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.
...
* 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.
...
* 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.
...
* 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.
...
* 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.
...
* 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.
...
* 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.
...
* 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.
...
* 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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
2f49007dd0
gnu: Add python-pairtools.
...
* gnu/packages/bioinformatics.scm (python-pairtools): New variable.
2020-06-03 15:01:19 +02:00
6742a84c63
gnu: Remove bedtools-2.26.
...
* gnu/packages/bioinformatics.scm (bedtools-2.26): Remove variable.
2020-06-03 14:07:58 +02:00
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
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
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
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
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
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
87a40d7203
Merge branch 'master' into core-updates
2020-05-05 20:43:21 +02:00
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
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
eca648b65b
gnu: Add miniasm.
...
* gnu/packages/bioinformatics.scm (miniasm): New variable.
2020-04-30 15:30:16 +02:00
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
545e12f40d
gnu: Add variant-tools.
...
* gnu/packages/bioinformatics.scm (variant-tools): New variable.
2020-04-28 12:23:28 +02:00
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
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
78799a6fdc
gnu: Update minimap2 to 2.17.
...
* gnu/packages/bioinformatics.scm (minimap2): Update to 2.17.
2020-04-27 21:34:10 +02:00
ccf70a80a1
gnu: Add python-deeptools.
...
* gnu/packages/bioinformatics.scm (python-deeptools): New variable.
2020-04-27 13:43:05 +02:00
c43edf6f30
gnu: Add python-deeptoolsintervals.
...
* gnu/packages/bioinformatics.scm (python-deeptoolsintervals): New variable.
2020-04-27 13:39:25 +02:00
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
7abe35febe
Merge branch 'master' into core-updates
2020-04-19 16:53:01 +02:00
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
d8fce2362b
gnu: Add python-hicmatrix.
...
* gnu/packages/bioinformatics.scm (python-hicmatrix): New variable.
2020-04-17 15:53:03 +02:00
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
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
bd21acf6c3
Merge branch 'master' into core-updates
2020-04-15 19:26:55 +02:00
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
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
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
fc58cb5bd2
Merge branch 'master' into core-updates
2020-04-13 20:26:21 +02:00
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
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
bdb90df764
Merge branch 'master' into core-updates
2020-04-11 00:10:23 +02:00
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
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
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
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
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
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
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
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
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
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
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
c4d769d359
Merge branch 'master' into core-updates
2020-03-18 19:41:08 +01:00
961d2ee269
Merge branch 'master' into core-updates
2020-03-14 13:13:40 +01:00
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
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
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
0c08e4bfa1
gnu: edirect: Update to 13.3.20200128.
...
* gnu/packages/bioinformatics.scm (edirect): Update to 13.3.20200128.
[source]: Remove bundled certificate authority tarball.
2020-03-12 16:50:23 +02:00
0b692ef2c6
gnu: r-qtl: Update to 1.46-2.
...
* gnu/packages/bioinformatics.scm (r-qtl): Update to 1.46-2.
2020-03-12 15:15:02 +01:00
d9a2a255f9
gnu: python-pybedtools: Update to 0.8.1.
...
* gnu/packages/bioinformatics.scm (python-pybedtools): Update to 0.8.1.
[arguments]: Add another test to the 'disable-broken-tests phase.
(python2-pybedtools)[native-inputs]: Add python2-pathlib.
2020-03-11 16:31:33 +02:00
173053790c
gnu: python-pyfaidx: Update to 0.5.8.
...
* gnu/packages/bioinformatics.scm (python-pyfaidx): Update to 0.5.8.
2020-03-11 15:45:33 +02:00
ea2822d7d6
gnu: Add python2-pyfaidx.
...
* gnu/packages/bioinformatics.scm (python2-pyfaidx): New variable.
2020-03-11 15:43:50 +02:00
ec11dcfe69
gnu: java-forester-1.005: Update source URI.
...
* gnu/packages/bioinformatics.scm (java-forester-1.005)[source]: Update URI.
[native-inputs]: Wrap long line.
2020-03-10 23:35:13 +01:00
c0f6446579
gnu: Fix build of python-velocyto.
...
* gnu/packages/bioinformatics.scm (python-velocyto): Add python-joblib to
native-inputs to make the test suite run succesfully.
2020-03-09 14:34:41 +01:00
830eac9c27
gnu: ngless: Update to 1.1.0.
...
* gnu/packages/bioinformatics.scm (ngless): Update to 1.1.0.
