b31c364467
gnu: r-maldiquant: Move to (gnu packages cran).
...
* gnu/packages/bioinformatics.scm (r-maldiquant): Move from here...
* gnu/packages/cran.scm (r-maldiquant): ...to here.
Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
2020-09-11 21:59:12 +02:00
30aaee3306
gnu: r-seqminer: Move to (gnu packages cran).
...
* gnu/packages/bioinformatics.scm (r-seqminer): Move from here...
* gnu/packages/cran.scm (r-seqminer): ...to here.
Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
2020-09-11 21:59:07 +02:00
66a8e62070
gnu: r-qtl2: Move to (gnu packages cran).
...
* gnu/packages/bioinformatics.scm (r-qtl2): Move from here...
* gnu/packages/cran.scm (r-qtl2): ...to here.
Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
2020-09-11 21:59:03 +02:00
496a52dc41
gnu: r-qtl: Move to (gnu packages cran).
...
* gnu/packages/bioinformatics.scm (r-qtl): Move from here...
* gnu/packages/cran.scm (r-qtl): ...to here.
Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
2020-09-11 21:58:58 +02:00
66be746dc0
gnu: Move r-bisquerna.
...
* gnu/packages/bioinformatics.scm (r-bisquerna): Move to ...
* gnu/packages/cran.scm: ... here.
2020-09-10 16:38:43 +02:00
0f8db4dc88
Revert "gnu: Add r-loomr."
...
This reverts commit 1f56ec08af
2020-09-09 18:14:48 +02:00
0574446be8
gnu: Add r-bisquerna.
...
* gnu/packages/bioinformatics.scm (r-bisquerna): New variable.
2020-09-09 17:02:55 +02:00
1f56ec08af
gnu: Add r-loomr.
...
* gnu/packages/bioinformatics.scm (r-loomr): New variable.
2020-09-09 16:56:02 +02:00
44f93ed6ed
gnu: seqmagick: Update to 0.8.0.
...
* gnu/packages/bioinformatics.scm (seqmagick): Update to 0.8.0.
2020-09-05 22:32:33 +02:00
de3c03a471
Merge remote-tracking branch 'origin/master' into staging
2020-09-05 22:30:04 +03:00
319de44a09
gnu: delly: Update to 0.8.3.
...
* gnu/packages/bioinformatics.scm (delly): Update to 0.8.3.
[inputs]: Order alphabetically.
2020-08-30 22:55:48 +03:00
e8bbb29b59
gnu: vcflib: Install pkgconfig file.
...
* gnu/packages/bioinformatics.scm (vcflib)[arguments]: Adjust custom
'install phase to add vcflib.pc.
2020-08-27 18:18:55 +03:00
6d8dd5bad7
gnu: vcflib: Use shared libraries.
...
* gnu/packages/bioinformatics.scm (vcflib)[source]: Add patch. Add
snippet to adjust files for new locations.
[inputs]: Add fastahack, smithwaterman, tabixpp, xz.
[native-inputs]: Add pkg-config. Remove the package-source of fastahack,
fsom, smithwaterman, tabixpp.
[arguments]: Remove make-flags. Add custom phase to add the output lib
directory to the rpath. Adjust custom 'unpack-submodule-sources for the
change in native-inputs. Adjust custom 'install phase to also install
libraries and headers.
* gnu/packages/patches/vcflib-use-shared-libraries.patch: New file.
* gnu/local.mk (dist_patch_DATA): Register it.
2020-08-27 18:18:55 +03:00
4bbcbe93cd
gnu: fastahack: Install pkgconfig file.
...
* gnu/packages/bioinformatics.scm (fastahack)[arguments]: Adjust custom
'install phase to add fastahack.pc.
2020-08-27 18:09:28 +03:00
f075bf09bd
gnu: fastahack: Build and install shared library and headers.
...
* gnu/packages/bioinformatics.scm (fastahack)[arguments]: Add phase to
build PIE objects. Add custom phase to build dynamic library. Adjust
custom 'install phase to install shared library and headers.
2020-08-27 18:08:13 +03:00
5c78997188
gnu: smithwaterman: Install pkgconfig file.
...
* gnu/packages/bioinformatics.scm (smithwaterman)[arguments]: Adjust
custom 'install phase to add smithwaterman.pc file.
2020-08-27 18:06:25 +03:00
afa352223f
gnu: smithwaterman: Build and install shared library and headers.
...
