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.
...
* gnu/packages/bioinformatics.scm (mantis)[supported-systems]: New field.
2019-01-07 15:47:34 +02:00
e942813aac
gnu: Add mantis.
...
* 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.
...
* 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.
...
* 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.
...
* 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.
...
* 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.
...
* gnu/packages/bioinformatics.scm (mosaik)[inputs]: Add ZLIB:STATIC.
2018-11-24 15:57:56 +01:00
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
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
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
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
4f70db97a0
Merge branch 'master' into core-updates
2018-11-20 01:14:12 +01:00
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
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
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
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
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
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
ee66a13563
gnu: Add jamm.
...
* 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.
...
* 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.
...
* 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.
...
* 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.
...
* 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
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
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
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
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
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
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
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
9f527c9199
gnu: sailfish: Use INVOKE.
...
* gnu/packages/bioinformatics.scm (sailfish)[arguments]: Use INVOKE instead of
SYSTEM*.
2018-11-08 09:52:46 +01:00
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
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
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
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
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
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
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
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
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
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
0881d62f25
gnu: newick-utils: Remove custom autoconf phase.
...
* gnu/packages/bioinformatics.scm (newick-utils)[arguments]: Remove.
2018-11-08 09:10:58 +01:00
e35dce0170
gnu: mash: Remove custom autoconf phase.
...
* gnu/packages/bioinformatics.scm (mash)[arguments]: Remove autoconf phase.
2018-11-08 09:10:20 +01:00
31c41a8cfe
gnu: vsearch: Remove custom autogen phase.
...
* gnu/packages/bioinformatics.scm (vsearch)[arguments]: Remove.
2018-11-08 09:04:34 +01:00
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
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
c098c49b3e
gnu: sailfish: Fetch sources from git.
...
* gnu/packages/bioinformatics.scm (sailfish)[source]: Fetch from git.
2018-11-08 08:53:54 +01:00
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
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
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
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
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
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
7145f4e519
gnu: ritornello: Fetch sources from git.
...
* gnu/packages/bioinformatics.scm (ritornello)[source]: Fetch from git.
2018-11-07 23:17:35 +01:00
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
6236524409
gnu: sortmerna: Fetch sources from git.
...
* gnu/packages/bioinformatics.scm (sortmerna)[source]: Fetch from git.
2018-11-07 23:17:35 +01:00
273df99d7d
gnu: vsearch: Fetch source from git.
...
* gnu/packages/bioinformatics.scm (vsearch)[source]: Fetch from git.
2018-11-07 23:17:35 +01:00
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
37e285be43
gnu: preseq: Fetch sources from git.
...
* gnu/packages/bioinformatics.scm (preseq)[source]: Fetch from git.
2018-11-07 23:17:35 +01:00
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
019fcdf20a
gnu: seqtk: Fetch sources from git.
...
* gnu/packages/bioinformatics.scm (seqtk)[source]: Fetch from git.
2018-11-07 23:17:34 +01:00
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
d9ba126d17
gnu: python2-biom-format: Fix build.
...
This is a follow-up to commit 239716fb0b
2018-11-07 23:17:34 +01:00
4715d4af17
gnu: raxml: Fetch sources from git.
...
* gnu/packages/bioinformatics.scm (raxml)[source]: Fetch from git.
2018-11-07 23:17:34 +01:00
5e242b02c3
gnu: pyicoteo: Fetch sources from git.
...
* gnu/packages/bioinformatics.scm (pyicoteo)[source]: Fetch from git.
2018-11-07 23:17:34 +01:00
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
55698df260
gnu: libgff: Fetch sources from git.
...
* gnu/packages/bioinformatics.scm (libgff)[source]: Fetch from git.
2018-11-07 21:41:56 +01:00
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
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
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
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
9d94ca0ebf
gnu: minced: Fetch sources from git.
...
* gnu/packages/bioinformatics.scm (minced)[source]: Fetch from git.
2018-11-07 21:41:55 +01:00
b58d9e4aa2
gnu: metabat: Fetch sources from git.
...
* gnu/packages/bioinformatics.scm (metabat)[source]: Fetch from git.
2018-11-07 21:41:55 +01:00
5c1f35e71b
gnu: mash: Update to 2.1.
