics.scm (r-biocparallel): Update to 1.16.5.
2019-01-12 23:35:17 +01:00
Ricardo Wurmus 52c977a05b
gnu: r-limma: Update to 3.38.3.
* gnu/packages/bioinformatics.scm (r-limma): Update to 3.38.3.
2019-01-12 23:35:17 +01:00
Ricardo Wurmus 3fd48846eb
gnu: r-variantannotation: Update to 1.28.8.
* gnu/packages/bioinformatics.scm (r-variantannotation): Update to 1.28.8.
2019-01-12 23:35:17 +01:00
Ricardo Wurmus a619850930
gnu: r-edger: Update to 3.24.3.
* gnu/packages/bioinformatics.scm (r-edger): Update to 3.24.3.
2019-01-12 23:35:17 +01:00
Ricardo Wurmus 00f105fe20
gnu: r-biocviews: Update to 1.50.10.
* gnu/packages/bioinformatics.scm (r-biocviews): Update to 1.50.10.
2019-01-12 23:35:16 +01:00
Ricardo Wurmus 9c1b2b2ae0
gnu: r-systempiper: Update to 1.16.1.
* gnu/packages/bioinformatics.scm (r-systempiper): Update to 1.16.1.
2019-01-12 23:35:16 +01:00
Ricardo Wurmus 3b8c884285
gnu: r-rbgl: Update to 1.58.1.
* gnu/packages/bioinformatics.scm (r-rbgl): Update to 1.58.1.
2019-01-12 23:35:16 +01:00
Ricardo Wurmus ffe16ef33c
gnu: r-dexseq: Update to 1.28.1.
* gnu/packages/bioinformatics.scm (r-dexseq): Update to 1.28.1.
2019-01-12 23:35:16 +01:00
Ricardo Wurmus f7e95c50b8
gnu: r-deseq2: Update to 1.22.2.
* gnu/packages/bioinformatics.scm (r-deseq2): Update to 1.22.2.
2019-01-12 23:35:16 +01:00
Ricardo Wurmus feb561f721
gnu: r-scran: Update to 1.10.2.
* gnu/packages/bioinformatics.scm (r-scran): Update to 1.10.2.
2019-01-12 23:35:16 +01:00
Ricardo Wurmus 80c4e75b87
gnu: r-seqminer: Update to 7.1.
* gnu/packages/bioinformatics.scm (r-seqminer): Update to 7.1.
2019-01-12 23:35:16 +01:00
Ricardo Wurmus 3bc0667f3c
gnu: r-bookdown: Update to 0.9.
* gnu/packages/bioinformatics.scm (r-bookdown): Update to 0.9.
2019-01-12 23:35:16 +01:00
Ricardo Wurmus 24155bf40d
gnu: Move Java compression packages to new module.
* gnu/packages/compression.scm (bitshuffle-for-snappy): Export variable.
(java-snappy, java-snappy-1, java-iq80-snappy, java-jbzip2, java-tukaani-xz):
Move these variables from here...
* gnu/packages/java-compression.scm: ...to this new file.
* gnu/local.mk (GNU_SYSTEM_MODULES): Add it.
* gnu/packages/java.scm, gnu/packages/bioinformatics.scm: Adjust module
references.
2019-01-12 12:14:28 +01:00
Ricardo Wurmus e7c6bc45ed
gnu: jamm: Remove broken "build" phase.
* gnu/packages/bioinformatics.scm (jamm)[arguments]: Remove "build" phase.
2019-01-11 06:08:43 +01:00
Efraim Flashner 6fd2ed23ac
gnu: mantis: Limit to x86_64-linux.
* gnu/packages/bioinformatics.scm (mantis)[supported-systems]: New field.
2019-01-07 15:47:34 +02:00
Ricardo Wurmus e942813aac
gnu: Add mantis.
* gnu/packages/bioinformatics.scm (mantis): New variable.
2019-01-07 11:56:18 +01:00
Pierre Neidhardt 8894668cd2
gnu: discrover: Comment on attempt of minimal texlive-union.
* gnu/packages/bioinformatics.scm (discrover): Comment on attempt of minimal
  texlive-union.
2018-12-20 12:07:40 +01:00
Efraim Flashner 2f3977b9a7
gnu: gess: Don't hardcode python version.
* gnu/packages/bioinformatics.scm (gess)[arguments]: Replace hardcoded
python version with parameterized one.
2018-12-17 12:08:05 +02:00
Christopher Baines 9718265eec
gnu: mash: Use C++ 14.
I'm looking to upgrade capnproto, and mash fails to build with 0.7. Therefore,
tweak the compilation to allow it to build with 0.7. The package also builds
with the current version of capnproto. I got the idea of changing the c++
version from here [1].

1: https://github.com/marbl/Mash/issues/98

* gnu/packages/bioinformatics.scm (mash)[arguments]: Add new use-c++14 phase.
2018-12-05 20:29:12 +00:00
Ricardo Wurmus 42c3e00c20
gnu: pigx-rnaseq: Update to 0.0.5.
* gnu/packages/bioinformatics.scm (pigx-rnaseq): Update to 0.0.5.
[inputs]: Replace snakemake-4 with snakemake.
2018-12-04 16:21:50 +01:00
Marius Bakke 4b2d1dc4dc
gnu: bless: Adjust to zlib static output.
* gnu/packages/bioinformatics.scm (bless)[inputs]: Add ZLIB:STATIC.
[arguments]: Adjust #:make-flags accordingly.
2018-11-24 19:32:48 +01:00
Marius Bakke f028823c0f
gnu: mosaik: Fix FTBFS from b90289dadc.
* gnu/packages/bioinformatics.scm (mosaik)[inputs]: Add ZLIB:STATIC.
2018-11-24 15:57:56 +01:00
Ricardo Wurmus d57ec906ba
gnu: pigx-scrnaseq: Use latest snakemake.
* gnu/packages/bioinformatics.scm (pigx-scrnaseq)[inputs]: Replace snakemake-4
with snakemake.
2018-11-23 16:30:48 +01:00
Ricardo Wurmus 92d9a1e2c6
gnu: pigx-bsseq: Use latest snakemake.
* gnu/packages/bioinformatics.scm (pigx-bsseq)[inputs]: Replace snakemake-4
with snakemake.
2018-11-23 16:30:16 +01:00
Ricardo Wurmus c068d00746
gnu: pigx-chipseq: Use latest snakemake.
* gnu/packages/bioinformatics.scm (pigx-chipseq)[inputs]: Replace snakemake-4
with snakemake.
2018-11-23 16:29:35 +01:00
Ricardo Wurmus 93d229cb86
gnu: python-loompy: Remove python-typing.
* gnu/packages/bioinformatics.scm (python-loompy)[propagated-inputs]: Remove
python-typing.
