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2617 Commits

Author SHA1 Message Date
Efraim Flashner
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
Efraim Flashner
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
Efraim Flashner
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
Efraim Flashner
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
Efraim Flashner
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
Efraim Flashner
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
Ricardo Wurmus
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
Ricardo Wurmus
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
Ricardo Wurmus
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
Ricardo Wurmus
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
Ricardo Wurmus
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
Ricardo Wurmus
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
Ricardo Wurmus
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
Ricardo Wurmus
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
Ricardo Wurmus
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
Ricardo Wurmus
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
Ricardo Wurmus
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
Ricardo Wurmus
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
Ricardo Wurmus
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
Ricardo Wurmus
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
Ricardo Wurmus
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
Ricardo Wurmus
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
Ricardo Wurmus
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
Ricardo Wurmus
a62aadf216
gnu: Add phast. 
* gnu/packages/bioinformatics.scm (phast): New variable.
 2020-08-10 21:58:38 +02:00
Ricardo Wurmus
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
Jakub Kądziołka
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
Marius Bakke
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
Jakub Kądziołka
56f12a65a0
gnu: r-rhdf5lib: Fix libsz substitution. 
This is a follow-up to commit b7f051db14 -
in the new version, some of the format strings being replaced gained
quotes. This commit fixes build of dependents of r-rhdf5lib, such as
r-hdf5array.

* gnu/packages/bioinformatics (r-rhdf5lib): Remove all instances of libsz.a.
 2020-07-19 15:54:48 +02:00
Tobias Geerinckx-Rice
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
Tobias Geerinckx-Rice
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
Ricardo Wurmus
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
Ricardo Wurmus
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
Ricardo Wurmus
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
Ricardo Wurmus
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
Ricardo Wurmus
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
Ricardo Wurmus
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
Ludovic Courtès
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
Ricardo Wurmus
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
Ricardo Wurmus
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
Efraim Flashner
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
Efraim Flashner
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
Ricardo Wurmus
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
Ricardo Wurmus
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
Ricardo Wurmus
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
Efraim Flashner
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
Efraim Flashner
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
Pierre Langlois
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
Pierre Langlois
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
Pierre Langlois
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
Ricardo Wurmus
ebcebc59ab
gnu: r-hdf5array: Update to 1.16.1. 
* gnu/packages/bioinformatics.scm (r-hdf5array): Update to 1.16.1.
 2020-06-22 12:15:49 +02:00
Ricardo Wurmus
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
Ricardo Wurmus
f65d5e84de
gnu: r-biomart: Update to 2.44.1. 
* gnu/packages/bioinformatics.scm (r-biomart): Update to 2.44.1.
 2020-06-22 12:15:49 +02:00
Ricardo Wurmus
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
Ricardo Wurmus
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
Ricardo Wurmus
8b00728144
gnu: r-limma: Update to 3.44.3. 
* gnu/packages/bioinformatics.scm (r-limma): Update to 3.44.3.
 2020-06-15 12:00:21 +02:00
Ricardo Wurmus
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
Ricardo Wurmus
a3b55161c7
gnu: r-delayedmatrixstats: Update to 1.10.0. 
* gnu/packages/bioinformatics.scm (r-delayedmatrixstats): Update to 1.10.0.
[native-inputs]: Add r-knitr.
 2020-06-13 01:19:47 +02:00
Ricardo Wurmus
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
Ricardo Wurmus
7039b53945
gnu: r-scater: Update to 1.16.1. 
* 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
Ricardo Wurmus
9e7acf2f14
gnu: r-singlecellexperiment: Update to 1.10.1. 
* gnu/packages/bioinformatics.scm (r-singlecellexperiment): Update to 1.10.1.
[native-inputs]: Add r-knitr.
 2020-06-13 01:19:46 +02:00
Ricardo Wurmus
16dd6bacaa
gnu: r-beachmat: Update to 2.4.0. 
* gnu/packages/bioinformatics.scm (r-beachmat): Update to 2.4.0.
[native-inputs]: Add r-knitr.
 2020-06-13 01:19:46 +02:00
Ricardo Wurmus
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
Ricardo Wurmus
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
Ricardo Wurmus
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
Ricardo Wurmus
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
Ricardo Wurmus
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
Ricardo Wurmus
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
Ricardo Wurmus
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
Ricardo Wurmus
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
Ricardo Wurmus
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
Ricardo Wurmus
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
Ricardo Wurmus
aab0e28fc1
gnu: r-snpstats: Update to 1.38.0. 