...
* gnu/packages/bioinformatics.scm (mash): Update to 2.1.
2018-11-07 21:41:55 +01:00
497fc04d8f
gnu: mash: Fetch sources from git.
...
* gnu/packages/bioinformatics.scm (mash)[source]: Fetch from git.
2018-11-07 21:41:55 +01:00
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
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
f0731591a5
gnu: idr: Fetch sources from git.
...
* gnu/packages/bioinformatics.scm (idr)[source]: Fetch from git.
2018-11-07 20:41:58 +01:00
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
57be690d91
gnu: hisat2: Use versioned source URL.
...
* gnu/packages/bioinformatics.scm (hisat2)[source]: Use versioned URL.
2018-11-07 20:32:29 +01:00
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
8d75adbf03
gnu: grit: Fetch sources from git.
...
* gnu/packages/bioinformatics.scm (grit)[source]: Fetch from git.
2018-11-07 20:27:10 +01:00
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
b113f39019
gnu: gemma: Fetch sources from git.
...
* gnu/packages/bioinformatics.scm (gemma)[source]: Fetch from git.
2018-11-07 20:26:45 +01:00
91b71cfbba
gnu: fxtract: Fetch sources from git.
...
* gnu/packages/bioinformatics.scm (fxtract)[source]: Fetch from git.
2018-11-07 19:55:50 +01:00
7ca49ab57a
gnu: ribodiff: Fetch sources from git.
...
* gnu/packages/bioinformatics.scm (ribodiff)[source]: Fetch from git.
2018-11-07 19:48:21 +01:00
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
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
383cb7b8e6
gnu: bioawk: Fetch sources from git.
...
* gnu/packages/bioinformatics.scm (bioawk)[source]: Fetch from git.
2018-11-07 19:06:30 +01:00
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
8e58319c45
gnu: bamtools: Fetch sources from git.
...
* gnu/packages/bioinformatics.scm (bamtools)[source]: Fetch from git.
2018-11-07 18:44:30 +01:00
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
fff67cc8a7
gnu: prodigal: Fetch sources from git.
...
* gnu/packages/bioinformatics.scm (prodigal)[source]: Fetch from git.
2018-11-07 17:19:53 +01:00
9255198423
gnu: r-mzr: Update to 2.16.0.
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* 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
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
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
611a255d2b
gnu: r-rhdf5: Update to 2.26.0.
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* gnu/packages/bioinformatics.scm (r-rhdf5): Update to 2.26.0.
2018-11-07 12:27:16 +01:00
a1c2bf8e54
gnu: r-rcas: Update to 1.8.0.
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* 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
900ce2bafd
gnu: r-delayedmatrixstats: Update to 1.4.0.
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* 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
70a3a76ba7
gnu: r-scran: Update to 1.10.1.
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* 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
48f2791496
gnu: r-scater: Update to 1.10.0.
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* 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
f93ec63ccf
gnu: r-singlecellexperiment: Update to 1.4.0.
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* gnu/packages/bioinformatics.scm (r-singlecellexperiment): Update to 1.4.0.
2018-11-07 12:27:16 +01:00
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
807d961cc9
gnu: r-methylkit: Update to 1.6.3.
...
* gnu/packages/bioinformatics.scm (r-methylkit): Update to 1.6.3.
2018-10-30 21:42:20 +01:00
ac0166450d
gnu: r-wgcna: Update to 1.66.
...
* gnu/packages/bioinformatics.scm (r-wgcna): Update to 1.66.
2018-10-30 21:42:09 +01:00
1182460750
gnu: r-go-db: Update to 3.6.0.
...
* gnu/packages/bioinformatics.scm (r-go-db): Update to 3.6.0.
2018-10-30 21:42:00 +01:00
466bf3af89
gnu: r-genomicfeatures: Update to 1.32.3.
...
* gnu/packages/bioinformatics.scm (r-genomicfeatures): Update to 1.32.3.
2018-10-30 21:41:12 +01:00
dd0216e0e7
gnu: r-delayedarray: Update to 0.6.6.
...
* gnu/packages/bioinformatics.scm (r-delayedarray): Update to 0.6.6.
2018-10-30 21:40:57 +01:00
72408357fa
gnu: r-genomicranges: Update to 1.32.7.
