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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
cb66fb101f
gnu: Add r-scde.
...
* gnu/packages/bioinformatics.scm (r-scde): New variable.
2019-03-06 15:55:54 +01:00
afeb10a056
gnu: Add bowtie1.
...
* gnu/packages/bioinformatics.scm (bowtie1): New variable.
2019-03-06 15:32:45 +01:00
4fc9b5b1dd
gnu: Add genrich.
...
* gnu/packages/bioinformatics.scm (genrich): New variable.
2019-03-06 13:28:45 +01:00
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
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
a27ca96f10
gnu: Add velvet.
...
* gnu/packages/bioinformatics.scm (velvet): New variable.
2019-03-01 12:55:35 +01:00
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
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
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
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
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
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
9846ec0bea
gnu: Add python-pyfit-sne.
...
* gnu/packages/bioinformatics.scm (python-pyfit-sne): New variable.
2019-02-15 11:03:26 +01:00
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
385d7546e1
gnu: Add cnvkit.
...
* gnu/packages/bioinformatics.scm (cnvkit): New variable.
2019-02-12 15:41:02 +01:00
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
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
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
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
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
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
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
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
fdb0b40b0e
gnu: pepr: Use PYPI-URI.
...
* gnu/packages/bioinformatics.scm (pepr)[source]: Use PYPI-URI.
2019-01-25 23:27:25 +01:00
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
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
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
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
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
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
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
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
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
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
Andreas Enge
Marius Bakke
Maxim Cournoyer
Ricardo Wurmus