* gnu/packages/bioinformatics.scm (r-snpstats): Update to 1.38.0.
 2020-06-13 01:19:45 +02:00
Ricardo Wurmus
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
Ricardo Wurmus
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
Ricardo Wurmus
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
Ricardo Wurmus
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
Ricardo Wurmus
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
Ricardo Wurmus
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
Ricardo Wurmus
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
Ricardo Wurmus
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
Ricardo Wurmus
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
Ricardo Wurmus
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
Ricardo Wurmus
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
Ricardo Wurmus
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
Ricardo Wurmus
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
Ricardo Wurmus
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
Ricardo Wurmus
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
Ricardo Wurmus
019bc36732
gnu: r-aroma-light: Update to 3.18.0. 
* gnu/packages/bioinformatics.scm (r-aroma-light): Update to 3.18.0.
 2020-06-13 01:19:44 +02:00
Ricardo Wurmus
f6ddf20891
gnu: r-msnid: Update to 1.22.0. 
* gnu/packages/bioinformatics.scm (r-msnid): Update to 1.22.0.
 2020-06-13 01:19:44 +02:00
Ricardo Wurmus
10a7ee2609
gnu: r-msnbase: Update to 2.14.2. 
* gnu/packages/bioinformatics.scm (r-msnbase): Update to 2.14.2.
[native-inputs]: Add r-knitr.
 2020-06-13 01:19:44 +02:00
Ricardo Wurmus
7b4fc6ae0a
gnu: r-pcamethods: Update to 1.80.0. 
* gnu/packages/bioinformatics.scm (r-pcamethods): Update to 1.80.0.
 2020-06-13 01:19:44 +02:00
Ricardo Wurmus
8eb579883d
gnu: r-mzid: Update to 1.26.0. 
* gnu/packages/bioinformatics.scm (r-mzid): Update to 1.26.0.
[native-inputs]: Add r-knitr.
 2020-06-13 01:19:44 +02:00
Ricardo Wurmus
8e0d11d88b
gnu: r-vsn: Update to 3.56.0. 
* gnu/packages/bioinformatics.scm (r-vsn): Update to 3.56.0.
 2020-06-13 01:19:44 +02:00
Ricardo Wurmus
736f6cfe66
gnu: r-affy: Update to 1.66.0. 
* gnu/packages/bioinformatics.scm (r-affy): Update to 1.66.0.
 2020-06-13 01:19:44 +02:00
Ricardo Wurmus
d93af7d632
gnu: r-affyio: Update to 1.58.0. 
* gnu/packages/bioinformatics.scm (r-affyio): Update to 1.58.0.
 2020-06-13 01:19:43 +02:00
Ricardo Wurmus
157eb89707
gnu: r-protgenerics: Update to 1.20.0. 
* gnu/packages/bioinformatics.scm (r-protgenerics): Update to 1.20.0.
 2020-06-13 01:19:43 +02:00
Ricardo Wurmus
d95a1cb10e
gnu: r-sva: Update to 3.36.0. 
* gnu/packages/bioinformatics.scm (r-sva): Update to 3.36.0.
[propagated-inputs]: Add r-edger.
 2020-06-13 01:19:43 +02:00
Ricardo Wurmus
c336d54d5f
gnu: r-methylkit: Update to 1.14.2. 
* gnu/packages/bioinformatics.scm (r-methylkit): Update to 1.14.2.
 2020-06-13 01:19:43 +02:00
Ricardo Wurmus
3475ad075b
gnu: r-copywriter: Update to 2.20.0. 
* gnu/packages/bioinformatics.scm (r-copywriter): Update to 2.20.0.
 2020-06-13 01:19:43 +02:00
Ricardo Wurmus
6a25fb9b6c
gnu: r-chipseq: Update to 1.38.0. 
* gnu/packages/bioinformatics.scm (r-chipseq): Update to 1.38.0.
 2020-06-13 01:19:43 +02:00
Ricardo Wurmus
43dec928d2
gnu: r-annotationfilter: Update to 1.12.0. 
* gnu/packages/bioinformatics.scm (r-annotationfilter): Update to 1.12.0.
[native-inputs]: Add r-knitr.
 2020-06-13 01:19:43 +02:00
Ricardo Wurmus
05716c1b1c
gnu: r-rhdf5: Update to 2.32.0. 
* gnu/packages/bioinformatics.scm (r-rhdf5): Update to 2.32.0.
[native-inputs]: Add r-knitr.