...
* gnu/packages/bioinformatics.scm (r-genomicranges): Update to 1.32.7.
2018-10-30 21:40:48 +01:00
9dad1957ab
gnu: r-limma: Update to 3.36.5.
...
* gnu/packages/bioinformatics.scm (r-limma): Update to 3.36.5.
2018-10-30 21:40:40 +01:00
57cf6a14f0
gnu: r-edger: Update to 3.22.5.
...
* gnu/packages/bioinformatics.scm (r-edger): Update to 3.22.5.
2018-10-30 21:40:32 +01:00
eb890466fa
gnu: r-genomeinfodbdata: Update to 1.1.0.
...
* gnu/packages/bioinformatics.scm (r-genomeinfodbdata): Update to 1.1.0.
2018-10-30 21:40:22 +01:00
e563acb96b
gnu: r-iranges: Update to 2.14.12.
...
* gnu/packages/bioinformatics.scm (r-iranges): Update to 2.14.12.
2018-10-30 21:40:12 +01:00
192c19f484
gnu: r-vegan: Update to 2.5-3.
...
* gnu/packages/bioinformatics.scm (r-vegan): Update to 2.5-3.
2018-10-30 21:40:00 +01:00
f8ee22fc8b
gnu: flexbar: Update to 3.4.0.
...
* gnu/packages/bioinformatics.scm (flexbar): Update to 3.4.0.
[source]: Fetch from git.
[arguments]: Adjust check and install phases.
[home-page]: Update to new home at Github.
[license]: Change to bsd-3.
2018-10-21 23:06:47 +02:00
4d93a9a36c
gnu: seqan: Update to 2.4.0.
...
* gnu/packages/bioinformatics.scm (seqan): Update to 2.4.0.
[native-inputs]: Replace bzip2 with xz.
(seqan-1): New variable.
(tophat)[inputs]: Use seqan-1.
2018-10-21 23:06:47 +02:00
4b8f4536ce
gnu: khmer: Update to 2.1.2.
...
* gnu/packages/bioinformatics.scm (khmer): Update to 2.1.2.
[source]: Fetch from git; remove bundled libraries in snippet.
[arguments]: Remove "set-paths" phase; remove "post-install-check" phase;
remove "reset-gzip-timestamps" phase.
[native-inputs]: Remove seqan and python-nose; add python-cython,
python-pytest, and python-pytest-runner.
[inputs]: Remove gcc-4.9.
2018-10-21 23:06:47 +02:00
50e33c3a8c
gnu: python-screed: Update to 1.0.
...
* gnu/packages/bioinformatics.scm (python-screed): Update to 1.0.
[arguments]: Run tests after installation.
[native-inputs]: Add python-pytest, python-pytest-cov, and
python-pytest-runner; remove python-nose.
2018-10-21 23:06:47 +02:00
0db75f7a79
gnu: fasttree: Use INVOKE.
...
* gnu/packages/bioinformatics.scm (fasttree)[arguments]: Use INVOKE; simplify
install phase.
2018-10-21 23:06:46 +02:00
38622ccd14
gnu: express-beta-diversity: Update to 1.0.8.
...
* gnu/packages/bioinformatics.scm (express-beta-diversity): Update to 1.0.8.
[source]: Fetch from git.
[arguments]: Use INVOKE; remove "exit-source" build phase; simplify.
2018-10-21 23:06:46 +02:00
c96ca68f31
gnu: edirect: Update to 10.2.20181018.
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* gnu/packages/bioinformatics.scm (edirect): Update to 10.2.20181018.
[arguments]: Add simple check phase; simplify other phases.
[inputs]: Add perl-xml-simple.
2018-10-21 23:06:46 +02:00
949fa34b84
gnu: eigensoft: Update to 7.2.1.
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* gnu/packages/bioinformatics.scm (eigensoft): Update to 7.2.1.
[arguments]: Remove Makefile modification.
2018-10-21 23:06:46 +02:00
5748fe5fcc
gnu: discrover: Fetch from git.
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* gnu/packages/bioinformatics.scm (discrover)[source]: Fetch from git.
2018-10-21 23:06:46 +02:00
1c06399358
gnu: diamond: Fetch from git.