2018-11-23 15:59:44 +01:00
Marius Bakke 4f70db97a0
Merge branch 'master' into core-updates 2018-11-20 01:14:12 +01:00
Roel Janssen c2e26dc156
gnu: r-ensembldb: Update to 2.6.2.
* gnu/packages/bioinformatics.scm (r-ensembldb): Update to 2.6.2.
2018-11-19 16:46:32 +01:00
Roel Janssen e038819138
gnu: r-msnbase: Update to 2.8.1.
* gnu/packages/bioinformatics.scm (r-msnbase): Update to 2.8.1.
2018-11-19 16:46:00 +01:00
Roel Janssen 4535a7b0f5
gnu: r-genomeinfodb: Update to 1.18.1.
* gnu/packages/bioinformatics.scm (r-genomeinfodb): Update to 1.18.1.
2018-11-19 16:33:35 +01:00
pimi 30f0d21b40
gnu: Add nanopolish.
* gnu/packages/bioinformatics.scm (nanopolish): New variable.

Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
2018-11-15 22:23:57 +01:00
Roel Janssen 2d86eaff5b
gnu: sambamba: Update to 0.6.8.
* gnu/packages/bioinformatics.scm (sambamba): Update to 0.6.8.
2018-11-15 13:09:01 +01:00
Mark H Weaver 2e0f69057a
gnu: bioinformatics: Return #t from all phases and snippets.
* gnu/packages/bioinformatics.scm (bamtools, ribotaper, bioawk)
(codingquarry, fraggenescan, minced, pplacer, star, subread, sailfish)
(salmon): Return #t from all phases and snippets, use 'invoke' where
appropriate, and remove vestigal plumbing.
2018-11-14 23:44:18 -05:00
Ricardo Wurmus ee66a13563
gnu: Add jamm.
* gnu/packages/bioinformatics.scm (jamm): New variable.
2018-11-14 15:13:20 +01:00
Ricardo Wurmus 51b262f310
gnu: r-txdb-mmusculus-ucsc-mm10-knowngene: Update to 3.4.4.
* gnu/packages/bioinformatics.scm (r-txdb-mmusculus-ucsc-mm10-knowngene):
Update to 3.4.4.
2018-11-13 23:34:40 +01:00
Ricardo Wurmus d34959b8d4
gnu: r-org-mm-eg-db: Update to 3.7.0.
* gnu/packages/bioinformatics.scm (r-org-mm-eg-db): Update to 3.7.0.
2018-11-13 23:34:40 +01:00
Ricardo Wurmus 314511b862
gnu: r-org-dm-eg-db: Update to 3.7.0.
* gnu/packages/bioinformatics.scm (r-org-dm-eg-db): Update to 3.7.0.
2018-11-13 23:34:39 +01:00
Ricardo Wurmus 76bd16bcf6
gnu: r-org-ce-eg-db: Update to 3.7.0.
* gnu/packages/bioinformatics.scm (r-org-ce-eg-db): Update to 3.7.0.
2018-11-13 23:34:39 +01:00
Ricardo Wurmus fc7683fa30
gnu: r-org-hs-eg-db: Update to 3.7.0.
* gnu/packages/bioinformatics.scm (r-org-hs-eg-db): Update to 3.7.0.
2018-11-13 23:34:39 +01:00
Ricardo Wurmus cb9e6ed702
gnu: r-genomationdata: Update to 1.14.0.
* gnu/packages/bioinformatics.scm (r-genomationdata): Update to 1.14.0.
2018-11-13 23:34:39 +01:00
Ricardo Wurmus 13e70f6304
gnu: r-go-db: Update to 3.7.0.
* gnu/packages/bioinformatics.scm (r-go-db): Update to 3.7.0.
2018-11-13 23:34:39 +01:00
Ricardo Wurmus 13a574652b
gnu: r-genomeinfodbdata: Update to 1.2.0.
* gnu/packages/bioinformatics.scm (r-genomeinfodbdata): Update to 1.2.0.
2018-11-13 23:34:39 +01:00
Ricardo Wurmus 5f9b38ba34
gnu: r-s4vectors: Update to 0.20.1.
* gnu/packages/bioinformatics.scm (r-s4vectors): Update to 0.20.1.
2018-11-11 23:13:48 +01:00
Ricardo Wurmus 03a415365a
gnu: r-ensembldb: Update to 2.6.1.
* gnu/packages/bioinformatics.scm (r-ensembldb): Update to 2.6.1.
2018-11-09 19:41:54 +01:00
Ricardo Wurmus 88514b9124
gnu: r-biostrings: Update to 2.50.1.
* gnu/packages/bioinformatics.scm (r-biostrings): Update to 2.50.1.
2018-11-09 19:41:53 +01:00
Ricardo Wurmus 77bea84ba1
gnu: r-biocviews: Update to 1.50.5.
* gnu/packages/bioinformatics.scm (r-biocviews): Update to 1.50.5.
2018-11-09 19:41:53 +01:00
Ricardo Wurmus a1e83a9856
gnu: pplacer-scripts: Use INVOKE.
* gnu/packages/bioinformatics.scm (pplacer-scripts)[arguments]: Use INVOKE and
return #T unconditionally.
2018-11-08 10:06:35 +01:00
Ricardo Wurmus ce49fdcce9
gnu: roary: Use INVOKE.
* gnu/packages/bioinformatics.scm (roary)[arguments]: Use INVOKE and return #T
unconditionally.
2018-11-08 09:58:05 +01:00
Ricardo Wurmus a9542937c8
gnu: seek: Use INVOKE.
* gnu/packages/bioinformatics.scm (seek)[arguments]: Use INVOKE and return #T
unconditionally; patch "gen_tools_am" shebang in "bootstrap" phase.
2018-11-08 09:54:22 +01:00
Ricardo Wurmus 9f527c9199
gnu: sailfish: Use INVOKE.
* gnu/packages/bioinformatics.scm (sailfish)[arguments]: Use INVOKE instead of
SYSTEM*.
2018-11-08 09:52:46 +01:00
Ricardo Wurmus 86c6928ea3
gnu: vsearch: Update to 2.9.1.
* gnu/packages/bioinformatics.scm (vsearch): Update to 2.9.1.
* gnu/packages/patches/vsearch-unbundle-cityhash.patch: Update.
2018-11-08 09:46:42 +01:00
Ricardo Wurmus 15c9609482
gnu: sra-tools: Update to 2.9.3.
* gnu/packages/bioinformatics.scm (sra-tools): Update to 2.9.3.
[arguments]: Remove build phase patch-away-glibc-conflict.
2018-11-08 09:46:05 +01:00
Ricardo Wurmus b17333414f
gnu: plink-ng: Fetch sources from git.
* gnu/packages/bioinformatics.scm (plink-ng)[source]: Fetch from git.