* gnu/packages/bioinformatics.scm (smithwaterman)[arguments]: Add custom
phase to build PIE objects. Add custom 'build-dynamic phase to build
dynamic library. Adjust custom 'install phase to install shared library
and headers.
2020-08-27 18:05:20 +03:00
261bc778b6
gnu: tabixpp: Install pkgconfig file.
...
* gnu/packages/bioinformatics.scm (tabixpp)[arguments]: Adjust custom
'install phase to add tabixpp.pc file.
2020-08-27 18:03:13 +03:00
35cb1bc527
gnu: tabixpp: Build and install shared library and headers.
...
* gnu/packages/bioinformatics.scm (tabixpp)[arguments]: Adjust custom
'build phase to build shared library. Adjust custom 'install phase to
install libraries and header.
2020-08-27 18:02:16 +03:00
4e0acfe5e7
gnu: r-complexheatmap: Update to 2.4.3.
...
* gnu/packages/bioinformatics.scm (r-complexheatmap): Update to 2.4.3.
2020-08-20 21:25:34 +02:00
e9d2cab0bf
gnu: r-gage: Update to 2.38.3.
...
* gnu/packages/bioinformatics.scm (r-gage): Update to 2.38.3.
[propagated-inputs]: Add r-go-db.
2020-08-20 21:25:34 +02:00
9da4a25b33
gnu: r-annotationhub: Update to 2.20.2.
...
* gnu/packages/bioinformatics.scm (r-annotationhub): Update to 2.20.2.
2020-08-20 21:25:34 +02:00
67f8477fb5
gnu: r-delayedarray: Update to 0.14.1.
...
* gnu/packages/bioinformatics.scm (r-delayedarray): Update to 0.14.1.
2020-08-20 21:25:33 +02:00
b414add3d1
gnu: r-annotationdbi: Update to 1.50.3.
...
* gnu/packages/bioinformatics.scm (r-annotationdbi): Update to 1.50.3.
2020-08-20 21:25:33 +02:00
e9128480d4
gnu: r-biocviews: Update to 1.56.2.
...
* gnu/packages/bioinformatics.scm (r-biocviews): Update to 1.56.2.
2020-08-20 21:25:33 +02:00
6e5be7ffad
gnu: pigx-chipseq: Update to 0.0.43.
...
* gnu/packages/bioinformatics.scm (pigx-chipseq): Update to 0.0.43.
2020-08-19 12:12:42 +02:00
346ea4b5fc
gnu: bowtie1: Add missing Python input.
...
Reported-by: Marcel Schilling <marcel.schilling@mdc-berlin.de>
* gnu/packages/bioinformatics.scm (bowtie1)[inputs]: Add python-wrapper.
2020-08-18 12:38:38 +02:00
4d55432fd0
gnu: pigx-bsseq: Update to 0.1.2.
...
* gnu/packages/bioinformatics.scm (pigx-bsseq): Update to 0.1.2.
[inputs]: Add r-ggrepel, bwa-meth, methyldackel, multiqc, and samblaster.
2020-08-16 15:57:27 +02:00
6f5530b9bc
gnu: pigx-scrnaseq: Use statically linked Pandoc.
...
* gnu/packages/bioinformatics.scm (pigx-scrnaseq)[inputs]: Use pandoc and
pandoc-citeproc instead of ghc-pandoc and ghc-pandoc-citeproc.
2020-08-16 15:57:27 +02:00
ac6eba4eb4
gnu: pigx-bsseq: Use statically linked Pandoc.
...
* gnu/packages/bioinformatics.scm (pigx-bsseq)[inputs]: Use pandoc and
pandoc-citeproc instead of ghc-pandoc and ghc-pandoc-citeproc.
2020-08-16 15:57:27 +02:00
c0ad6dc976
gnu: pigx-chipseq: Use statically linked Pandoc.
...
* gnu/packages/bioinformatics.scm (pigx-chipseq)[inputs]: Use pandoc and
pandoc-citeproc instead of ghc-pandoc and ghc-pandoc-citeproc.
2020-08-16 15:57:27 +02:00
2cb9f0f2a6
gnu: pigx-rnaseq: Use statically linked Pandoc.
...
* gnu/packages/bioinformatics.scm (pigx-rnaseq)[inputs]: Use pandoc and
pandoc-citeproc instead of ghc-pandoc and ghc-pandoc-citeproc.
2020-08-16 15:57:27 +02:00
19afa4d58f
gnu: r-rcas: Use pandoc instead of ghc-pandoc.
...