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* gnu/packages/bioinformatics.scm (diamond)[source]: Fetch from git.
2018-10-21 23:06:46 +02:00
7a1e62ca67
gnu: delly: Update to 0.7.9.
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* gnu/packages/bioinformatics.scm (delly): Update to 0.7.9.
[source]: Fetch from git.
[arguments]: Add phase install-templates; use default install phase.
[native-inputs]: Remove python-2.
[home-page]: Use new home page.
* gnu/packages/patches/delly-use-system-libraries.patch: Delete file.
* gnu/local.mk (dist_patch_DATA): Remove patch.
2018-10-21 23:06:46 +02:00
4d494a4fa3
gnu: deeptools: Update to 3.1.3.
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* gnu/packages/bioinformatics.scm (deeptools): Update to 3.1.3.
2018-10-21 23:06:46 +02:00
42643fc24d
gnu: python-dendropy: Fetch from git.
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* gnu/packages/bioinformatics.scm (python-dendropy)[source]: Fetch from git.
2018-10-21 23:06:46 +02:00
6b31040ae6
gnu: python-py2bit: Update to 0.3.0.
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* gnu/packages/bioinformatics.scm (python-py2bit): Update to 0.3.0.
2018-10-21 23:06:45 +02:00
6b7260bad1
gnu: cutadapt: Update to 1.18.
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* gnu/packages/bioinformatics.scm (cutadapt): Update to 1.18.
[inputs]: Add python-dnaio.
2018-10-21 23:06:45 +02:00
a5b0038cbd
gnu: Add python-dnaio.
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* gnu/packages/bioinformatics.scm (python-dnaio): New variable.
2018-10-21 23:06:45 +02:00
7321920cd3
gnu: crossmap: Update to 0.2.9.
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* gnu/packages/bioinformatics.scm (crossmap): Update to 0.2.9.
* gnu/packages/patches/crossmap-allow-system-pysam.patch: Delete file.
* gnu/local.mk (dist_patch_DATA): Remove patch.
2018-10-21 23:06:45 +02:00
8640f9ec91
gnu: python-twobitreader: Update to 3.1.6.
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* gnu/packages/bioinformatics.scm (python-twobitreader): Update to 3.1.6.
[source]: Fetch from git.
2018-10-21 23:06:45 +02:00
f5cec0068a
gnu: Add python-bx-python.
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* gnu/packages/bioinformatics.scm (python-bx-python): New variable.
(python2-bx-python): Define in terms of python-bx-python.
2018-10-21 23:06:45 +02:00
2ba2d62c69
gnu: python2-bx-python: Update to 0.8.2.
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* gnu/packages/bioinformatics.scm (python2-bx-python): Update to 0.8.2.
[source]: Remove obsolete snippet.
[inputs]: Move python2-numpy from here...
[propagated-inputs]: ...to here; add python2-six.
[native-inputs]: Add python2-lzo and python2-cython.
[home-page]: Update to new home at Github.
2018-10-21 23:06:45 +02:00
1d18ee6dfd
gnu: bwa-pssm: Fetch from git.
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* gnu/packages/bioinformatics.scm (bwa-pssm)[source]: Fetch from git.
2018-10-21 23:06:45 +02:00
9a6808e0c0
gnu: tophat: Update to 2.1.1.
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* gnu/packages/bioinformatics.scm (tophat): Update to 2.1.1.
* gnu/packages/patches/tophat-build-with-later-seqan.patch: Delete file.
* gnu/local.mk (dist_patch_DATA): Remove patch.
2018-10-21 23:06:45 +02:00
617c478506
gnu: python2-dendropy: Disable failing test.
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* gnu/packages/bioinformatics.scm (python2-dendropy)[arguments]: Disable
failing test.
2018-10-21 22:31:56 +10:00
21c837405a
gnu: bowtie: Update to 2.3.4.3.
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* gnu/packages/bioinformatics.scm (bowtie): Update to 2.3.4.3.
[source]: Fetch from git.
[inputs]: Replace python-2 with python-wrapper; move perl, perl-clone,
perl-test-deep, and perl-test-simple from here...
[native-inputs]: ...to here.
[arguments]: Simplify check phase.