2018-11-08 09:30:59 +01:00
Ricardo Wurmus 87408854ec
gnu: ncbi-vdb: Update to 2.9.3.
* gnu/packages/bioinformatics.scm (ncbi-vdb): Update to 2.9.3.
2018-11-08 09:30:16 +01:00
Ricardo Wurmus 8d3eaa9262
gnu: ngs-sdk: Update to 2.9.3.
* gnu/packages/bioinformatics.scm (ngs-sdk): Update to 2.9.3.
2018-11-08 09:29:58 +01:00
Ricardo Wurmus 3da3cedf76
gnu: ngs-sdk: Use INVOKE.
* gnu/packages/bioinformatics.scm (ngs-sdk)[arguments]: Use INVOKE and
return #T unconditionally.
2018-11-08 09:15:05 +01:00
Ricardo Wurmus e78e54d029
gnu: emboss: Use INVOKE.
* gnu/packages/bioinformatics.scm (emboss)[arguments]: Use INVOKE and
return #T unconditionally.
2018-11-08 09:14:09 +01:00
Ricardo Wurmus 8b685c4720
gnu: taxtastic: Use INVOKE.
* gnu/packages/bioinformatics.scm (taxtastic)[arguments]: Use INVOKE and
return #T unconditionally.
2018-11-08 09:13:35 +01:00
Ricardo Wurmus 2e2d88539c
gnu: sra-tools: Use INVOKE.
* gnu/packages/bioinformatics.scm (sra-tools)[arguments]: Use INVOKE and
return #T unconditionally.
2018-11-08 09:12:43 +01:00
Ricardo Wurmus 179416467f
gnu: muscle: Use INVOKE.
* gnu/packages/bioinformatics.scm (muscle)[arguments]: Use INVOKE and
return #T unconditionally.
2018-11-08 09:11:38 +01:00
Ricardo Wurmus 0881d62f25
gnu: newick-utils: Remove custom autoconf phase.
* gnu/packages/bioinformatics.scm (newick-utils)[arguments]: Remove.
2018-11-08 09:10:58 +01:00
Ricardo Wurmus e35dce0170
gnu: mash: Remove custom autoconf phase.
* gnu/packages/bioinformatics.scm (mash)[arguments]: Remove autoconf phase.
2018-11-08 09:10:20 +01:00
Ricardo Wurmus 31c41a8cfe
gnu: vsearch: Remove custom autogen phase.
* gnu/packages/bioinformatics.scm (vsearch)[arguments]: Remove.
2018-11-08 09:04:34 +01:00
Ricardo Wurmus c527d36f02
gnu: java-picard-1.113: Use INVOKE.
* gnu/packages/bioinformatics.scm (java-picard-1.113)[arguments]: Use INVOKE
and return #T unconditionally.
2018-11-08 09:02:34 +01:00
Ricardo Wurmus e438c96558
gnu: fraggenescan: Use INVOKE.
* gnu/packages/bioinformatics.scm (fraggenescan)[arguments]: Use INVOKE in
build phases and return #T unconditionally.
2018-11-08 08:58:46 +01:00
Ricardo Wurmus c098c49b3e
gnu: sailfish: Fetch sources from git.
* gnu/packages/bioinformatics.scm (sailfish)[source]: Fetch from git.
2018-11-08 08:53:54 +01:00
Ricardo Wurmus 4031e7f1ec
gnu: ngs-sdk: Fetch sources from git.
* gnu/packages/bioinformatics.scm (ngs-sdk)[source]: Fetch from git.
2018-11-08 08:53:53 +01:00
Ricardo Wurmus 6a7d9ee39f
gnu: ncbi-vdb: Use INVOKE and end phases on #T.
* gnu/packages/bioinformatics.scm (ncbi-vdb)[arguments]: Use INVOKE and
unconditionally end phases with #T.
2018-11-08 08:53:53 +01:00
Ricardo Wurmus 3398dfb764
gnu: ncbi-vdb: Fetch sources from git.
* gnu/packages/bioinformatics.scm (ncbi-vdb)[source]: Fetch from git.
[arguments]: Add phase to make checkout writable.
2018-11-08 08:53:53 +01:00
Ricardo Wurmus e0f1aa2d2b
gnu: tadbit: Fetch sources from git.
* gnu/packages/bioinformatics.scm (tadbit)[source]: Fetch from git.
[version]: Use "2.0.0" instead of "2.0".
2018-11-08 08:53:50 +01:00
Ricardo Wurmus f3f34b132c
gnu: filevercmp: Fetch sources from git.
* gnu/packages/bioinformatics.scm (filevercmp)[source]: Fetch from git.
[arguments]: Add #T to the end of the install phase.
2018-11-07 23:17:36 +01:00
Ricardo Wurmus 3b888065da
gnu: ritornello: Update to 2.0.1.
* gnu/packages/bioinformatics.scm (ritornello): Update to 2.0.1.
[arguments]: Adjust file patching.
2018-11-07 23:17:36 +01:00
Ricardo Wurmus 7145f4e519
gnu: ritornello: Fetch sources from git.
* gnu/packages/bioinformatics.scm (ritornello)[source]: Fetch from git.
2018-11-07 23:17:35 +01:00
Ricardo Wurmus e0a8fc85dd
gnu: snap-aligner: Fetch sources from git.
* gnu/packages/bioinformatics.scm (snap-aligner)[source]: Fetch from git.
[arguments]: Use INVOKE.
2018-11-07 23:17:35 +01:00
Ricardo Wurmus 6236524409
gnu: sortmerna: Fetch sources from git.
* gnu/packages/bioinformatics.scm (sortmerna)[source]: Fetch from git.
2018-11-07 23:17:35 +01:00
Ricardo Wurmus 273df99d7d
gnu: vsearch: Fetch source from git.
* gnu/packages/bioinformatics.scm (vsearch)[source]: Fetch from git.
2018-11-07 23:17:35 +01:00
Ricardo Wurmus 67caa4b773
gnu: preseq: Update to 2.0.3.
* gnu/packages/bioinformatics.scm (preseq): Update to 2.0.3.
2018-11-07 23:17:35 +01:00
Ricardo Wurmus 37e285be43
gnu: preseq: Fetch sources from git.
* gnu/packages/bioinformatics.scm (preseq)[source]: Fetch from git.
2018-11-07 23:17:35 +01:00
Ricardo Wurmus 63f3255e13
gnu: seqtk: Update to 1.3.
* gnu/packages/bioinformatics.scm (seqtk): Update to 1.3.
[source]: Remove outdated snippet.
[arguments]: Use INVOKE and return #T unconditionally.
2018-11-07 23:17:35 +01:00
Ricardo Wurmus 019fcdf20a
gnu: seqtk: Fetch sources from git.
* gnu/packages/bioinformatics.scm (seqtk)[source]: Fetch from git.