* gnu/packages/bioinformatics.scm (r-rcas)[propagated-inputs]: Replace
ghc-pandoc with pandoc.
2020-08-16 15:57:25 +02:00
e6bdc6949b
gnu: hisat2: Use pandoc instead of ghc-pandoc.
...
* gnu/packages/bioinformatics.scm (hisat2)[native-inputs]: Replace ghc-pandoc
with pandoc.
2020-08-15 10:10:39 +02:00
bcdc61bfa1
gnu: tophat: Hide default GCC.
...
* gnu/packages/bioinformatics.scm (tophat)[arguments]: Add build phase
"hide-default-gcc".
2020-08-12 21:55:06 +02:00
8ca7141c02
gnu: r-seurat: Update to 3.2.0.
...
* gnu/packages/bioinformatics.scm (r-seurat): Update to 3.2.0.
[propagated-inputs]: Remove r-tsne; add r-jsonlite, r-miniui, r-shiny, r-spatstat, and r-tibble.
2020-08-12 13:57:10 +02:00
a62aadf216
gnu: Add phast.
...
* gnu/packages/bioinformatics.scm (phast): New variable.
2020-08-10 21:58:38 +02:00
92b34df789
gnu: clipper: Update to 2.0.
...
* gnu/packages/bioinformatics.scm (clipper): Update to 2.0.
[source]: Remove snippet.
[arguments]: Build with Python 3; remove phase "fix-typo", add phase
"make-files-writable".
[inputs]: Replace all Python 2 variants with Python 3 variants.
[native-inputs]: Add python-setuptools-git.
2020-08-07 12:53:23 +02:00
6a7bdbfa2d
gnu: paml: Fix build.
...
* gnu/packages/bioinformatics.scm (paml)[snippet]: Fix permissions
before repacking the source tarball.
2020-07-30 03:48:50 +02:00
e1409c764f
gnu: check: Update to 0.15.1.
...
* gnu/packages/check.scm (check): Update to 0.15.1.
(check-0.14): New public variable.
* gnu/packages/backup.scm (burp)[native-inputs]: Change from CHECK to
CHECK-0.14.
* gnu/packages/bioinformatics.scm (libsbml)[native-inputs]: Likewise.
* gnu/packages/databases.scm (recutils)[native-inputs]: Likewise.
* gnu/packages/electronics.scm (libsigrokdecode)[native-inputs]: Likewise.
* gnu/packages/enlightenment.scm (efl, edi)[native-inputs]: Likewise.
* gnu/packages/gnome.scm (gdm)[inputs]: Likewise.
* gnu/packages/gtk.scm (girara)[native-inputs]: Likewise.
* gnu/packages/messaging.scm (pidgin)[native-inputs]: Likewise.
* gnu/packages/networking.scm (iodine)[native-inputs]: Likewise.
* gnu/packages/pulseaudio.scm (pulseaudio)[native-inputs]: Likewise.
* gnu/packages/sssd.scm (sssd)[native-inputs]: Likewise.
* gnu/packages/web.scm (libwapcaplet)[native-inputs]: Likewise.
2020-07-25 16:16:11 +02:00
56f12a65a0
gnu: r-rhdf5lib: Fix libsz substitution.
...
This is a follow-up to commit b7f051db14
2020-07-19 15:54:48 +02:00
fe39c70195
gnu: Use HTTPS for mdc-berlin.de home pages.
...
* gnu/packages/bioinformatics.scm (r-genomation, r-genomationdata, pigx-rnaseq)
(pigx-chipseq, pigx-bsseq, pigx-scrnaseq, pigx)[home-page]: Use HTTPS.
2020-07-16 20:12:06 +02:00
c980589260
gnu: Use HTTPS for biojava.org home pages.
...
* gnu/packages/bioinformatics.scm (java-biojava-core)
(java-biojava-phylo, java-biojava-alignment, java-biojava-phylo-4.0)
(java-biojava-alignment-4.0)[home-page]: Use HTTPS.
2020-07-16 20:12:06 +02:00
b7f051db14
gnu: r-rhdf5lib: Update to 1.10.1.
...
* gnu/packages/bioinformatics.scm (r-rhdf5lib): Update to 1.10.1.
2020-07-16 10:08:05 +02:00
82eafe32a2
gnu: r-qtl2: Update to 0.22-11.
...
* gnu/packages/bioinformatics.scm (r-qtl2): Update to 0.22-11.
2020-07-16 10:08:05 +02:00
16e16586d2
gnu: r-genomicfeatures: Update to 1.40.1.