2018-10-20 23:37:34 +02:00
f45093429c
gnu: blast+: Use INVOKE and return #T unconditionally.
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* gnu/packages/bioinformatics.scm (blast+)[arguments]: Use INVOKE and
return #T unconditionally.
2018-10-20 23:37:34 +02:00
f8b697a385
gnu: bedops: Update to 2.4.35.
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* gnu/packages/bioinformatics.scm (bedops): Update to 2.4.35.
[source]: Fetch from git.
2018-10-20 23:37:34 +02:00
337d72fb44
gnu: bedops: Use INVOKE.
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* gnu/packages/bioinformatics.scm (bedops)[arguments]: Use INVOKE.
2018-10-20 23:37:34 +02:00
c793f4d8fb
gnu: bamm: Fetch from git and use INVOKE.
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* gnu/packages/bioinformatics.scm (bamm)[source]: Fetch from git.
[arguments]: Use INVOKE and return #T unconditionally.
2018-10-20 23:37:34 +02:00
95758e2faf
gnu: aragorn: Use invoke and simplify.
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* gnu/packages/bioinformatics.scm (aragorn)[arguments]: Use INVOKE in build
phase; simplify install phase.
2018-10-20 23:37:33 +02:00
8b4102b903
gnu: clipper: Update to 1.2.1.
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* gnu/packages/bioinformatics.scm (clipper): Update to 1.2.1.
[source]: Fetch from git.
[arguments]: Add fix-typo phase.
2018-10-20 23:37:33 +02:00
895cf8278a
gnu: python-pybedtools: Update to 0.7.10.
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* gnu/packages/bioinformatics.scm (python2-pybedtools): Update to 0.7.10.
[arguments]: Disable broken tests.
[propagated-inputs]: Replace bedtools with bedtools-2.26; add
python-matplotlib, python-pysam, and python-pyyaml.
[native-inputs]: Remove python-pyyaml; add kentutils, python-numpy,
python-pandas, and python-six.
(python-pybedtools): New variable.
2018-10-20 23:37:33 +02:00
129363b762
gnu: Add bedtools-2.26.
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* gnu/packages/bioinformatics.scm (bedtools-2.26): New variable.
2018-10-20 23:37:28 +02:00
e8a7eab169
gnu: kallisto: Update to 0.44.0.
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* gnu/packages/bioinformatics.scm (kallisto): Update to 0.44.0.
[source]: Fetch from git.
[arguments]: Add build phase to use htslib from Guix.
[inputs]: Add htslib.
2018-10-11 16:12:11 +02:00
b6bd8b108a
gnu: Add filtlong.
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* gnu/packages/bioinformatics.scm (filtlong): New variable.
Co-authored-by: Ludovic Courtès <ludo@gnu.org>
2018-10-08 18:32:42 +02:00
d71078bc75
gnu: Add ngless.
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* gnu/packages/bioinformatics.scm (ngless): New variable.
2018-10-05 23:59:27 +02:00
357450dca0
gnu: bioruby: Update to 1.5.2.
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This works with Ruby 2.5.
* gnu/packages/bioinformatics.scm (bioruby): Update to 1.5.2.
2018-10-05 21:25:39 +01:00
a6798218be
gnu: samtools-0.1: Adjust to match changes in samtools.
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* gnu/packages/bioinformatics.scm (samtools-0.1)[arguments]: Override make
flags.
2018-10-05 09:21:54 +02:00
8e72f0f319
gnu: deeptools: Update to 3.1.2.
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* gnu/packages/bioinformatics.scm (deeptools): Update to 3.1.2.
[source]: Fetch from git.
[arguments]: Delete reset-gzip-timestamps phase.
[inputs]: Add python-plotly.
2018-10-05 09:21:54 +02:00
939882f734
gnu: python-pysam: Update to 0.15.1.
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* gnu/packages/bioinformatics.scm (python-pysam): Update to 0.15.1.
[source]: Fetch from git.
[arguments]: Delete tests requiring internet access; use "invoke".
[inputs]: Add curl.
2018-10-05 09:21:54 +02:00
f79b59e311
gnu: bcftools: Update to 1.9.
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* gnu/packages/bioinformatics.scm (bcftools): Update to 1.9.