2018-11-07 23:17:34 +01:00
Ricardo Wurmus b9d0c3564b
gnu: raxml: Update to 8.2.12.
* gnu/packages/bioinformatics.scm (raxml): Update to 8.2.12.
2018-11-07 23:17:34 +01:00
Ricardo Wurmus d9ba126d17
gnu: python2-biom-format: Fix build.
This is a follow-up to commit 239716fb0b.

* gnu/packages/bioinformatics.scm (python2-biom-format)[arguments]: Modify
phases of base package.
2018-11-07 23:17:34 +01:00
Ricardo Wurmus 4715d4af17
gnu: raxml: Fetch sources from git.
* gnu/packages/bioinformatics.scm (raxml)[source]: Fetch from git.
2018-11-07 23:17:34 +01:00
Ricardo Wurmus 5e242b02c3
gnu: pyicoteo: Fetch sources from git.
* gnu/packages/bioinformatics.scm (pyicoteo)[source]: Fetch from git.
2018-11-07 23:17:34 +01:00
Ricardo Wurmus 2b773a9273
gnu: sra-tools: Fetch sources from git.
* gnu/packages/bioinformatics.scm (sra-tools)[source]: Fetch from git.
2018-11-07 21:41:56 +01:00
Ricardo Wurmus 55698df260
gnu: libgff: Fetch sources from git.
* gnu/packages/bioinformatics.scm (libgff)[source]: Fetch from git.
2018-11-07 21:41:56 +01:00
Ricardo Wurmus 4257c10ad2
gnu: kentutils: Fetch sources from git.
* gnu/packages/bioinformatics.scm (kentutils)[source]: Fetch from git.
[arguments]: Add phase "fix-permissions".
2018-11-07 21:41:55 +01:00
Ricardo Wurmus 1a20bcadf3
gnu: r-seqgl: Fetch sources from git.
* gnu/packages/bioinformatics.scm (r-seqgl)[source]: Fetch from git.
2018-11-07 21:41:55 +01:00
Ricardo Wurmus a2b9d6a8d0
gnu: pplacer: Fetch sources from git.
* gnu/packages/bioinformatics.scm (pplacer)[source]: Fetch from git.
[arguments]: Make files writable; use INVOKE.
2018-11-07 21:41:55 +01:00
Ricardo Wurmus 6052264b56
gnu: minced: Update to 0.3.2.
* gnu/packages/bioinformatics.scm (minced): Update to 0.3.2.
2018-11-07 21:41:55 +01:00
Ricardo Wurmus 9d94ca0ebf
gnu: minced: Fetch sources from git.
* gnu/packages/bioinformatics.scm (minced)[source]: Fetch from git.
2018-11-07 21:41:55 +01:00
Ricardo Wurmus b58d9e4aa2
gnu: metabat: Fetch sources from git.
* gnu/packages/bioinformatics.scm (metabat)[source]: Fetch from git.
2018-11-07 21:41:55 +01:00
Ricardo Wurmus 5c1f35e71b
gnu: mash: Update to 2.1.
* gnu/packages/bioinformatics.scm (mash): Update to 2.1.
2018-11-07 21:41:55 +01:00
Ricardo Wurmus 497fc04d8f
gnu: mash: Fetch sources from git.
* gnu/packages/bioinformatics.scm (mash)[source]: Fetch from git.
2018-11-07 21:41:55 +01:00
Ricardo Wurmus 2dc28391f3
gnu: kaiju: Update to 1.6.3.
* gnu/packages/bioinformatics.scm (kaiju): Update to 1.6.3.
2018-11-07 20:47:22 +01:00
Ricardo Wurmus 6fe323bf2e
gnu: kaiju: Fetch sources from git.
* gnu/packages/bioinformatics.scm (kaiju)[source]: Fetch from git.
[arguments]: Remove redundant installation step.
2018-11-07 20:46:36 +01:00
Ricardo Wurmus f0731591a5
gnu: idr: Fetch sources from git.
* gnu/packages/bioinformatics.scm (idr)[source]: Fetch from git.
2018-11-07 20:41:58 +01:00
Ricardo Wurmus b8a6230df3
gnu: java-htsjdk: Fetch sources from git.
* gnu/packages/bioinformatics.scm (java-htsjdk)[source]: Fetch from git.
2018-11-07 20:36:07 +01:00
Ricardo Wurmus 57be690d91
gnu: hisat2: Use versioned source URL.
* gnu/packages/bioinformatics.scm (hisat2)[source]: Use versioned URL.
2018-11-07 20:32:29 +01:00
Ricardo Wurmus c8f02c1dcb
gnu: grit: Update to 2.0.5.
* gnu/packages/bioinformatics.scm (grit): Update to 2.0.5.
[arguments]: Simplify.
2018-11-07 20:30:44 +01:00
Ricardo Wurmus 8d75adbf03
gnu: grit: Fetch sources from git.
* gnu/packages/bioinformatics.scm (grit)[source]: Fetch from git.
2018-11-07 20:27:10 +01:00
Ricardo Wurmus 152bebd9e0
gnu: gemma: Update to 0.98.
* gnu/local.mk (dist_patch_DATA): Remove patch.
* gnu/packages/patches/gemma-intel-compat.patch: Remove file.
* gnu/packages/bioinformatics.scm (gemma): Update to 0.98.
[source]: Remove patch.
[inputs]: Add eigen, gfortran:lib, and openblas.
[arguments]: Add phase "find-eigen".
2018-11-07 20:26:46 +01:00
Ricardo Wurmus b113f39019
gnu: gemma: Fetch sources from git.
* gnu/packages/bioinformatics.scm (gemma)[source]: Fetch from git.
2018-11-07 20:26:45 +01:00
Ricardo Wurmus 91b71cfbba
gnu: fxtract: Fetch sources from git.
* gnu/packages/bioinformatics.scm (fxtract)[source]: Fetch from git.
2018-11-07 19:55:50 +01:00
Ricardo Wurmus 7ca49ab57a
gnu: ribodiff: Fetch sources from git.
* gnu/packages/bioinformatics.scm (ribodiff)[source]: Fetch from git.
2018-11-07 19:48:21 +01:00
Ricardo Wurmus 239716fb0b
gnu: python-biom-format: Update to 2.1.7.
* gnu/packages/bioinformatics.scm (python-biom-format): Update to 2.1.7.
[arguments]: Add phases "use-cython", "disable-broken-test", and
"make-files-writable".
[propagated-inputs]: Add python-flake8.
[native-inputs]: Add python-cython, python-pytest, and python-pytest-cov.
2018-11-07 19:47:07 +01:00
Ricardo Wurmus 007a81d5cf
gnu: python-biom-format: Fetch source from git.
* gnu/packages/bioinformatics.scm (python-biom-format)[source]: Fetch from
git.
2018-11-07 19:10:36 +01:00
Ricardo Wurmus 383cb7b8e6
gnu: bioawk: Fetch sources from git.