...
* gnu/packages/bioinformatics.scm (r-genomicfeatures): Update to 1.40.1.
2020-07-16 10:08:05 +02:00
02f3a622e2
gnu: r-summarizedexperiment: Update to 1.18.2.
...
* gnu/packages/bioinformatics.scm (r-summarizedexperiment): Update to 1.18.2.
2020-07-16 10:08:05 +02:00
b80f141f86
gnu: r-delayedmatrixstats: Update to 1.10.1.
...
* gnu/packages/bioinformatics.scm (r-delayedmatrixstats): Update to 1.10.1.
2020-07-16 10:08:03 +02:00
15597255e6
gnu: r-rhdf5: Update to 2.32.2.
...
* gnu/packages/bioinformatics.scm (r-rhdf5): Update to 2.32.2.
2020-07-16 10:08:03 +02:00
b0e7b6992f
gnu: Remove ".git" from " https://github/…/….git ".
...
Until now, 'lookup-origin' and thus 'lookup-origin-revision' in (guix
swh) would sometimes return #f for these because the ".git" URLs are
redirects to the non-".git" URLs. Consequently, 'guix lint -c archival'
would keep saying "scheduled Software Heritage archival"; likewise, the
fallback download code would fail.
* gnu/packages/ada.scm,
gnu/packages/admin.scm,
gnu/packages/aidc.scm,
gnu/packages/algebra.scm,
gnu/packages/android.scm,
gnu/packages/animation.scm,
gnu/packages/arcan.scm,
gnu/packages/assembly.scm,
gnu/packages/audio.scm,
gnu/packages/authentication.scm,
gnu/packages/avr.scm,
gnu/packages/axoloti.scm,
gnu/packages/backup.scm,
gnu/packages/bash.scm,
gnu/packages/benchmark.scm,
gnu/packages/bioconductor.scm,
gnu/packages/bioinformatics.scm,
gnu/packages/bittorrent.scm,
gnu/packages/boost.scm,
gnu/packages/build-tools.scm,
gnu/packages/c.scm,
gnu/packages/calendar.scm,
gnu/packages/cdrom.scm,
gnu/packages/check.scm,
gnu/packages/chemistry.scm,
gnu/packages/chez.scm,
gnu/packages/clojure.scm,
gnu/packages/code.scm,
gnu/packages/compression.scm,
gnu/packages/compton.scm,
gnu/packages/coq.scm,
gnu/packages/cpp.scm,
gnu/packages/cran.scm,
gnu/packages/crypto.scm,
gnu/packages/curl.scm,
gnu/packages/databases.scm,
gnu/packages/datastructures.scm,
gnu/packages/debug.scm,
gnu/packages/disk.scm,
gnu/packages/distributed.scm,
gnu/packages/django.scm,
gnu/packages/dlang.scm,
gnu/packages/dns.scm,
gnu/packages/docker.scm,
gnu/packages/education.scm,
gnu/packages/efi.scm,
gnu/packages/elixir.scm,
gnu/packages/emacs-xyz.scm,
gnu/packages/embedded.scm,
gnu/packages/emulators.scm,
gnu/packages/engineering.scm,
gnu/packages/erlang.scm,
gnu/packages/fabric-management.scm,
gnu/packages/file-systems.scm,
gnu/packages/finance.scm,
gnu/packages/firmware.scm,
gnu/packages/flashing-tools.scm,
gnu/packages/fonts.scm,
gnu/packages/fontutils.scm,
gnu/packages/fpga.scm,
gnu/packages/game-development.scm,
gnu/packages/games.scm,
gnu/packages/genealogy.scm,
gnu/packages/genimage.scm,
gnu/packages/geo.scm,
gnu/packages/gimp.scm,
gnu/packages/gl.scm,
gnu/packages/gnome-xyz.scm,
gnu/packages/gnome.scm,
gnu/packages/gnuzilla.scm,
gnu/packages/golang.scm,
gnu/packages/gpodder.scm,
gnu/packages/graph.scm,
gnu/packages/graphics.scm,
gnu/packages/graphviz.scm,
gnu/packages/groff.scm,
gnu/packages/groovy.scm,
gnu/packages/gtk.scm,
gnu/packages/guile-xyz.scm,
gnu/packages/guile.scm,
gnu/packages/hardware.scm,
gnu/packages/haskell-apps.scm,