2020-03-08 23:37:09 +01:00
46a864e7c1
gnu: taxtastic: Update to 0.8.11.
...
* gnu/packages/bioinformatics.scm (taxtastic): Update to 0.8.11.
[source]: Fetch from Github.
[arguments]: Build with default Python; add phases 'prepare-directory,
'python37-compatibility, and update 'check phase.
[propagated-inputs]: Replace Python 2 variants with Python 3 variants.
2020-03-08 22:50:16 +01:00
d56553edc3
gnu: r-methylkit: Add r-knitr.
...
* gnu/packages/bioinformatics.scm (r-methylkit)[native-inputs]: Add r-knitr.
2020-03-07 19:42:34 +01:00
3b7c644569
gnu: r-vsn: Add r-knitr.
...
* gnu/packages/bioinformatics.scm (r-vsn)[native-inputs]: Add r-knitr.
2020-03-07 19:31:46 +01:00
858e642e4c
gnu: python-scanpy: Update to 1.4.5.1.
...
* gnu/packages/bioinformatics.scm (python-scanpy): Update to 1.4.5.1.
[source]: Fetch from pypi.
[propagated-inputs]: Add python-legacy-api-wrap, python-packaging,
python-patsy, and python-umap-learn.
[native-inputs]: Add python-setuptools-scm.
2020-03-06 09:16:48 +01:00
4d5d07f75c
gnu: gess: Use WRAP-SCRIPT.
...
* gnu/packages/bioinformatics.scm (gess)[arguments]: Use WRAP-SCRIPT.
[inputs]: Add guile-3.0 for wrapper.
2020-03-03 11:33:58 +01:00
9309fe355e
gnu: gess: Override PYTHONPATH.
...
* gnu/packages/bioinformatics.scm (gess)[arguments]: Override PYTHONPATH
instead of augmenting it.
2020-03-03 11:33:58 +01:00
1284df4ef6
gnu: r-seqminer: Update to 8.0.
...
* gnu/packages/bioinformatics.scm (r-seqminer): Update to 8.0.
2020-03-02 21:53:48 +01:00
f73b75e00c
gnu: r-hdf5array: Update to 1.14.3.
...
* gnu/packages/bioinformatics.scm (r-hdf5array): Update to 1.14.3.
2020-03-01 23:37:58 +01:00
6c1f5a1b7e
gnu: r-rsamtools: Update to 2.2.3.
...
* gnu/packages/bioinformatics.scm (r-rsamtools): Update to 2.2.3.
2020-03-01 23:37:52 +01:00
9bbf3f9de2
gnu: r-edger: Update to 3.28.1.
...
* gnu/packages/bioinformatics.scm (r-edger): Update to 3.28.1.
2020-03-01 23:37:40 +01:00
e3eb7ee474
gnu: r-seurat: Update to 3.1.4.
...
* gnu/packages/bioinformatics.scm (r-seurat): Update to 3.1.4.
[propagated-inputs]: Add r-patchwork.
2020-03-01 23:21:17 +01:00
643d90bf74
gnu: infernal: Update to 1.1.3.
...
* gnu/packages/bioinformatics.scm (infernal): Update to 1.1.3.
[native-inputs]: Add python.
2020-02-27 18:18:34 +01:00
e6cc426fbb
gnu: vcftools: Update to 0.1.16.
...
* gnu/packages/bioinformatics.scm (vcftools): Update to 0.1.16.
2020-02-27 18:18:34 +01:00
6c32e9b4dc
gnu: bedtools: Update to 2.29.2.
...
* gnu/packages/bioinformatics.scm (bedtools): Update to 2.29.2.
[native-inputs]: Replace python-2 with python-wrapper.
[license]: Change to Expat.
2020-02-27 17:38:17 +01:00
d24b3b0213
gnu: rseqc: Update to 3.0.1.
...
* gnu/packages/bioinformatics.scm (rseqc): Update to 3.0.1.
[source]: Remove snippet.
[arguments]: Remove to build with Python 3.
[inputs]: Replace python2-cython, python2-pysam, and python2-numpy with
python-cython, python-pysam, and python-numpy, respectively; add
python-bx-python and python-pybigwig.
[native-inputs]: Replace python2-nose with python-nose.
2020-02-27 17:38:17 +01:00
146430ea0e
gnu: proteinortho: Update to 6.0.14.
...
* gnu/packages/bioinformatics.scm (proteinortho): Update to 6.0.14.
[source]: Fetch from git; remove pre-built scripts.