* gnu/packages/bioinformatics.scm (bioawk)[source]: Fetch from git.
2018-11-07 19:06:30 +01:00
Ricardo Wurmus 20ee3e8b76
gnu: bedtools-2.18: Fetch sources from stable URL.
* gnu/packages/bioinformatics.scm (bedtools-2.18)[source]: Use stable release
tarball instead of generated tag tarball.
2018-11-07 18:52:46 +01:00
Ricardo Wurmus 8e58319c45
gnu: bamtools: Fetch sources from git.
* gnu/packages/bioinformatics.scm (bamtools)[source]: Fetch from git.
2018-11-07 18:44:30 +01:00
Ricardo Wurmus 21335fdbec
gnu: ngless: Install links to required tools.
* gnu/packages/bioinformatics.scm (ngless)[arguments]: Install links to tools.
[inputs]: Add prodigal, bwa, samtools, and minimap2.
2018-11-07 17:19:53 +01:00
Ricardo Wurmus fff67cc8a7
gnu: prodigal: Fetch sources from git.
* gnu/packages/bioinformatics.scm (prodigal)[source]: Fetch from git.
2018-11-07 17:19:53 +01:00
Ricardo Wurmus 9255198423
gnu: r-mzr: Update to 2.16.0.
* gnu/packages/bioinformatics.scm (r-mzr): Update to 2.16.0.
[inputs]: Remove netcdf.
[propagated-inputs]: Add r-ncdf4.
2018-11-07 12:27:16 +01:00
Ricardo Wurmus 37200dbcc3
gnu: r-rhdf5lib: Update to 1.4.0.
* gnu/packages/bioinformatics.scm (r-rhdf5lib): Update to 1.4.0.
[source]: Add snippet to remove bundled binaries.
[arguments]: Replace references to hdf5 with references to hdf5-1.10.
[native-inputs]: Likewise.
[propagated-inputs]: Replace hdf5 with hdf5-1.10.
2018-11-07 12:27:16 +01:00
Ricardo Wurmus 8e48d36f26
gnu: r-hdf5array: Update to 1.10.0.
* gnu/packages/bioinformatics.scm (r-hdf5array): Update to 1.10.0.
2018-11-07 12:27:16 +01:00
Ricardo Wurmus 611a255d2b
gnu: r-rhdf5: Update to 2.26.0.
* gnu/packages/bioinformatics.scm (r-rhdf5): Update to 2.26.0.
2018-11-07 12:27:16 +01:00
Ricardo Wurmus a1c2bf8e54
gnu: r-rcas: Update to 1.8.0.
* gnu/packages/bioinformatics.scm (r-rcas): Update to 1.8.0.
[native-inputs]: Remove r-testthat and ghc-pandoc-citeproc.
[propagated-inputs]: Add r-annotationdbi, r-genomeinfodb, and r-genomicranges;
remove r-bsgenome-mmusculus-ucsc-mm9, r-bsgenome-celegans-ucsc-ce10,
r-bsgenome-dmelanogaster-ucsc-dm3, r-org-ce-eg-db, r-org-dm-eg-db, and
r-org-mm-eg-db.
2018-11-07 12:27:16 +01:00
Ricardo Wurmus 900ce2bafd
gnu: r-delayedmatrixstats: Update to 1.4.0.
* gnu/packages/bioinformatics.scm (r-delayedmatrixstats): Update to 1.4.0.
[propagated-inputs]: Add r-biocparallel and r-hdf5array.
2018-11-07 12:27:16 +01:00
Ricardo Wurmus 70a3a76ba7
gnu: r-scran: Update to 1.10.1.
* gnu/packages/bioinformatics.scm (r-scran): Update to 1.10.1.
[propagated-inputs]: Add r-biocneighbors; remove r-dt, r-fnn, r-ggplot2,
r-shiny, and r-viridis.
2018-11-07 12:27:16 +01:00
Ricardo Wurmus 48f2791496
gnu: r-scater: Update to 1.10.0.
* gnu/packages/bioinformatics.scm (r-scater): Update to 1.10.0.
[propagated-inputs]: Add r-biocparallel; remove r-biobase, r-data-table,
r-edger, r-limma, r-rhdf5, r-rjson, r-shiny, r-shinydashboard, and r-tximport.
2018-11-07 12:27:16 +01:00
Ricardo Wurmus f93ec63ccf
gnu: r-singlecellexperiment: Update to 1.4.0.
* gnu/packages/bioinformatics.scm (r-singlecellexperiment): Update to 1.4.0.
2018-11-07 12:27:16 +01:00
Ricardo Wurmus 3c833608f3
gnu: r-beachmat: Update to 1.4.0.
* gnu/packages/bioinformatics.scm (r-beachmat): Update to 1.4.0.
[propagated-inputs]: Add r-biocgenerics.
2018-11-07 12:27:16 +01:00
Ricardo Wurmus edb91244c3
gnu: r-qvalue: Update to 2.14.0.
* gnu/packages/bioinformatics.scm (r-qvalue): Update to 2.14.0.
2018-11-07 12:27:16 +01:00
Ricardo Wurmus d055f199a9
gnu: r-hitc: Update to 1.26.0.
* gnu/packages/bioinformatics.scm (r-hitc): Update to 1.26.0.
2018-11-07 12:27:16 +01:00
Ricardo Wurmus 8023912934
gnu: r-fithic: Update to 1.8.0.
* gnu/packages/bioinformatics.scm (r-fithic): Update to 1.8.0.
2018-11-07 12:27:16 +01:00
Ricardo Wurmus 7468a76480
gnu: r-sushi: Update to 1.20.0.
* gnu/packages/bioinformatics.scm (r-sushi): Update to 1.20.0.
2018-11-07 12:27:16 +01:00
Ricardo Wurmus 85b16c05e8
gnu: r-gwascat: Update to 2.14.0.
* gnu/packages/bioinformatics.scm (r-gwascat): Update to 2.14.0.
2018-11-07 12:27:16 +01:00
Ricardo Wurmus d57445c9b2
gnu: r-gviz: Update to 1.26.0.
* gnu/packages/bioinformatics.scm (r-gviz): Update to 1.26.0.
2018-11-07 12:27:16 +01:00
Ricardo Wurmus ea55326dc7
gnu: r-gqtlstats: Update to 1.14.0.
* gnu/packages/bioinformatics.scm (r-gqtlstats): Update to 1.14.0.
2018-11-07 12:27:16 +01:00
Ricardo Wurmus da679b5202
gnu: r-ldblock: Update to 1.12.0.
* gnu/packages/bioinformatics.scm (r-ldblock): Update to 1.12.0.
2018-11-07 12:27:16 +01:00
Ricardo Wurmus 4b91335566
gnu: r-erma: Update to 0.14.0.