gnu/packages/haskell-xyz.scm,
gnu/packages/hexedit.scm,
gnu/packages/i2p.scm,
gnu/packages/ibus.scm,
gnu/packages/image-processing.scm,
gnu/packages/image-viewers.scm,
gnu/packages/image.scm,
gnu/packages/ipfs.scm,
gnu/packages/java-graphics.scm,
gnu/packages/java-maths.scm,
gnu/packages/java.scm,
gnu/packages/javascript.scm,
gnu/packages/jrnl.scm,
gnu/packages/julia.scm,
gnu/packages/jupyter.scm,
gnu/packages/kodi.scm,
gnu/packages/language.scm,
gnu/packages/lego.scm,
gnu/packages/less.scm,
gnu/packages/libusb.scm,
gnu/packages/linux.scm,
gnu/packages/lirc.scm,
gnu/packages/lisp-xyz.scm,
gnu/packages/llvm.scm,
gnu/packages/logging.scm,
gnu/packages/lolcode.scm,
gnu/packages/lua.scm,
gnu/packages/lxde.scm,
gnu/packages/lxqt.scm,
gnu/packages/machine-learning.scm,
gnu/packages/mail.scm,
gnu/packages/markup.scm,
gnu/packages/maths.scm,
gnu/packages/maven.scm,
gnu/packages/mes.scm,
gnu/packages/messaging.scm,
gnu/packages/monitoring.scm,
gnu/packages/mpd.scm,
gnu/packages/music.scm,
gnu/packages/networking.scm,
gnu/packages/node-xyz.scm,
gnu/packages/ocaml.scm,
gnu/packages/ocr.scm,
gnu/packages/onc-rpc.scm,
gnu/packages/opencl.scm,
gnu/packages/opencog.scm,
gnu/packages/pantheon.scm,
gnu/packages/password-utils.scm,
gnu/packages/patchutils.scm,
gnu/packages/pdf.scm,
gnu/packages/perl6.scm,
gnu/packages/phabricator.scm,
gnu/packages/popt.scm,
gnu/packages/printers.scm,
gnu/packages/prolog.scm,
gnu/packages/protobuf.scm,
gnu/packages/pulseaudio.scm,
gnu/packages/python-crypto.scm,
gnu/packages/python-web.scm,
gnu/packages/python-xyz.scm,
gnu/packages/qt.scm,
gnu/packages/radio.scm,
gnu/packages/rails.scm,
gnu/packages/rdf.scm,
gnu/packages/rednotebook.scm,
gnu/packages/rpc.scm,
gnu/packages/rsync.scm,
gnu/packages/ruby.scm,
gnu/packages/rust.scm,
gnu/packages/scheme.scm,
gnu/packages/screen.scm,
gnu/packages/security-token.scm,
gnu/packages/selinux.scm,
gnu/packages/serialization.scm,
gnu/packages/shells.scm,
gnu/packages/shellutils.scm,
gnu/packages/simh.scm,
gnu/packages/sml.scm,
gnu/packages/ssh.scm,
gnu/packages/statistics.scm,
gnu/packages/stenography.scm,
gnu/packages/sync.scm,
gnu/packages/syncthing.scm,
gnu/packages/synergy.scm,
gnu/packages/telephony.scm,
gnu/packages/terminals.scm,
gnu/packages/tex.scm,
gnu/packages/texinfo.scm,
gnu/packages/text-editors.scm,
gnu/packages/textutils.scm,
gnu/packages/time.scm,
gnu/packages/tmux.scm,
gnu/packages/tor.scm,
gnu/packages/toys.scm,
gnu/packages/version-control.scm,
gnu/packages/video.scm,
gnu/packages/vim.scm,
gnu/packages/virtualization.scm,
gnu/packages/vlang.scm,
gnu/packages/vnc.scm,
gnu/packages/vpn.scm,
gnu/packages/web-browsers.scm,
gnu/packages/web.scm,
gnu/packages/wireservice.scm,
gnu/packages/wm.scm,
gnu/packages/wxwidgets.scm,
gnu/packages/xdisorg.scm,
gnu/packages/xml.scm,
gnu/packages/xorg.scm,
tests/lint.scm: Remove trailing ".git" from 'git-reference' URL.
2020-07-12 23:08:15 +02:00
bd978be3ae
gnu: r-annotationdbi: Update to 1.50.1.
...
* gnu/packages/bioinformatics.scm (r-annotationdbi): Update to 1.50.1.
2020-07-02 12:45:53 +02:00
3d5334c390
gnu: blast+: Update to 2.10.1.