[arguments]: Set make-flags; update wrap-programs phase to wrap all scripts.
[inputs]: Add guile-3.0, diamond, python-wrapper, lapack, and openblas; remove
python-2.
[native-inputs]: Add which.
[license]: Update to GPLv3+
2020-02-26 14:07:32 +01:00
9207575669
gnu: diamond: Update to 0.9.30.
...
* gnu/packages/bioinformatics.scm (diamond): Update to 0.9.30.
2020-02-26 14:07:32 +01:00
b38dd34f40
gnu: crossmap: Update to 0.3.8.
...
* gnu/packages/bioinformatics.scm (crossmap): Update to 0.3.8.
[arguments]: Remove to build with default Python.
[inputs]: Add python-pybigwig; replace python2-bx-python, python2-numpy, and
python2-pysam with their Python 3 variants.
[native-inputs]: Replace python2-cython and python2-nose with their Python 3
variants.
2020-02-26 14:07:32 +01:00
640d910427
gnu: macs: Update to 2.2.6.
...
* gnu/packages/bioinformatics.scm (macs): Update to 2.2.6.
[source]: Fetch from git.
[arguments]: Enable tests, build with default Python.
[inputs]: Replace python2-numpy with python-numpy.
[native-inputs]: Add python-pytest.
2020-02-26 12:53:23 +01:00
59c5f85d06
gnu: Remove python-loompy-for-pigx-scrnaseq.
...
* gnu/packages/bioinformatics.scm (python-loompy-for-pigx-scrnaseq): Remove
variable.
2020-02-26 08:59:11 +01:00
4f19106770
gnu: pigx-scrnaseq: Update to 1.1.3.
...
* gnu/packages/bioinformatics.scm (pigx-scrnaseq): Update to 1.1.3.
[arguments]: Remove.
[inputs]: Remove dropseq-tools and java-picard; add flexbar, jellyfish, and
r-seurat; replace python-loompy-for-pigx-scrnaseq with python-loompy.
2020-02-26 08:58:06 +01:00
788de3aec8
gnu: jamm: Update to 1.0.7.6.
...
* gnu/packages/bioinformatics.scm (jamm): Update to 1.0.7.6.
2020-02-25 15:37:27 +01:00
f55084b782
gnu: r-scran: Update to 1.14.6.
...
* gnu/packages/bioinformatics.scm (r-scran): Update to 1.14.6.
2020-02-19 23:00:58 +01:00
9374f550e6
gnu: r-hdf5array: Update to 1.14.2.
...
* gnu/packages/bioinformatics.scm (r-hdf5array): Update to 1.14.2.
2020-02-19 23:00:53 +01:00
f2b9f41234
gnu: r-gviz: Update to 1.30.3.
...
* gnu/packages/bioinformatics.scm (r-gviz): Update to 1.30.3.
2020-02-19 23:00:48 +01:00
3f4f3a7822
gnu: r-rhtslib: Update to 1.18.1.
...
* gnu/packages/bioinformatics.scm (r-rhtslib): Update to 1.18.1.
2020-02-19 23:00:42 +01:00
f0e330d68b
gnu: r-genomicfeatures: Update to 1.38.2.
...
* gnu/packages/bioinformatics.scm (r-genomicfeatures): Update to 1.38.2.
2020-02-19 23:00:36 +01:00
154babb9c4
gnu: r-rsamtools: Update to 2.2.2.
...
* gnu/packages/bioinformatics.scm (r-rsamtools): Update to 2.2.2.
2020-02-19 23:00:31 +01:00
e0ca7b3a14
gnu: r-limma: Update to 3.42.2.
...
* gnu/packages/bioinformatics.scm (r-limma): Update to 3.42.2.
2020-02-19 23:00:25 +01:00
0f72b7abd8
gnu: r-shortread: Update to 1.44.3.
...
* gnu/packages/bioinformatics.scm (r-shortread): Update to 1.44.3.
2020-02-19 23:00:20 +01:00
f45ada0fc8
gnu: r-seurat: Update to 3.1.3.
...
* gnu/packages/bioinformatics.scm (r-seurat): Update to 3.1.3.
[propagated-inputs]: Remove r-sdmtools.
2020-02-19 20:55:00 +01:00
db092c2a90
gnu: r-qtl: Update to 1.45-11.
...
* gnu/packages/bioinformatics.scm (r-qtl): Update to 1.45-11.
2020-02-19 20:54:45 +01:00
01005f4269
gn: edirect: Update to 12.1.20190829.
...
The previous version has disappeared upstream.