* gnu/packages/bioinformatics.scm (r-erma): Update to 0.14.0.
2018-11-07 12:27:15 +01:00
Ricardo Wurmus 220ac15e3f
gnu: r-snpstats: Update to 1.32.0.
* gnu/packages/bioinformatics.scm (r-snpstats): Update to 1.32.0.
2018-11-07 12:27:15 +01:00
Ricardo Wurmus 181a843143
gnu: r-gqtlbase: Update to 1.14.0.
* gnu/packages/bioinformatics.scm (r-gqtlbase): Update to 1.14.0.
2018-11-07 12:27:15 +01:00
Ricardo Wurmus f20c766413
gnu: r-ggbio: Update to 1.30.0.
* gnu/packages/bioinformatics.scm (r-ggbio): Update to 1.30.0.
2018-11-07 12:27:15 +01:00
Ricardo Wurmus e7a0bc1ccf
gnu: r-biovizbase: Update to 1.30.0.
* gnu/packages/bioinformatics.scm (r-biovizbase): Update to 1.30.0.
2018-11-07 12:27:15 +01:00
Ricardo Wurmus cdab2dcfea
gnu: r-organismdbi: Update to 1.24.0.
* gnu/packages/bioinformatics.scm (r-organismdbi): Update to 1.24.0.
[propagated-inputs]: Remove r-biocinstaller; add r-biocmanager.
2018-11-07 12:27:15 +01:00
Ricardo Wurmus e8e78c4966
gnu: r-ensembldb: Update to 2.6.0.
* gnu/packages/bioinformatics.scm (r-ensembldb): Update to 2.6.0.
2018-11-07 12:27:15 +01:00
Ricardo Wurmus 0c96e4b290
gnu: r-dirichletmultinomial: Update to 1.24.0.
* gnu/packages/bioinformatics.scm (r-dirichletmultinomial): Update to 1.24.0.
2018-11-07 12:27:15 +01:00
Ricardo Wurmus 5ae5a8ebfc
gnu: r-complexheatmap: Update to 1.20.0.
* gnu/packages/bioinformatics.scm (r-complexheatmap): Update to 1.20.0.
2018-11-07 12:27:15 +01:00
Ricardo Wurmus d78c6aca55
gnu: r-genomicfiles: Update to 1.18.0.
* gnu/packages/bioinformatics.scm (r-genomicfiles): Update to 1.18.0.
2018-11-07 12:27:15 +01:00
Ricardo Wurmus 122e099e72
gnu: r-gage: Update to 2.32.0.
* gnu/packages/bioinformatics.scm (r-gage): Update to 2.32.0.
2018-11-07 12:27:15 +01:00
Ricardo Wurmus 4984212786
gnu: r-keggrest: Update to 1.22.0.
* gnu/packages/bioinformatics.scm (r-keggrest): Update to 1.22.0.
2018-11-07 12:27:15 +01:00
Ricardo Wurmus 95df764c01
gnu: r-fastseg: Update to 1.28.0.
* gnu/packages/bioinformatics.scm (r-fastseg): Update to 1.28.0.
2018-11-07 12:27:15 +01:00
Ricardo Wurmus 147633d4c1
gnu: r-annotationhub: Update to 2.14.1.
* gnu/packages/bioinformatics.scm (r-annotationhub): Update to 2.14.1.
[propagated-inputs]: Remove r-biocinstaller; add r-biocmanager.
2018-11-07 12:27:15 +01:00
Ricardo Wurmus d7ea34bf99
gnu: r-interactivedisplaybase: Update to 1.20.0.
* gnu/packages/bioinformatics.scm (r-interactivedisplaybase): Update to 1.20.0.
2018-11-07 12:27:15 +01:00
Ricardo Wurmus b03951f26b
gnu: r-edaseq: Update to 2.16.0.
* gnu/packages/bioinformatics.scm (r-edaseq): Update to 2.16.0.
2018-11-07 12:27:15 +01:00
Ricardo Wurmus 7812e6b82e
gnu: r-deseq: Update to 1.34.0.
* gnu/packages/bioinformatics.scm (r-deseq): Update to 1.34.0.
2018-11-07 12:27:15 +01:00
Ricardo Wurmus 800954eba4
gnu: r-aroma-light: Update to 3.12.0.
* gnu/packages/bioinformatics.scm (r-aroma-light): Update to 3.12.0.
2018-11-07 12:27:15 +01:00
Ricardo Wurmus 675d91a035
gnu: r-msnid: Update to 1.16.0.
* gnu/packages/bioinformatics.scm (r-msnid): Update to 1.16.0.
2018-11-07 12:27:14 +01:00
Ricardo Wurmus 762aca7270
gnu: r-msnbase: Update to 2.8.0.
* gnu/packages/bioinformatics.scm (r-msnbase): Update to 2.8.0.
2018-11-07 12:27:14 +01:00
Ricardo Wurmus 73d7475246
gnu: r-pcamethods: Update to 1.74.0.
* gnu/packages/bioinformatics.scm (r-pcamethods): Update to 1.74.0.
2018-11-07 12:27:14 +01:00
Ricardo Wurmus 2c4311dc7c
gnu: r-mzid: Update to 1.20.0.
* gnu/packages/bioinformatics.scm (r-mzid): Update to 1.20.0.
2018-11-07 12:27:14 +01:00
Ricardo Wurmus 0e16fc4699
gnu: r-vsn: Update to 3.50.0.
* gnu/packages/bioinformatics.scm (r-vsn): Update to 3.50.0.
2018-11-07 12:27:14 +01:00
Ricardo Wurmus 2b085484c0
gnu: r-affy: Update to 1.60.0.
* gnu/packages/bioinformatics.scm (r-affy): Update to 1.60.0.
[propagated-inputs]: Remove r-biocinstaller; add r-biocmanager.
2018-11-07 12:27:14 +01:00
Ricardo Wurmus 511abd7add
gnu: r-affyio: Update to 1.52.0.
* gnu/packages/bioinformatics.scm (r-affyio): Update to 1.52.0.
2018-11-07 12:27:14 +01:00
Ricardo Wurmus 691ce09fd3
gnu: r-protgenerics: Update to 1.14.0.
* gnu/packages/bioinformatics.scm (r-protgenerics): Update to 1.14.0.
2018-11-07 12:27:14 +01:00
Ricardo Wurmus 8af8688339
gnu: r-sva: Update to 3.30.0.
* gnu/packages/bioinformatics.scm (r-sva): Update to 3.30.0.
2018-11-07 12:27:14 +01:00
Ricardo Wurmus 18604a76e4
gnu: r-methylkit: Update to 1.8.0.
* gnu/packages/bioinformatics.scm (r-methylkit): Update to 1.8.0.
2018-11-07 12:27:14 +01:00
Ricardo Wurmus 739a856db8
gnu: r-copywriter: Update to 2.14.0.
