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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
e7c6bc45ed
gnu: jamm: Remove broken "build" phase.
...
* gnu/packages/bioinformatics.scm (jamm)[arguments]: Remove "build" phase.
2019-01-11 06:08:43 +01:00
6fd2ed23ac
gnu: mantis: Limit to x86_64-linux.
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* gnu/packages/bioinformatics.scm (mantis)[supported-systems]: New field.
2019-01-07 15:47:34 +02:00
e942813aac
gnu: Add mantis.
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* gnu/packages/bioinformatics.scm (mantis): New variable.
2019-01-07 11:56:18 +01:00
8894668cd2
gnu: discrover: Comment on attempt of minimal texlive-union.
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* gnu/packages/bioinformatics.scm (discrover): Comment on attempt of minimal
texlive-union.
2018-12-20 12:07:40 +01:00
2f3977b9a7
gnu: gess: Don't hardcode python version.
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* gnu/packages/bioinformatics.scm (gess)[arguments]: Replace hardcoded
python version with parameterized one.
2018-12-17 12:08:05 +02:00
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
42c3e00c20
gnu: pigx-rnaseq: Update to 0.0.5.
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* 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
4b2d1dc4dc
gnu: bless: Adjust to zlib static output.
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* gnu/packages/bioinformatics.scm (bless)[inputs]: Add ZLIB:STATIC.
[arguments]: Adjust #:make-flags accordingly.
2018-11-24 19:32:48 +01:00
f028823c0f
gnu: mosaik: Fix FTBFS from b90289dadc.
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* gnu/packages/bioinformatics.scm (mosaik)[inputs]: Add ZLIB:STATIC.
2018-11-24 15:57:56 +01:00
d57ec906ba
gnu: pigx-scrnaseq: Use latest snakemake.
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* gnu/packages/bioinformatics.scm (pigx-scrnaseq)[inputs]: Replace snakemake-4
with snakemake.
2018-11-23 16:30:48 +01:00
92d9a1e2c6
gnu: pigx-bsseq: Use latest snakemake.
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* gnu/packages/bioinformatics.scm (pigx-bsseq)[inputs]: Replace snakemake-4
with snakemake.
2018-11-23 16:30:16 +01:00
c068d00746
gnu: pigx-chipseq: Use latest snakemake.
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* gnu/packages/bioinformatics.scm (pigx-chipseq)[inputs]: Replace snakemake-4
with snakemake.
2018-11-23 16:29:35 +01:00
93d229cb86
gnu: python-loompy: Remove python-typing.
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* gnu/packages/bioinformatics.scm (python-loompy)[propagated-inputs]: Remove
python-typing.
2018-11-23 15:59:44 +01:00
4f70db97a0
Merge branch 'master' into core-updates
2018-11-20 01:14:12 +01:00
c2e26dc156
gnu: r-ensembldb: Update to 2.6.2.
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* gnu/packages/bioinformatics.scm (r-ensembldb): Update to 2.6.2.
2018-11-19 16:46:32 +01:00
e038819138
gnu: r-msnbase: Update to 2.8.1.
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* gnu/packages/bioinformatics.scm (r-msnbase): Update to 2.8.1.
2018-11-19 16:46:00 +01:00
4535a7b0f5
gnu: r-genomeinfodb: Update to 1.18.1.
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* gnu/packages/bioinformatics.scm (r-genomeinfodb): Update to 1.18.1.
2018-11-19 16:33:35 +01:00
30f0d21b40
gnu: Add nanopolish.
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* gnu/packages/bioinformatics.scm (nanopolish): New variable.
Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
2018-11-15 22:23:57 +01:00
2d86eaff5b
gnu: sambamba: Update to 0.6.8.
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* gnu/packages/bioinformatics.scm (sambamba): Update to 0.6.8.
2018-11-15 13:09:01 +01:00
2e0f69057a
gnu: bioinformatics: Return #t from all phases and snippets.
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* 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
ee66a13563
gnu: Add jamm.
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* gnu/packages/bioinformatics.scm (jamm): New variable.
2018-11-14 15:13:20 +01:00
51b262f310
gnu: r-txdb-mmusculus-ucsc-mm10-knowngene: Update to 3.4.4.
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* gnu/packages/bioinformatics.scm (r-txdb-mmusculus-ucsc-mm10-knowngene):
Update to 3.4.4.
2018-11-13 23:34:40 +01:00
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
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
76bd16bcf6
gnu: r-org-ce-eg-db: Update to 3.7.0.
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* gnu/packages/bioinformatics.scm (r-org-ce-eg-db): Update to 3.7.0.
2018-11-13 23:34:39 +01:00
fc7683fa30
gnu: r-org-hs-eg-db: Update to 3.7.0.
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* gnu/packages/bioinformatics.scm (r-org-hs-eg-db): Update to 3.7.0.
2018-11-13 23:34:39 +01:00
cb9e6ed702
gnu: r-genomationdata: Update to 1.14.0.
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* gnu/packages/bioinformatics.scm (r-genomationdata): Update to 1.14.0.
2018-11-13 23:34:39 +01:00
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
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