* gnu/packages/bioinformatics.scm (edirect): Update to 12.1.20190829.
2020-02-18 13:34:20 +02:00
bf71edd3df
gnu: python2-pbcore: Remove python2-sphinx dependency.
...
* gnu/packages/bioinformatics.scm (python2-pbcore)[arguments]: Add #:phases.
[native-inputs]: Remove PYTHON2-SPHINX.
2020-02-13 16:47:22 +01:00
94600c3960
gnu: r-gviz: Update to 1.30.1.
...
* gnu/packages/bioinformatics.scm (r-gviz): Update to 1.30.1.
2020-01-27 20:48:36 +01:00
c7b98a84d9
gnu: r-genomicfeatures: Update to 1.38.1.
...
* gnu/packages/bioinformatics.scm (r-genomicfeatures): Update to 1.38.1.
2020-01-27 20:48:36 +01:00
caf4290bd8
gnu: r-s4vectors: Update to 0.24.3.
...
* gnu/packages/bioinformatics.scm (r-s4vectors): Update to 0.24.3.
2020-01-27 20:48:36 +01:00
c6b4b4e719
gnu: r-diversitree: Update to 0.9-13.
...
* gnu/packages/bioinformatics.scm (r-diversitree): Update to 0.9-13.
2020-01-27 16:33:27 +01:00
87858bc526
gnu: ocaml: Switch to ocaml 4.09 by default.
...
Bap and earley cannot be updated as they do not support 4.09 yet. Bap requires
the janestreet packages, which cannot be upgraded as no version supports
4.09 and 4.07 at the same time. Moreover, newer versions of the
janestreet packages have a different dependency graph, which will
require a whole new set of packages. We cannot simply use
package-with-ocaml4.07 on them.
* gnu/packages/ocaml.scm (ocaml-sqlite3, ocaml-ppx-tools, ocaml-gen)
(ocaml-sedlex, ocaml-pcre, ocaml-expect, ocaml-ezjsonm, ocaml-uri)
(ocaml-piqilib, ocaml-piqi, ocaml-charinfo-width, ocaml-zed)
(ocaml-lambda-term, ocaml-utop, ocaml-ppx-inline-test, ocaml-earley)
(ocaml-merlin, ocaml-gsl, ocaml-gsl-1, ocaml-sexplib0, ocaml-parsexp)
(ocaml-sexplib, ocaml-base, ocaml-stdio, ocaml-ppxlib, ocaml-ppx-compare)
(ocaml-fieldslib, ocaml-variantslib, ocaml-ppx-fields-conv)
(ocaml-ppx-sexp-conv, ocaml-ppx-variants-conv, ocaml-ppx-custom-printf)
(ocaml-bin-prot, ocaml-ppx-hash, ocaml-ppx-enumerate, ocaml-ppx-bench)
(ocaml-ppx-here, ocaml-ppx-typerep, ocaml-ppx-sexp-value)
(ocaml-ppx-sexp-message, ocaml-ppx-pipebang, ocaml-ppx-optional)
(ocaml-ppx-optcomp, ocaml-ppx-fail, ocaml-ppx-let, ocaml-ppx-assert)
(ocaml-ppx-expect, ocaml-ppx-js-style, ocaml-ppx-typerep-conv)
(ocaml-ppx-base, ocaml-ppx-bin-prot, ocaml-ppx-jane)
(ocaml-splittable-random, ocaml-configurator, ocaml-spawn, ocaml-core)
(ocaml-core-kernel, ocaml-odoc, ocaml-fftw3, ocaml-lacaml): Rename to ...