 2020-06-13 01:19:43 +02:00
Ricardo Wurmus
876e05bfce
gnu: r-tximport: Update to 1.16.1. 
* gnu/packages/bioinformatics.scm (r-tximport): Update to 1.16.1.
 2020-06-13 01:19:43 +02:00
Ricardo Wurmus
40a4772f09
gnu: r-mutationalpatterns: Update to 2.0.0. 
* gnu/packages/bioinformatics.scm (r-mutationalpatterns): Update to 2.0.0.
 2020-06-13 01:19:43 +02:00
Ricardo Wurmus
3c53617efc
gnu: r-rcas: Update to 1.14.0. 
* gnu/packages/bioinformatics.scm (r-rcas): Update to 1.14.0.
[propagated-inputs]: Remove r-annotationdbi, r-biomart, r-dbi, r-knitr,
r-motifrg, r-org-hs-eg-db, and r-topgo; add r-bsgenome, r-gprofiler2,
r-iranges, and r-ranger.
[native-inputs]: Add r-knitr.
 2020-06-13 01:19:43 +02:00
Ricardo Wurmus
261d931406
gnu: r-bamsignals: Update to 1.20.0. 
* gnu/packages/bioinformatics.scm (r-bamsignals): Update to 1.20.0.
[native-inputs]: Add r-knitr.
 2020-06-13 01:19:43 +02:00
Ricardo Wurmus
8f08457f05
gnu: r-rhtslib: Update to 1.20.0. 
* gnu/packages/bioinformatics.scm (r-rhtslib): Update to 1.20.0.
[native-inputs]: Add r-knitr.
 2020-06-13 01:19:42 +02:00
Ricardo Wurmus
52ce0d299d
gnu: r-zlibbioc: Update to 1.34.0. 
* gnu/packages/bioinformatics.scm (r-zlibbioc): Update to 1.34.0.
 2020-06-13 01:19:42 +02:00
Ricardo Wurmus
239ca0f3bd
gnu: r-motifrg: Update to 1.31.0. 
* gnu/packages/bioinformatics.scm (r-motifrg): Update to 1.31.0.
 2020-06-13 01:19:42 +02:00
Ricardo Wurmus
40ba4e8466
gnu: r-seqlogo: Update to 1.54.3. 
* gnu/packages/bioinformatics.scm (r-seqlogo): Update to 1.54.3.
 2020-06-13 01:19:42 +02:00
Ricardo Wurmus
837e7634d9
gnu: r-genomation: Update to 1.20.0. 
* gnu/packages/bioinformatics.scm (r-genomation): Update to 1.20.0.
[native-inputs]: Add r-knitr.
 2020-06-13 01:19:42 +02:00
Ricardo Wurmus
2d537b5afc
gnu: r-seqpattern: Update to 1.20.0. 
* gnu/packages/bioinformatics.scm (r-seqpattern): Update to 1.20.0.
 2020-06-13 01:19:42 +02:00
Ricardo Wurmus
e6df69a84d
gnu: r-impute: Update to 1.62.0. 
* gnu/packages/bioinformatics.scm (r-impute): Update to 1.62.0.
 2020-06-13 01:19:42 +02:00
Ricardo Wurmus
d9b23ec47c
gnu: r-bsgenome: Update to 1.56.0. 
* gnu/packages/bioinformatics.scm (r-bsgenome): Update to 1.56.0.
[propagated-inputs]: Add r-matrixstats.
 2020-06-13 01:19:42 +02:00
Ricardo Wurmus
543fd63c2e
gnu: r-topgo: Update to 2.40.0. 
* gnu/packages/bioinformatics.scm (r-topgo): Update to 2.40.0.
 2020-06-13 01:19:42 +02:00
Ricardo Wurmus
a285314e29
gnu: r-genomicfeatures: Update to 1.40.0. 
* gnu/packages/bioinformatics.scm (r-genomicfeatures): Update to 1.40.0.
[native-inputs]: Add r-knitr.
 2020-06-13 01:19:42 +02:00
Ricardo Wurmus
f85794edb8
gnu: r-rtracklayer: Update to 1.48.0. 
* gnu/packages/bioinformatics.scm (r-rtracklayer): Update to 1.48.0.
 2020-06-13 01:19:42 +02:00
Ricardo Wurmus
58613ca1e5
gnu: r-genomicalignments: Update to 1.24.0. 
* gnu/packages/bioinformatics.scm (r-genomicalignments): Update to 1.24.0.