...
* gnu/packages/bioinformatics.scm (blast+): Update to 2.10.1.
2020-06-30 18:49:11 +02:00
5e5bcba295
gnu: r-qtl2: Update synopsis, description.
...
* gnu/packages/bioinformatics.scm (r-qtl2)[synopsis]: Use upstream's
synopsis.
[description]: Same.
2020-06-28 10:18:47 +03:00
54bb476670
gnu: r-qtl2: Update to 0.22-8.
...
* gnu/packages/bioinformatics.scm (r-qtl2): Update to 0.22-8.
[source]: Download from cran.
2020-06-28 10:15:21 +03:00
fb4804d03d
gnu: r-scater: Update to 1.16.2.
...
* gnu/packages/bioinformatics.scm (r-scater): Update to 1.16.2.
2020-06-28 05:46:19 +02:00
e66f81cf63
gnu: r-biocviews: Update to 1.56.1.
...
* gnu/packages/bioinformatics.scm (r-biocviews): Update to 1.56.1.
2020-06-28 05:46:19 +02:00
fa7871af77
gnu: r-dexseq: Update to 1.34.1.
...
* gnu/packages/bioinformatics.scm (r-dexseq): Update to 1.34.1.
2020-06-28 05:46:19 +02:00
de0f36f0aa
gnu: miniasm: Make sure all phases return #t.
...
* gnu/packages/bioinformatics.scm (miniasm)[arguments]: Make custom
'install phase return #t.
2020-06-23 16:04:51 +03:00
896f18210b
gnu: miniasm: Don't use unstable tarball.
...
* gnu/packages/bioinformatics.scm (miniasm)[source]: Download using
git-fetch.
2020-06-23 16:04:04 +03:00
6e31d6f3c4
gnu: python-plotly: Update to 4.8.1.
...
But keep version 2.4.1 around for packages that still need it and for python2
support.
* gnu/packages/graph.scm (python-plotly): Update to 4.8.1.
[source]: Use git-fetch so that tests are also included.
[arguments]: Enable tests.
[home-page]: Follow redirect.
(python-plotly-2.4.1): New variable.
(python2-plotly): Inherit from python-plotly-2.4.1.
* gnu/packages/bioinformatics.scm (python-deeptools)[native-inputs]: Depend on
python-plotly-2.4.1.
Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2020-06-22 15:44:16 +02:00
20b545f768
gnu: python-pandas: Update to 1.0.5.
...
But also keep version 0.25.3 around for packages requiring an earlier
versions, as well as version 0.24.2 for a version with python2.
* gnu/packages/python-science.scm (python-pandas): Update to 1.0.5.
[arguments]: Adapt 'patch-which phase. Add new 'prepare-x phase. Do not
delete tests that depend on "moto", they are skipped automatically.
[propagated-inputs]: Add python-jinja2.
[inputs]: Add xsel and xclip.
[native-inputs]: Add xorg-server-for-tests so we can test clipboard support.
(python-pandas-0.24): New variable.
(python2-pandas): Inherit from python-pandas-0.25.
* gnu/packages/bioinformatics.scm (python-biom-format)[propagated-inputs]:
Switch to python-pandas-0.25.
Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2020-06-22 15:44:08 +02:00
3a79adab41
gnu: deeptools: Deprecate in favor of python-deeptools.
...
And make sure python-deeptools's tests are running.
* gnu/packages/bioinformatics.scm (python-deeptools): Fetch source using git.
[native-inputs]: Add python-mock and python-nose.
(deeptools): Mark as deprecated.
Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2020-06-22 15:43:59 +02:00
ebcebc59ab
gnu: r-hdf5array: Update to 1.16.1.
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* gnu/packages/bioinformatics.scm (r-hdf5array): Update to 1.16.1.
2020-06-22 12:15:49 +02:00
b07e53bb09
gnu: r-rhdf5: Update to 2.32.1.
...
* gnu/packages/bioinformatics.scm (r-rhdf5): Update to 2.32.1.
2020-06-22 12:15:49 +02:00
f65d5e84de
gnu: r-biomart: Update to 2.44.1.
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* gnu/packages/bioinformatics.scm (r-biomart): Update to 2.44.1.
2020-06-22 12:15:49 +02:00
55401384dc
gnu: r-genomeinfodb: Update to 1.24.2.
...
* gnu/packages/bioinformatics.scm (r-genomeinfodb): Update to 1.24.2.
2020-06-22 12:15:49 +02:00
acba72b914
gnu: express: Update to 1.5.3.