(ocaml4.07-sqlite3, ocaml4.07-ppx-tools, ocaml4.07-gen, ocaml4.07-sedlex)
(ocaml4.07-pcre, ocaml4.07-expect, ocaml4.07-ezjsonm, ocaml4.07-uri)
(ocaml4.07-piqilib, ocaml4.07-piqi, ocaml4.07-charinfo-width)
(ocaml4.07-zed, ocaml4.07-lambda-term, ocaml4.07-utop)
(ocaml4.07-ppx-inline-test, ocaml4.07-earley, ocaml4.07-merlin)
(ocaml4.07-gsl, ocaml4.07-gsl-1, ocaml4.07-sexplib0, ocaml4.07-parsexp)
(ocaml4.07-sexplib, ocaml4.07-base, ocaml4.07-stdio, ocaml4.07-ppxlib)
(ocaml4.07-ppx-compare, ocaml4.07-fieldslib, ocaml4.07-variantslib)
(ocaml4.07-ppx-fields-conv, ocaml4.07-ppx-sexp-conv)
(ocaml4.07-ppx-variants-conv, ocaml4.07-ppx-custom-printf)
(ocaml4.07-bin-prot, ocaml4.07-ppx-hash, ocaml4.07-ppx-enumerate)
(ocaml4.07-ppx-bench, ocaml4.07-ppx-here, ocaml4.07-ppx-typerep)
(ocaml4.07-ppx-sexp-value, ocaml4.07-ppx-sexp-message)
(ocaml4.07-ppx-pipebang, ocaml4.07-ppx-optional, ocaml4.07-ppx-optcomp)
(ocaml4.07-ppx-fail, ocaml4.07-ppx-let, ocaml4.07-ppx-assert)
(ocaml4.07-ppx-expect, ocaml4.07-ppx-js-style)
(ocaml4.07-ppx-typerep-conv, ocaml4.07-ppx-base, ocaml4.07-ppx-bin-prot)
(ocaml4.07-ppx-jane, ocaml4.07-splittable-random)
(ocaml4.07-configurator, ocaml4.07-spawn, ocaml4.07-core)
(ocaml4.07-core-kernel, ocaml4.07-odoc, ocaml4.07-fftw3)
(ocaml4.07-lacaml): ... to this and use ocaml 4.07.
(bap, unison): Use ocaml-4.07.
* gnu/packages/bioinformatics.scm (pplacer): Use ocaml-4.07.
2020-01-27 03:56:06 +01:00
a19fb6a436
gnu: Use HTTPS for (gnu packages bioinformatics) home pages.
...
* gnu/packages/bioinformatics (bamm, ribodiff, python-biopython)
(discrover, hisat, hisat2, htseq, fastqc, htslib, python2-pbcore, roary)
(sortmerna, r-qtl, multiqc, r-deseq, r-fastseg, sambamba, trim-galore)
(gess, kentutils, bismark, kallisto, sailfish, python-hicexplorer)
(pplacer, python2-checkm-genome, r-velocyto)[home-page]: Use HTTPS.
2020-01-21 02:15:32 +01:00
72607005e4
gnu: r-gage: Update home page.
...
* gnu/packages/bioinformatics.scm (r-gage)[home-page]: Update.
2020-01-21 02:15:32 +01:00
0388046068
gnu: sra-tools: Update home page.
...
* gnu/packages/bioinformatics.scm (sra-tools)[home-page]: Update.
2020-01-21 02:15:31 +01:00
0eeaf1ac3c
gnu: raxml: Update home page.
...
* gnu/packages/bioinformatics.scm (raxml)[home-page]: Update.
2020-01-21 02:15:31 +01:00
5832b88c45
gnu: prodigal: Update home page.
...
* gnu/packages/bioinformatics.scm (prodigal)[home-page]: Use source code repository as home page.
2020-01-21 02:15:31 +01:00
030fe2fb7e
gnu: miso: Update home page.
...
* gnu/packages/bioinformatics.scm (miso)[home-page]: Update.
2020-01-21 02:15:31 +01:00
b725655fce
gnu: grit: Update home page.
...
* gnu/packages/bioinformatics.scm (grit)[home-page]: Use source code
repository as home page.
2020-01-21 02:15:31 +01:00
b56f2b6366
gnu: express-beta-diversity: Update home page.
...
The original is not coming back:
<https://github.com/dparks1134/ExpressBetaDiversity/issues/11 >.
* gnu/packages/bioinformatics.scm (express-beta-diversity)[home-page]:
Use source code repository as home page.
2020-01-21 02:15:31 +01:00
568bd2e382
gnu: dendropy: Update home page.
...
* gnu/packages/bioinformatics.scm (dendropy)[home-page]: Update.
2020-01-21 02:15:31 +01:00
99db6db7be
gnu: Use HTTPS for bioconductor.org.
...
* gnu/packages/bioinformatics.scm (r-homo-sapiens)[source]: Use HTTPS.
* gnu/packages/bioconductor.scm (r-bsgenome-mmusculus-ucsc-mm9-masked,
r-cghcall, r-diffbind, r-cghbase, r-ripseeker, r-chippeakanno,
r-qdnaseq, r-marray, r-multtest)[home-page]: Likewise.
* gnu/packages/graph.scm (r-rgraphviz)[home-page]: Likewise.
2020-01-21 00:43:39 +01:00
f1fa954a7d
gnu: edirect: Use HTTPS home page.