* gnu/packages/bioinformatics.scm (r-copywriter): Update to 2.14.0.
2018-11-07 12:27:14 +01:00
Ricardo Wurmus 2e9d8116fb
gnu: r-chipseq: Update to 1.32.0.
* gnu/packages/bioinformatics.scm (r-chipseq): Update to 1.32.0.
2018-11-07 12:27:14 +01:00
Ricardo Wurmus cec8f0920b
gnu: r-annotationfilter: Update to 1.6.0.
* gnu/packages/bioinformatics.scm (r-annotationfilter): Update to 1.6.0.
2018-11-07 12:27:14 +01:00
Ricardo Wurmus d2b60be596
gnu: r-tximport: Update to 1.10.0.
* gnu/packages/bioinformatics.scm (r-tximport): Update to 1.10.0.
2018-11-07 12:27:14 +01:00
Ricardo Wurmus ad90921ddc
gnu: r-mutationalpatterns: Update to 1.8.0.
* gnu/packages/bioinformatics.scm (r-mutationalpatterns): Update to 1.8.0.
2018-11-07 12:27:14 +01:00
Ricardo Wurmus 338f860cc6
gnu: r-bamsignals: Update to 1.14.0.
* gnu/packages/bioinformatics.scm (r-bamsignals): Update to 1.14.0.
2018-11-07 12:27:14 +01:00
Ricardo Wurmus 48196899cd
gnu: r-rhtslib: Update to 1.14.0.
* gnu/packages/bioinformatics.scm (r-rhtslib): Update to 1.14.0.
2018-11-07 12:27:14 +01:00
Ricardo Wurmus 7d7c702c03
gnu: r-zlibbioc: Update to 1.28.0.
* gnu/packages/bioinformatics.scm (r-zlibbioc): Update to 1.28.0.
2018-11-07 12:27:14 +01:00
Ricardo Wurmus 2919fefe12
gnu: r-motifrg: Update to 1.26.0.
* gnu/packages/bioinformatics.scm (r-motifrg): Update to 1.26.0.
2018-11-07 12:27:13 +01:00
Ricardo Wurmus 34f1c60c78
gnu: r-seqlogo: Update to 1.48.0.
* gnu/packages/bioinformatics.scm (r-seqlogo): Update to 1.48.0.
2018-11-07 12:27:13 +01:00
Ricardo Wurmus c5b0815c44
gnu: r-genomation: Update to 1.14.0.
* gnu/packages/bioinformatics.scm (r-genomation): Update to 1.14.0.
2018-11-07 12:27:13 +01:00
Ricardo Wurmus 45ba2caedb
gnu: r-seqpattern: Update to 1.14.0.
* gnu/packages/bioinformatics.scm (r-seqpattern): Update to 1.14.0.
2018-11-07 12:27:13 +01:00
Ricardo Wurmus d11bc259a8
gnu: r-impute: Update to 1.56.0.
* gnu/packages/bioinformatics.scm (r-impute): Update to 1.56.0.
2018-11-07 12:27:13 +01:00
Ricardo Wurmus 78ecdbc00a
gnu: r-bsgenome: Update to 1.50.0.
* gnu/packages/bioinformatics.scm (r-bsgenome): Update to 1.50.0.
2018-11-07 12:27:13 +01:00
Ricardo Wurmus 44fa14dfa3
gnu: r-topgo: Update to 2.34.0.
* gnu/packages/bioinformatics.scm (r-topgo): Update to 2.34.0.
2018-11-07 12:27:13 +01:00
Ricardo Wurmus 8a0d57d26e
gnu: r-genomicfeatures: Update to 1.34.1.
* gnu/packages/bioinformatics.scm (r-genomicfeatures): Update to 1.34.1.
2018-11-07 12:27:13 +01:00
Ricardo Wurmus c5f1d1ce80
gnu: r-rtracklayer: Update to 1.42.0.
* gnu/packages/bioinformatics.scm (r-rtracklayer): Update to 1.42.0.
2018-11-07 12:27:13 +01:00
Ricardo Wurmus 52b95337e8
gnu: r-genomicalignments: Update to 1.18.0.
* gnu/packages/bioinformatics.scm (r-genomicalignments): Update to 1.18.0.
2018-11-07 12:27:13 +01:00
Ricardo Wurmus 9fd4350e5a
gnu: r-summarizedexperiment: Update to 1.12.0.
* gnu/packages/bioinformatics.scm (r-summarizedexperiment): Update to 1.12.0.
2018-11-07 12:27:13 +01:00
Ricardo Wurmus de4c38f80b
gnu: r-delayedarray: Update to 0.8.0.
* gnu/packages/bioinformatics.scm (r-delayedarray): Update to 0.8.0.
2018-11-07 12:27:13 +01:00
Ricardo Wurmus 7f3778eb06
gnu: r-rsamtools: Update to 1.34.0.
* gnu/packages/bioinformatics.scm (r-rsamtools): Update to 1.34.0.
2018-11-07 12:27:13 +01:00
Ricardo Wurmus 4804c59227
gnu: r-biostrings: Update to 2.50.0.
* gnu/packages/bioinformatics.scm (r-biostrings): Update to 2.50.0.
2018-11-07 12:27:13 +01:00
Ricardo Wurmus cd8828918f
gnu: r-biocparallel: Update to 1.16.0.
* gnu/packages/bioinformatics.scm (r-biocparallel): Update to 1.16.0.
2018-11-07 12:27:13 +01:00
Ricardo Wurmus 3359d44210
gnu: r-biomart: Update to 2.38.0.
* gnu/packages/bioinformatics.scm (r-biomart): Update to 2.38.0.
2018-11-07 12:27:13 +01:00
Ricardo Wurmus 3986e0dee5
gnu: r-annotationdbi: Update to 1.44.0.
* gnu/packages/bioinformatics.scm (r-annotationdbi): Update to 1.44.0.
2018-11-07 12:27:13 +01:00
Ricardo Wurmus 5b82e12a99
gnu: r-biobase: Update to 2.42.0.
* gnu/packages/bioinformatics.scm (r-biobase): Update to 2.42.0.
2018-11-07 12:27:13 +01:00
Ricardo Wurmus 8d3906a95f
gnu: r-genomicranges: Update to 1.34.0.
* gnu/packages/bioinformatics.scm (r-genomicranges): Update to 1.34.0.
2018-11-07 12:27:12 +01:00
Ricardo Wurmus fb10fb72ba
gnu: r-xvector: Update to 0.22.0.
* gnu/packages/bioinformatics.scm (r-xvector): Update to 0.22.0.
2018-11-07 12:27:12 +01:00
Ricardo Wurmus 78d2ffdc73
gnu: r-limma: Update to 3.38.2.
* gnu/packages/bioinformatics.scm (r-limma): Update to 3.38.2.