 2020-06-13 01:19:42 +02:00
Ricardo Wurmus
87c98cf701
gnu: r-summarizedexperiment: Update to 1.18.1. 
* gnu/packages/bioinformatics.scm (r-summarizedexperiment): Update to 1.18.1.
[native-inputs]: Add r-knitr.
 2020-06-13 01:19:41 +02:00
Ricardo Wurmus
46e103a1b5
gnu: r-delayedarray: Update to 0.14.0. 
* gnu/packages/bioinformatics.scm (r-delayedarray): Update to 0.14.0.
[propagated-inputs]: Remove r-biocparallel.
 2020-06-13 01:19:41 +02:00
Ricardo Wurmus
1f9c87a442
gnu: r-rsamtools: Update to 2.4.0. 
* gnu/packages/bioinformatics.scm (r-rsamtools): Update to 2.4.0.
 2020-06-13 01:19:41 +02:00
Ricardo Wurmus
d3491d4dad
gnu: r-biostrings: Update to 2.56.0. 
* gnu/packages/bioinformatics.scm ( r-biostrings): Update to 2.56.0.
[propagated-inputs]: Add r-crayon.
 2020-06-13 01:19:41 +02:00
Ricardo Wurmus
cb486f16da
gnu: r-biocparallel: Update to 1.22.0. 
* gnu/packages/bioinformatics.scm (r-biocparallel): Update to 1.22.0.
[native-inputs]: Add r-knitr.
 2020-06-13 01:19:41 +02:00
Ricardo Wurmus
e87e6cc89d
gnu: r-biomart: Update to 2.44.0. 
* gnu/packages/bioinformatics.scm (r-biomart): Update to 2.44.0.
 2020-06-13 01:19:41 +02:00
Ricardo Wurmus
920224771f
gnu: r-annotationdbi: Update to 1.50.0. 
* gnu/packages/bioinformatics.scm (r-annotationdbi): Update to 1.50.0.
[native-inputs]: Add r-knitr.
 2020-06-13 01:19:41 +02:00
Ricardo Wurmus
7d91e3bed4
gnu: r-biobase: Update to 2.48.0. 
* gnu/packages/bioinformatics.scm (r-biobase): Update to 2.48.0.
 2020-06-13 01:19:41 +02:00
Ricardo Wurmus
087a97f8df
gnu: r-genomicranges: Update to 1.40.0. 
* gnu/packages/bioinformatics.scm (r-genomicranges): Update to 1.40.0.
[native-inputs]: Add r-knitr.
 2020-06-13 01:19:41 +02:00
Ricardo Wurmus
e0d40fa275
gnu: r-xvector: Update to 0.28.0. 
* gnu/packages/bioinformatics.scm (r-xvector): Update to 0.28.0.
 2020-06-13 01:19:41 +02:00
Ricardo Wurmus
49c766d0bb
gnu: r-limma: Update to 3.44.1. 
* gnu/packages/bioinformatics.scm (r-limma): Update to 3.44.1.
 2020-06-13 01:19:41 +02:00
Ricardo Wurmus
cdd83b2e22
gnu: r-variantannotation: Update to 1.34.0. 
* gnu/packages/bioinformatics.scm (r-variantannotation): Update to 1.34.0.
 2020-06-13 01:19:41 +02:00
Ricardo Wurmus
c14d59d9ad
gnu: r-edger: Update to 3.30.3. 
* gnu/packages/bioinformatics.scm (r-edger): Update to 3.30.3.
 2020-06-13 01:19:41 +02:00
Ricardo Wurmus
506735eea6
gnu: r-genomeinfodb: Update to 1.24.0. 
* gnu/packages/bioinformatics.scm (r-genomeinfodb): Update to 1.24.0.
 2020-06-13 01:19:40 +02:00
Ricardo Wurmus
8a38b676da
gnu: r-iranges: Update to 2.22.2. 
* gnu/packages/bioinformatics.scm (r-iranges): Update to 2.22.2.
 2020-06-13 01:19:40 +02:00
Ricardo Wurmus
f189f536be
gnu: r-s4vectors: Update to 0.26.1. 
* gnu/packages/bioinformatics.scm (r-s4vectors): Update to 0.26.1.
 2020-06-13 01:19:40 +02:00
Ricardo Wurmus
1a9de6cfe8
gnu: r-bioccheck: Update to 1.24.0. 
* gnu/packages/bioinformatics.scm (r-bioccheck): Update to 1.24.0.
[native-inputs]: Add r-knitr.