[arguments]: Remove obsolete make flags.
2018-10-05 09:21:54 +02:00
4ae4a15232
gnu: samtools: Update to 1.9.
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* gnu/packages/bioinformatics.scm (samtools): Update to 1.9.
[origin]: Remove bundled htslib sources.
[arguments]: Remove obsolete make-flags.
2018-10-05 09:21:54 +02:00
bd5f5eece9
gnu: htslib: Update to 1.9.
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* gnu/packages/bioinformatics.scm (htslib): Update to 1.9.
2018-10-05 09:21:50 +02:00
0f1622220a
gnu: Add r-absfiltergsea.
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* gnu/packages/bioinformatics.scm (r-absfiltergsea): New variable.
2018-10-02 16:23:49 -04:00
3f0f49d708
gnu: Add poretools.
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* gnu/packages/bioinformatics.scm (poretools): New variable.
2018-10-02 16:05:14 -04:00
f2bc53af70
gnu: Add porechop.
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* gnu/packages/bioinformatics.scm (porechop): New variable.
2018-09-30 14:09:48 -04:00
e72702475d
gnu: Add r-bseqsc.
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* gnu/packages/bioinformatics.scm (r-bseqsc): New variable.
2018-09-24 13:31:20 +02:00
28829c040f
gnu: Add r-cssam.
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* gnu/packages/bioinformatics.scm (r-cssam): New variable.
2018-09-24 13:31:20 +02:00
a434730f2e
gnu: Add r-xbioc.
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* gnu/packages/bioinformatics.scm (r-xbioc): New variable.
2018-09-24 13:31:20 +02:00
05fb1e0017
gnu: hmmer: Update to 3.2.1.
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* gnu/packages/bioinformatics.scm (hmmer): Update to 3.2.1.
[origin]: Remove patch.
[license]: Change to BSD-3.
[supported-systems]: New field.
* gnu/packages/patches/hmmer-remove-cpu-specificity.patch: Delete file.
* gnu/local.mk (dist_patch_DATA): Remove it.
2018-09-22 09:16:47 +10:00
7e27393f82
gnu: Add r-pore.
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* gnu/packages/bioinformatics.scm (r-pore): New variable.
Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2018-09-21 17:04:37 +02:00
89ee8a6edf
gnu: rsem: Update to 1.3.1.
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* gnu/packages/bioinformatics.scm (rsem): Update to 1.3.1.
[source]: Fetch from git; remove patch; delete bundled samtools.
[arguments]: Pass make flags; adjust phases.
[inputs]: Remove ncurses and samtools-0.1; add htslib-1.3.
* gnu/packages/patches/rsem-makefile.patch: Remove patch.
* gnu/local.mk (dist_patch_DATA): Remove it.
2018-09-20 17:55:26 +02:00
1dd153b3aa
gnu: Add python-hic2cool.
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* gnu/packages/bioinformatics.scm (python-hic2cool): New variable.
2018-09-14 09:15:49 +02:00
875d068176
Adjust all users of (gnu packages ldc) to use (gnu packages dlang).
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This is a followup to commit 98d6543f86
2018-09-10 15:44:32 -04:00
5bfa7510d1
gnu: Add python-pygenometracks.
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* gnu/packages/bioinformatics.scm (python-pygenometracks): New variable.
2018-09-10 16:50:26 +02:00
1189c7f1b0
gnu: Add python-hicexplorer.
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* gnu/packages/bioinformatics.scm (python-hicexplorer): New variable.
2018-09-10 16:50:26 +02:00
5bb9e0af8d
gnu: Add python-cooler.
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* gnu/packages/bioinformatics.scm (python-cooler): New variable.
2018-09-10 16:50:26 +02:00
80f4db91b1
gnu: Add python-pyfaidx.
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* gnu/packages/bioinformatics.scm (python-pyfaidx): New variable.
2018-09-10 16:50:26 +02:00
1f41f01c14
gnu: Add python-pypairix.
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* gnu/packages/bioinformatics.scm (python-pypairix): New variable.
2018-09-10 16:50:26 +02:00
a9d496b353
gnu: Add python-intervaltree.
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* gnu/packages/bioinformatics.scm (python-intervaltree): New variable.