...
* gnu/packages/bioinformatics.scm (express): Update to 1.5.3.
[source]: Fetch from Github.
[arguments]: Add phase "remove-update-check".
2020-06-22 09:07:51 +02:00
8b00728144
gnu: r-limma: Update to 3.44.3.
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* gnu/packages/bioinformatics.scm (r-limma): Update to 3.44.3.
2020-06-15 12:00:21 +02:00
9ae4bd0b77
gnu: r-mzr: Update to 2.22.0.
...
* gnu/packages/bioinformatics.scm (r-mzr): Update to 2.22.0.
[native-inputs]: Add r-knitr.
2020-06-13 01:20:02 +02:00
a3b55161c7
gnu: r-delayedmatrixstats: Update to 1.10.0.
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* gnu/packages/bioinformatics.scm (r-delayedmatrixstats): Update to 1.10.0.
[native-inputs]: Add r-knitr.
2020-06-13 01:19:47 +02:00
47c7670c43
gnu: r-scran: Update to 1.16.0.
...
* gnu/packages/bioinformatics.scm (r-scran): Update to 1.16.0.
[propagated-inputs]: Add r-iranges.
[native-inputs]: Add r-knitr.
2020-06-13 01:19:47 +02:00
7039b53945
gnu: r-scater: Update to 1.16.1.
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* gnu/packages/bioinformatics.scm (r-scater): Update to 1.16.1.
[propagated-inputs]: Add r-rlang.
[native-inputs]: Add r-knitr.
2020-06-13 01:19:46 +02:00
9e7acf2f14
gnu: r-singlecellexperiment: Update to 1.10.1.
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* gnu/packages/bioinformatics.scm (r-singlecellexperiment): Update to 1.10.1.
[native-inputs]: Add r-knitr.
2020-06-13 01:19:46 +02:00
16dd6bacaa
gnu: r-beachmat: Update to 2.4.0.
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* gnu/packages/bioinformatics.scm (r-beachmat): Update to 2.4.0.
[native-inputs]: Add r-knitr.
2020-06-13 01:19:46 +02:00
87d5444d9f
gnu: r-rhdf5lib: Update to 1.10.0.
...
* gnu/packages/bioinformatics.scm (r-rhdf5lib): Update to 1.10.0.
[source]: Update snippet.
[arguments]: Replace ZLIB variables in Makevars.
[native-inputs]: Add r-knitr.
2020-06-13 01:19:46 +02:00
cf907680e8
gnu: r-hdf5array: Update to 1.16.0.
...
* gnu/packages/bioinformatics.scm (r-hdf5array): Update to 1.16.0.
2020-06-13 01:19:46 +02:00
46f188d1df
gnu: r-hitc: Update to 1.32.0.
...
* gnu/packages/bioinformatics.scm (r-hitc): Update to 1.32.0.
2020-06-13 01:19:46 +02:00
6be25cc2db
gnu: r-fithic: Update to 1.14.0.
...
* gnu/packages/bioinformatics.scm (r-fithic): Update to 1.14.0.
[native-inputs]: Add r-knitr.
2020-06-13 01:19:46 +02:00
a811751f49
gnu: r-sushi: Update to 1.26.0.
...
* gnu/packages/bioinformatics.scm (r-sushi): Update to 1.26.0.
2020-06-13 01:19:46 +02:00
ddef43a29d
gnu: r-gwascat: Update to 2.20.1.
...
* gnu/packages/bioinformatics.scm (r-gwascat): Update to 2.20.1.
[propagated-inputs]: Remove r-homo-sapiens; add r-ggplot2.
[native-inputs]: Add r-knitr.
2020-06-13 01:19:46 +02:00
522da60b29
gnu: r-gviz: Update to 1.32.0.
...
* gnu/packages/bioinformatics.scm (r-gviz): Update to 1.32.0.
[propagated-inputs]: Add r-ensembldb.
[native-inputs]: Add r-knitr.
2020-06-13 01:19:46 +02:00
a97897bc3d
gnu: r-gqtlstats: Update to 1.20.0.
...
* gnu/packages/bioinformatics.scm (r-gqtlstats): Update to 1.20.0.
[native-inputs]: Add r-knitr.
2020-06-13 01:19:46 +02:00
6caad43c18
gnu: r-ldblock: Update to 1.18.0.
...
* gnu/packages/bioinformatics.scm (r-ldblock): Update to 1.18.0.
[native-inputs]: Add r-knitr.