 2020-06-13 01:19:40 +02:00
Ricardo Wurmus
9f416be83d
gnu: r-biocstyle: Update to 2.16.0. 
* gnu/packages/bioinformatics.scm (r-biocstyle): Update to 2.16.0.
[native-inputs]: Add r-knitr.
 2020-06-13 01:19:40 +02:00
Ricardo Wurmus
1ca88fb8e9
gnu: r-biocviews: Update to 1.56.0. 
* gnu/packages/bioinformatics.scm (r-biocviews): Update to 1.56.0.
 2020-06-13 01:19:40 +02:00
Ricardo Wurmus
5de96ae98b
gnu: r-grohmm: Update to 1.22.0. 
* gnu/packages/bioinformatics.scm (r-grohmm): Update to 1.22.0.
 2020-06-13 01:19:40 +02:00
Ricardo Wurmus
bb18d11d85
gnu: r-systempiper: Update to 1.22.0. 
* gnu/packages/bioinformatics.scm (r-systempiper): Update to 1.22.0.
[propagated-inputs]: Add r-assertthat, r-magrittr, r-rsvg, r-dot, and
r-stringr; remove r-biocgenerics.
[native-inputs]: Add r-knitr.
 2020-06-13 01:19:40 +02:00
Ricardo Wurmus
681cca95b3
gnu: r-shortread: Update to 1.46.0. 
* gnu/packages/bioinformatics.scm (r-shortread): Update to 1.46.0.
 2020-06-13 01:19:40 +02:00
Ricardo Wurmus
3d2899dab5
gnu: r-gostats: Update to 2.54.0. 
* gnu/packages/bioinformatics.scm (r-gostats): Update to 2.54.0.
 2020-06-13 01:19:40 +02:00
Ricardo Wurmus
be414286bc
gnu: r-category: Update to 2.54.0. 
* gnu/packages/bioinformatics.scm (r-category): Update to 2.54.0.
 2020-06-13 01:19:40 +02:00
Ricardo Wurmus
a8613ff861
gnu: r-gseabase: Update to 1.50.1. 
* gnu/packages/bioinformatics.scm (r-gseabase): Update to 1.50.1.
[native-inputs]: Add r-knitr.
 2020-06-13 01:19:40 +02:00
Ricardo Wurmus
7d8b96e24b
gnu: r-rbgl: Update to 1.64.0. 
* gnu/packages/bioinformatics.scm (r-rbgl): Update to 1.64.0.
 2020-06-13 01:19:39 +02:00
Ricardo Wurmus
397568dbca
gnu: r-annotationforge: Update to 1.30.1. 
* gnu/packages/bioinformatics.scm (r-annotationforge): Update to 1.30.1.
[native-inputs]: Add r-knitr.
 2020-06-13 01:19:39 +02:00
Ricardo Wurmus
db5addba2c
gnu: r-dexseq: Update to 1.34.0. 
* gnu/packages/bioinformatics.scm (r-dexseq): Update to 1.34.0.
[native-inputs]: Add r-knitr.
 2020-06-13 01:19:39 +02:00
Ricardo Wurmus
3d7de4ed82
gnu: r-deseq2: Update to 1.28.1. 
* gnu/packages/bioinformatics.scm (r-deseq2): Update to 1.28.1.
[propagated-inputs]: Remove r-hmisc.
[native-inputs]: Add r-knitr.
 2020-06-13 01:19:39 +02:00
Ricardo Wurmus
5fdea056c9
gnu: r-genefilter: Update to 1.70.0. 
* gnu/packages/bioinformatics.scm (r-genefilter): Update to 1.70.0.
[native-inputs]: Add r-knitr.
 2020-06-13 01:19:39 +02:00
Ricardo Wurmus
a620d22ea8
gnu: r-gprofiler: Move to (gnu packages cran). 
* gnu/packages/bioinformatics.scm (r-gprofiler): Move this variable from here...
* gnu/packages/cran.scm (r-gprofiler): ...to here.
 2020-06-13 01:19:38 +02:00
Marius Bakke
fa7bd13e5b
gnu: rcas-web: Use guile2.2 version of Guile-Redis. 
* gnu/packages/bioinformatics.scm (rcas-web)[inputs]: Change from GUILE-REDIS
to GUILE2.2-REDIS.  While at it, rename the GUILE input to "guile" instead
of "guile-next".
 2020-06-06 15:35:40 +02:00
Ricardo Wurmus
0266094531
gnu: python-pypairix: Update to 0.3.7 and build programs. 