2018-09-10 16:50:26 +02:00
ab50580a9d
gnu: r-annotationhub: Update to 2.12.1.
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* gnu/packages/bioinformatics.scm (r-annotationhub): Update to 2.12.1.
2018-09-09 22:26:02 +02:00
d53aeeafcc
Add missing use-modules clause.
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This is a follow-up to commit 5dfe491290
2018-09-06 04:53:32 +02:00
00a43cb81c
gnu: pigx-scrnaseq: Use latest version of Pandoc.
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* gnu/packages/bioinformatics.scm (pigx-scrnaseq)[inputs]: Replace
"ghc-pandoc-citeproc-with-pandoc-1" with "ghc-pandoc-citeproc", and
"ghc-pandoc-1" with "ghc-pandoc".
2018-09-05 20:03:09 +02:00
c2b4f81e51
gnu: pigx-bsseq: Use latest version of Pandoc.
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* gnu/packages/bioinformatics.scm (pigx-bsseq)[inputs]: Replace
"ghc-pandoc-citeproc-with-pandoc-1" with "ghc-pandoc-citeproc", and
"ghc-pandoc-1" with "ghc-pandoc".
2018-09-05 20:03:09 +02:00
7cd40c8c5d
gnu: pigx-chipseq: Use latest version of Pandoc.
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* gnu/packages/bioinformatics.scm (pigx-chipseq)[inputs]: Replace
"ghc-pandoc-citeproc-with-pandoc-1" with "ghc-pandoc-citeproc", and
"ghc-pandoc-1" with "ghc-pandoc".
2018-09-05 20:03:09 +02:00
ca248f1db9
gnu: pigx-rnaseq: Use latest version of Pandoc.
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* gnu/packages/bioinformatics.scm (pigx-rnaseq)[inputs]: Replace
"ghc-pandoc-citeproc-with-pandoc-1" with "ghc-pandoc-citeproc", and
"ghc-pandoc-1" with "ghc-pandoc".
2018-09-05 20:03:09 +02:00
dff5640a59
gnu: r-rcas: Use standard version of ghc-pandoc-citeproc.
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* gnu/packages/bioinformatics.scm (r-rcas)[native-inputs]: Replace
"ghc-pandoc-citeproc-with-pandoc-1" with "ghc-pandoc-citeproc".
2018-09-05 20:03:09 +02:00
5dfe491290
gnu: r-graph: Move from bioinformatics to bioconductor.
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* gnu/packages/bioinformatics.scm (r-graph): Move from here...
* gnu/packages/bioconductor.scm (r-graph): ...to here.
2018-09-05 20:03:08 +02:00
f077174178
gnu: r-scran: Update to 1.8.4.
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* gnu/packages/bioinformatics.scm (r-scran): Update to 1.8.4.
2018-09-05 20:03:05 +02:00
8e44ff0c0d
gnu: r-scater: Update to 1.8.4.
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* gnu/packages/bioinformatics.scm (r-scater): Update to 1.8.4.
2018-09-05 20:03:05 +02:00
e69c07e61a
gnu: r-hdf5array: Update to 1.8.1.
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* gnu/packages/bioinformatics.scm (r-hdf5array): Update to 1.8.1.
2018-09-05 20:03:04 +02:00
16527f1cbc
gnu: r-ggbio: Update to 1.28.5.
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* gnu/packages/bioinformatics.scm (r-ggbio): Update to 1.28.5.
[propagated-inputs]: Add r-rlang.
2018-09-05 20:03:04 +02:00
70daf9362b
gnu: r-biovizbase: Update to 1.28.2.
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* gnu/packages/bioinformatics.scm (r-biovizbase): Update to 1.28.2.
[propagated-inputs]: Add r-rlang.
2018-09-05 20:03:04 +02:00
ff7c7d62f4
gnu: r-keggrest: Update to 1.20.1.
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* gnu/packages/bioinformatics.scm (r-keggrest): Update to 1.20.1.
2018-09-05 20:03:04 +02:00
3c55304688
gnu: r-edaseq: Update to 2.14.1.
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* gnu/packages/bioinformatics.scm (r-edaseq): Update to 2.14.1.
2018-09-05 20:03:04 +02:00
Ricardo Wurmus