2020-06-13 01:19:46 +02:00
87772ab4dd
gnu: r-erma: Update to 1.4.0.
...
* gnu/packages/bioinformatics.scm (r-erma): Update to 1.4.0.
[native-inputs]: Add r-knitr.
2020-06-13 01:19:45 +02:00
aab0e28fc1
gnu: r-snpstats: Update to 1.38.0.
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* gnu/packages/bioinformatics.scm (r-snpstats): Update to 1.38.0.
2020-06-13 01:19:45 +02:00
42d8cd9f97
gnu: r-gqtlbase: Update to 1.20.0.
...
* gnu/packages/bioinformatics.scm (r-gqtlbase): Update to 1.20.0.
[native-inputs]: Add r-knitr.
2020-06-13 01:19:45 +02:00
7038aeb210
gnu: r-ggbio: Update to 1.36.0.
...
* gnu/packages/bioinformatics.scm (r-ggbio): Update to 1.36.0.
[native-inputs]: Add r-knitr.
2020-06-13 01:19:45 +02:00
07518c3a34
gnu: r-biovizbase: Update to 1.36.0.
...
* gnu/packages/bioinformatics.scm (r-biovizbase): Update to 1.36.0.
2020-06-13 01:19:45 +02:00
7c26687871
gnu: r-organismdbi: Update to 1.30.0.
...
* gnu/packages/bioinformatics.scm (r-organismdbi): Update to 1.30.0.
2020-06-13 01:19:45 +02:00
39da6fbc40
gnu: r-ensembldb: Update to 2.12.1.
...
* gnu/packages/bioinformatics.scm (r-ensembldb): Update to 2.12.1.
[native-inputs]: Add r-knitr.
2020-06-13 01:19:45 +02:00
7a9e7e4844
gnu: r-dirichletmultinomial: Update to 1.30.0.
...
* gnu/packages/bioinformatics.scm (r-dirichletmultinomial): Update to 1.30.0.
2020-06-13 01:19:45 +02:00
ca5c92c0c7
gnu: r-complexheatmap: Update to 2.4.2.
...
* gnu/packages/bioinformatics.scm (r-complexheatmap): Update to 2.4.2.
[native-inputs]: Add r-knitr.
2020-06-13 01:19:45 +02:00
8323ff3376
gnu: r-genomicfiles: Update to 1.24.0.
...
* gnu/packages/bioinformatics.scm (r-genomicfiles): Update to 1.24.0.
2020-06-13 01:19:45 +02:00
817e4c8b68
gnu: r-gage: Update to 2.37.0.
...
* gnu/packages/bioinformatics.scm (r-gage): Update to 2.37.0.
2020-06-13 01:19:45 +02:00
d80a6cacaf
gnu: r-keggrest: Update to 1.28.0.
...
* gnu/packages/bioinformatics.scm (r-keggrest): Update to 1.28.0.
[native-inputs]: Add r-knitr.
2020-06-13 01:19:45 +02:00
3422533bd9
gnu: r-fastseg: Update to 1.34.0.
...
* gnu/packages/bioinformatics.scm (r-fastseg): Update to 1.34.0.
2020-06-13 01:19:44 +02:00
5fce232977
gnu: r-annotationhub: Update to 2.20.0.
...
* gnu/packages/bioinformatics.scm (r-annotationhub): Update to 2.20.0.
[native-inputs]: Add r-knitr.
2020-06-13 01:19:44 +02:00
334e8d7b79
gnu: r-interactivedisplaybase: Update to 1.26.3.
...
* gnu/packages/bioinformatics.scm (r-interactivedisplaybase): Update to
1.26.3.
[propagated-inputs]: Add r-dt.
[native-inputs]: Add r-knitr.
2020-06-13 01:19:44 +02:00
15990617eb
gnu: r-edaseq: Update to 2.22.0.
...
* gnu/packages/bioinformatics.scm (r-edaseq): Update to 2.22.0.
[native-inputs]: Add r-knitr.
2020-06-13 01:19:44 +02:00
c9059a3b0e
gnu: r-deseq: Update to 1.39.0.
...
* gnu/packages/bioinformatics.scm (r-deseq): Update to 1.39.0.
2020-06-13 01:19:44 +02:00
zimoun
Roel Janssen
Ricardo Wurmus
Andreas Enge
Efraim Flashner
Jakub Kądziołka
Marius Bakke
Tobias Geerinckx-Rice
Ludovic Courtès
Pierre Langlois