* gnu/packages/bioinformatics.scm (python-pypairix): Update to 0.3.7.
[source]: Fetch from github.
[arguments]: Add phases "build-programs" and "install-programs".
 2020-06-04 11:56:31 +02:00
Ricardo Wurmus
2f49007dd0
gnu: Add python-pairtools. 
* gnu/packages/bioinformatics.scm (python-pairtools): New variable.
 2020-06-03 15:01:19 +02:00
Ricardo Wurmus
6742a84c63
gnu: Remove bedtools-2.26. 
* gnu/packages/bioinformatics.scm (bedtools-2.26): Remove variable.
 2020-06-03 14:07:58 +02:00
Ricardo Wurmus
08542026ea
gnu: python-pybedtools: Disable unreliable test. 
* gnu/packages/bioinformatics.scm (python-pybedtools)[arguments]: Disable
test_intron_exon_reads test; run tests verbosely.

test_intron_exon_reads
 2020-06-03 14:07:48 +02:00
Nicolas Goaziou
98d6edb621
gnu: blast+: Use HTTPS home page URI. 
* gnu/packages/bioinformatics.scm (blast+)[home-page]: Use HTTPS URI.
 2020-05-27 01:48:37 +02:00
Nicolas Goaziou
f41f882272
gnu: bbmap: Use HTTPS home page URI. 
* gnu/packages/bioinformatics.scm (bbmap)[home-page]: Use HTTPS URI.
 2020-05-27 01:45:21 +02:00
Ricardo Wurmus
9dc50c8c47
gnu: sra-tools: Update to 2.10.6. 
* gnu/packages/bioinformatics.scm (sra-tools): Update to 2.10.6.
[arguments]: Replace CC variable in utf8proc Makefile.
[inputs]: Replace hdf5 with hdf5-1.10; add python-wrapper.
 2020-05-19 12:42:01 +02:00
Ricardo Wurmus
68de995674
gnu: ncbi-vdb: Update to 2.10.6. 
* gnu/packages/bioinformatics.scm (ncbi-vdb): Update to 2.10.6.
 2020-05-19 12:42:01 +02:00
Ricardo Wurmus
6437c598e7
gnu: ngs-sdk: Update to 2.10.5. 
* gnu/packages/bioinformatics.scm (ngs-sdk): Update to 2.10.5.
 2020-05-19 12:42:01 +02:00
Marius Bakke
87a40d7203
Merge branch 'master' into core-updates 2020-05-05 20:43:21 +02:00
Efraim Flashner
31def9a9df
gnu: Add grocsvs. 
* gnu/packages/bioinformatics.scm (grocsvs): New variable.
* gnu/packages/patches/grocsvs-dont-use-admiral.patch: New file.
* gnu/local.mk (dist_patch_DATA): Register it.
 2020-05-05 10:06:28 +03:00
Marius Bakke
8bf8cd9b85
Merge branch 'master' into core-updates 
Conflicts:
	gnu/local.mk
	gnu/packages/backup.scm
	gnu/packages/emacs-xyz.scm
	gnu/packages/guile.scm
	gnu/packages/lisp.scm
	gnu/packages/openldap.scm
	gnu/packages/package-management.scm
	gnu/packages/web.scm
	gnu/packages/xorg.scm
 2020-04-30 23:47:49 +02:00
Roel Janssen
eca648b65b
gnu: Add miniasm. 
* gnu/packages/bioinformatics.scm (miniasm): New variable.
 2020-04-30 15:30:16 +02:00
Ricardo Wurmus
4a148c6da3
gnu: python2-warpedlmm: Fix build. 
* gnu/packages/bioinformatics.scm (python2-warpedlmm)[propagated-inputs]: Add
python2-weave.
[arguments]: Disable tests and add "use-weave" phase.
 2020-04-30 13:08:33 +02:00
Ricardo Wurmus
545e12f40d
gnu: Add variant-tools. 
* gnu/packages/bioinformatics.scm (variant-tools): New variable.
 2020-04-28 12:23:28 +02:00
Ricardo Wurmus
9c726c485a
gnu: r-hdf5array: Update to 1.14.4. 
* gnu/packages/bioinformatics.scm (r-hdf5array): Update to 1.14.4.
 2020-04-28 08:44:04 +02:00
Ricardo Wurmus
cda0683295
gnu: r-seurat: Update to 3.1.5. 
* gnu/packages/bioinformatics.scm (r-seurat): Update to 3.1.5.