2018-11-07 12:27:12 +01:00
Ricardo Wurmus ca2945c316
gnu: r-variantannotation: Update to 1.28.1.
* gnu/packages/bioinformatics.scm (r-variantannotation): Update to 1.28.1.
2018-11-07 12:27:12 +01:00
Ricardo Wurmus 08cd2d5b59
gnu: r-edger: Update to 3.24.0.
* gnu/packages/bioinformatics.scm (r-edger): Update to 3.24.0.
2018-11-07 12:27:12 +01:00
Ricardo Wurmus 12871693fe
gnu: r-genomeinfodb: Update to 1.18.0.
* gnu/packages/bioinformatics.scm (r-genomeinfodb): Update to 1.18.0.
2018-11-07 12:27:12 +01:00
Ricardo Wurmus 9a8dd51979
gnu: r-iranges: Update to 2.16.0.
* gnu/packages/bioinformatics.scm (r-iranges): Update to 2.16.0.
2018-11-07 12:27:12 +01:00
Ricardo Wurmus a037453554
gnu: r-s4vectors: Update to 0.20.0.
* gnu/packages/bioinformatics.scm (r-s4vectors): Update to 0.20.0.
2018-11-07 12:27:12 +01:00
Ricardo Wurmus 70f2758f71
gnu: r-dnacopy: Update to 1.56.0.
* gnu/packages/bioinformatics.scm (r-dnacopy): Update to 1.56.0.
2018-11-07 12:27:12 +01:00
Ricardo Wurmus a127d3522a
gnu: r-bioccheck: Update to 1.18.0.
* gnu/packages/bioinformatics.scm (r-bioccheck): Update to 1.18.0.
[propagated-inputs]: Add r-knitr and r-biocmanager; remove r-biocinstaller.
2018-11-07 12:27:12 +01:00
Ricardo Wurmus 6087f5ce37
gnu: r-biocstyle: Update to 2.10.0.
* gnu/packages/bioinformatics.scm (r-biocstyle): Update to 2.10.0.
[propagated-inputs]: Add biocmanager.
2018-11-07 12:27:12 +01:00
Ricardo Wurmus c8dbb5fa7f
gnu: r-biocviews: Update to 1.50.1.
* gnu/packages/bioinformatics.scm (r-biocviews): Update to 1.50.1.
2018-11-07 12:27:12 +01:00
Ricardo Wurmus 36d7d823a4
gnu: r-biocinstaller: Update to 1.32.1.
* gnu/packages/bioinformatics.scm (r-biocinstaller): Update to 1.32.1.
2018-11-07 12:27:12 +01:00
Ricardo Wurmus 2f28ffd81d
gnu: r-biocgenerics: Update to 0.28.0.
* gnu/packages/bioinformatics.scm (r-biocgenerics): Update to 0.28.0.
2018-11-07 12:27:12 +01:00
Ricardo Wurmus 5c996cab4c
gnu: r-grohmm: Update to 1.16.0.
* gnu/packages/bioinformatics.scm (r-grohmm): Update to 1.16.0.
2018-11-07 12:27:12 +01:00
Ricardo Wurmus bf25930cf6
gnu: r-systempiper: Update to 1.16.0.
* gnu/packages/bioinformatics.scm (r-systempiper): Update to 1.16.0.
2018-11-07 12:27:12 +01:00
Ricardo Wurmus 9adf78c21e
gnu: r-shortread: Update to 1.40.0.
* gnu/packages/bioinformatics.scm (r-shortread): Update to 1.40.0.
2018-11-07 12:27:12 +01:00
Ricardo Wurmus 4a4b5b8537
gnu: r-gostats: Update to 2.48.0.
* gnu/packages/bioinformatics.scm (r-gostats): Update to 2.48.0.
2018-11-07 12:27:12 +01:00
Ricardo Wurmus 95ae5acc89
gnu: r-category: Update to 2.48.0.
* gnu/packages/bioinformatics.scm (r-category): Update to 2.48.0.
2018-11-07 12:26:34 +01:00
Ricardo Wurmus 6dfb0b25ae
gnu: r-gseabase: Update to 1.44.0.
* gnu/packages/bioinformatics.scm (r-gseabase): Update to 1.44.0.
2018-11-07 12:26:34 +01:00
Ricardo Wurmus 19a6149190
gnu: r-rbgl: Update to 1.58.0.
* gnu/packages/bioinformatics.scm (r-rbgl): Update to 1.58.0.
2018-11-07 12:26:34 +01:00
Ricardo Wurmus 2ff6604a53
gnu: r-annotationforge: Update to 1.24.0.
* gnu/packages/bioinformatics.scm (r-annotationforge): Update to 1.24.0.
2018-11-07 12:26:34 +01:00
Ricardo Wurmus 856444a0a1
gnu: r-dexseq: Update to 1.28.0.
* gnu/packages/bioinformatics.scm (r-dexseq): Update to 1.28.0.
2018-11-07 12:26:34 +01:00
Ricardo Wurmus b5c552e654
gnu: r-deseq2: Update to 1.22.1.
* gnu/packages/bioinformatics.scm (r-deseq2): Update to 1.22.1.
2018-11-07 12:26:34 +01:00
Ricardo Wurmus 85fb33a051
gnu: r-genefilter: Update to 1.64.0.
* gnu/packages/bioinformatics.scm (r-genefilter): Update to 1.64.0.
2018-11-07 12:26:34 +01:00
Ricardo Wurmus f4a95a0d15
gnu: r-geneplotter: Update to 1.60.0.
* gnu/packages/bioinformatics.scm (r-geneplotter): Update to 1.60.0.
2018-11-07 12:26:34 +01:00
Ricardo Wurmus dadd682c53
gnu: r-copynumber: Update to 1.22.0.
* gnu/packages/bioinformatics.scm (r-copynumber): Update to 1.22.0.
2018-11-07 12:26:34 +01:00
Ricardo Wurmus 090d4c0159
gnu: r-annotate: Update to 1.60.0.
* gnu/packages/bioinformatics.scm (r-annotate): Update to 1.60.0.
2018-11-07 12:26:34 +01:00
Ricardo Wurmus 6b451c0801
gnu: r-gprofiler: Update to 0.6.7.
* gnu/packages/bioinformatics.scm (r-gprofiler): Update to 0.6.7.
2018-10-30 21:42:48 +01:00
Ricardo Wurmus 4fc6609a0c
gnu: r-keggrest: Update to 1.20.2.
* gnu/packages/bioinformatics.scm (r-keggrest): Update to 1.20.2.
2018-10-30 21:42:39 +01:00
Ricardo Wurmus 67cfb83ff1
gnu: r-msnbase: Update to 2.6.4.
* gnu/packages/bioinformatics.scm (r-msnbase): Update to 2.6.4.
2018-10-30 21:42:31 +01:00