[propagated-inputs]: Remove r-metap.
 2020-04-28 08:44:04 +02:00
Roel Janssen
78799a6fdc
gnu: Update minimap2 to 2.17. 
* gnu/packages/bioinformatics.scm (minimap2): Update to 2.17.
 2020-04-27 21:34:10 +02:00
Roel Janssen
ccf70a80a1
gnu: Add python-deeptools. 
* gnu/packages/bioinformatics.scm (python-deeptools): New variable.
 2020-04-27 13:43:05 +02:00
Roel Janssen
c43edf6f30
gnu: Add python-deeptoolsintervals. 
* gnu/packages/bioinformatics.scm (python-deeptoolsintervals): New variable.
 2020-04-27 13:39:25 +02:00
Efraim Flashner
ee8de73814
gnu: python-scanpy: Update to 1.4.6. 
* gnu/packages/bioinformatics.scm (python-scanpy): Update to 1.4.6.
[arguments]: Add another network based test to skip.
[propagated-inputs]: Add python-tqdm.
 2020-04-26 15:03:50 +03:00
Marius Bakke
7abe35febe
Merge branch 'master' into core-updates 2020-04-19 16:53:01 +02:00
Ricardo Wurmus
974bf81776
gnu: python-pygenometracks: Update to 3.3. 
* gnu/packages/bioinformatics.scm (python-pygenometracks): Update to 3.3.
[arguments]: Add phase "relax-requirements"; disable tests.
[propagated-inputs]: Remove python-configparser and python-hicexplorer; add
python-gffutils, python-pysam, and python-tqdm.
 2020-04-17 15:53:03 +02:00
Ricardo Wurmus
d8fce2362b
gnu: Add python-hicmatrix. 
* gnu/packages/bioinformatics.scm (python-hicmatrix): New variable.
 2020-04-17 15:53:03 +02:00
Ricardo Wurmus
c55beaecd8
gnu: python-cooler: Update to 0.8.7. 
* gnu/packages/bioinformatics.scm (python-cooler): Update to 0.8.7.
[propagated-inputs]: Add python-asciitree, python-numpy, python-pyyaml, and
python-simplejson.
[native-inputs]: Remove python-nose, python-numpydoc, and python-sphinx; add
python-pytest.
 2020-04-17 15:53:03 +02:00
Ricardo Wurmus
4a085ffc16
gnu: python-pybigwig: Update to 0.3.17. 
* gnu/packages/bioinformatics.scm (python-pybigwig): Update to 0.3.17.
 2020-04-17 15:53:03 +02:00
Marius Bakke
bd21acf6c3
Merge branch 'master' into core-updates 2020-04-15 19:26:55 +02:00
Ricardo Wurmus
1971d11db9
gnu: r-delayedarray: Update to 0.12.3. 
* gnu/packages/bioinformatics.scm (r-delayedarray): Update to 0.12.3.
[native-inputs]: Add r-knitr.
 2020-04-14 16:41:00 +02:00
Ricardo Wurmus
679609e179
gnu: r-s4vectors: Update to 0.24.4. 
* gnu/packages/bioinformatics.scm (r-s4vectors): Update to 0.24.4.
 2020-04-14 16:41:00 +02:00
Ricardo Wurmus
fba62f8e92
gnu: pigx-chipseq: Update to 0.0.42. 
* gnu/packages/bioinformatics.scm (pigx-chipseq): Update to 0.0.42.
 2020-04-14 14:07:57 +02:00
Marius Bakke
fc58cb5bd2
Merge branch 'master' into core-updates 2020-04-13 20:26:21 +02:00
Vagrant Cascadian
7cc83f43c9
gnu: r-bamsignals: Fix grammar of "allows to efficiently obtain" to 
"efficiently obtains".

* gnu/packages/bioinformatics (r-bamsignals): Fix grammar.
 2020-04-12 14:59:48 -07:00
Vagrant Cascadian
f49369fad2
gnu: r-qtl: Fix grammar "allows to estimate" to "estimates". 
* gnu/packages/bioinformatics (r-qtl): Fix grammar.
 2020-04-12 14:43:50 -07:00
Marius Bakke
bdb90df764
Merge branch 'master' into core-updates 2020-04-11 00:10:23 +02:00
Marius Bakke
bdb56513e7
gnu: minimap2: Fix cond expression for Guile 3 compatibility. 
* gnu/packages/bioinformatics.scm (minimap2)[arguments]: Make the last COND
test the symbol else instead of _.
 2020-04-09 20:04:43 +02:00
Marius Bakke
2778302399
Merge branch 'master' into core-updates 
Conflicts:
	etc/news.scm
	gnu/local.mk
	gnu/packages/check.scm
	gnu/packages/cross-base.scm
	gnu/packages/gimp.scm
	gnu/packages/java.scm
	gnu/packages/mail.scm
	gnu/packages/sdl.scm
	gnu/packages/texinfo.scm
	gnu/packages/tls.scm
	gnu/packages/version-control.scm
 2020-04-08 13:00:50 +02:00
Jakub Kądziołka
7fe746e071
gnu: python-intervaltree: Update to 3.0.2. 
* gnu/packages/bioinformatics.scm (python-intervaltree): Update to 3.0.2.
[arguments]: Don't skip the tests, work around the problematic
sanity-check instead.
 2020-04-05 20:43:17 +02:00
Marius Bakke
f12f7a0464
gnu: sailfish: Fix build failure. 
* gnu/packages/bioinformatics.scm (sailfish)[arguments]: Prepend to
CPLUS_INCLUDE_PATH instead of overriding it.
 2020-04-03 19:11:05 +02:00
Ricardo Wurmus
0be3cc7f89
gnu: r-biomart: Update to 2.42.1. 
* gnu/packages/bioinformatics.scm (r-biomart): Update to 2.42.1.
[native-inputs]: Add r-knitr.
 2020-04-01 11:15:26 +02:00
Ricardo Wurmus
c5c6719f92
gnu: r-genomeinfodb: Update to 1.22.1. 
* gnu/packages/bioinformatics.scm (r-genomeinfodb): Update to 1.22.1.
[native-inputs]: Add r-knitr.
 2020-04-01 11:15:26 +02:00
Marius Bakke
18af687037
Merge branch 'master' into core-updates 
Conflicts:
	gnu/packages/icu4c.scm
	gnu/packages/man.scm
	gnu/packages/python-xyz.scm
	guix/scripts/environment.scm
	guix/scripts/pack.scm
	guix/scripts/package.scm
	guix/scripts/pull.scm
	guix/store.scm
 2020-03-27 00:12:15 +01:00
Roel Janssen
79c395dde3
gnu: Update sambamba to 0.7.1. 
* gnu/packages/bioinformatics.scm (sambamba): Update to 0.7.1;
  Remove unneeded undead input.
 2020-03-26 18:08:27 +01:00
Ricardo Wurmus
c649d31957
gnu: r-tximport: Update to 1.14.2. 
* gnu/packages/bioinformatics.scm (r-tximport): Update to 1.14.2.
[native-inputs]: Add r-knitr.
 2020-03-24 11:06:00 +01:00
Efraim Flashner
10d3fbf051
gnu: edirect: Install more programs. 
* gnu/packages/bioinformatics.scm (edirect)[arguments]: Add
'patch-programs phase to work around not finding binaries in the PATH.
Rewrite 'install phase to install many more scripts. Rewrite
'wrap-program to wrap more scripts with more programs.
[inputs]: Add edirect-go-programs.
[native-search-paths]: New field.
 2020-03-22 09:53:57 +02:00
Efraim Flashner
7d13a94215
gnu: Add edirect-go-programs. 
* gnu/packages/bioinformatics.scm (edirect-go-programs): New variable.
(edirect)[source]: Adjust snippet to not use non-free software.
 2020-03-22 09:53:57 +02:00
Marius Bakke
c4d769d359
Merge branch 'master' into core-updates 2020-03-18 19:41:08 +01:00
Marius Bakke
961d2ee269
Merge branch 'master' into core-updates 2020-03-14 13:13:40 +01:00
Ricardo Wurmus
57f6ac8d90
gnu: pigx-scrnaseq: Update to 1.1.4. 
* gnu/packages/bioinformatics.scm (pigx-scrnaseq): Update to 1.1.4.
 2020-03-17 20:29:19 +01:00
Ricardo Wurmus
bc6bf142d3
gnu: star: Update to 2.7.3a. 
* gnu/packages/bioinformatics.scm (star): Update to 2.7.3a.
 2020-03-16 13:59:20 +01:00
Marius Bakke
aaadd6e2e1
gnu: salmon: Adjust for C_INCLUDE_PATH changes. 
* gnu/packages/bioinformatics.scm (salmon)[arguments]: Append Eigen headers to
C_INCLUDE_PATH instead of CPATH.
 2020-03-13 00:18:57 +01:00