...
* gnu/packages/bioinformatics.scm (edirect)[home-page]: Use HTTPS.
2020-01-19 06:09:02 +01:00
7699e32289
gnu: kentutils: Build with OpenSSL 1.0.
...
* gnu/packages/bioinformatics.scm (kentutils)[inputs]: Change from OPENSSL to
OPENSSL-1.0.
2020-01-16 19:20:20 +01:00
d64124df89
gnu: r-delayedarray: Update to 0.12.2.
...
* gnu/packages/bioinformatics.scm (r-delayedarray): Update to 0.12.2.
2020-01-16 06:53:31 +01:00
f7b5c1a02f
gnu: r-iranges: Update to 2.20.2.
...
* gnu/packages/bioinformatics.scm (r-iranges): Update to 2.20.2.
2020-01-16 06:53:31 +01:00
fdf69f1ee0
gnu: r-s4vectors: Update to 0.24.2.
...
* gnu/packages/bioinformatics.scm (r-s4vectors): Update to 0.24.2.
2020-01-16 06:53:31 +01:00
7241b44ad4
gnu: r-biocstyle: Update to 2.14.4.
...
* gnu/packages/bioinformatics.scm (r-biocstyle): Update to 2.14.4.
2020-01-16 06:53:30 +01:00
2604ecb3a9
gnu: smithwaterman: Update to 0.0.0-2.2610e25.
...
* gnu/packages/bioinformatics.scm (smithwaterman): Update to 0.0.0-2.2610e25.
[arguments]: Add make-flags to build static library. Adjust custom
'install phase to install static library.
2020-01-09 14:30:38 +02:00
0ab7f6c5f4
gnu: vcflib: Update to 1.0.1.
...
* gnu/packages/bioinformatics.scm (vcflib): Update to 1.0.1.
[source]: Download using url-fetch.
[native-inputs]: Sort alphabetically. Move perl, python ...
[inputs]: ... to here.
[arguments]: Add make-flags. Update custom 'build phase.
(tabixpp-freebayes): Remove variable.
(freebayes)[native-inputs]: Use tabixpp-source over tabixpp-freebayes.
2020-01-09 14:30:38 +02:00
2e3efa6e55
gnu: fastahack: Update to 1.0.0.
...
* gnu/packages/bioinformatics.scm (fastahack): Update to 1.0.0.
2020-01-09 14:30:38 +02:00
de933b71ee
gnu: Add intervaltree.
...
* gnu/packages/bioinformatics.scm (intervaltree): New variable.
(vcflib, freebayes)[native-inputs]: Use packaged intervaltree's source.
2020-01-09 14:30:38 +02:00
612d6a8e5b
gnu: tabixpp: Update to 1.1.0.
...
* gnu/packages/bioinformatics.scm (tabixpp): Update to 1.1.0.
[source]: Add snippet to remove vendored library.
[arguments]: Adjust custom 'build phase to fix INCLUDES.
2020-01-09 14:30:37 +02:00
2673620f24
gnu: bwa: Install static library.
...
* gnu/packages/bioinformatics.scm (bwa)[arguments]: Install static
library.
2020-01-09 14:30:34 +02:00
ba42da245b
gnu: uglify-js: Move back next to sbcl-cl-uglify-js definition.
...
This fixes the bug which prevented uglify-js from being defined properly, and
cascaded back to all Common Lisp packages.
* gnu/packages/bioinformatics.scm: Replace javascript module with lisp-xyz.
* gnu/packages/cran.scm: Use lisp-xyz module.
* gnu/packages/javascript.scm (uglify-js): Move from here...
* gnu/packages/lisp-xyz.scm: ... To here.
* gnu/packages/web.scm: Replace javascript module with lisp-xyz.
* guix/build-system/minify.scm: Find uglify-js in the lisp-xyz module.
2020-01-03 15:03:36 +01:00
04b181cb15
gnu: r-topgo: Update to 2.38.1.
...
* gnu/packages/bioinformatics.scm (r-topgo): Update to 2.38.1.
2019-12-27 21:30:25 +01:00
4997ff5c1b
gnu: r-summarizedexperiment: Update to 1.16.1.
...
* gnu/packages/bioinformatics.scm (r-summarizedexperiment): Update to 1.16.1.
2019-12-27 21:30:25 +01:00
ba17429d67
gnu: r-delayedarray: Update to 0.12.1.
...
* gnu/packages/bioinformatics.scm (r-delayedarray): Update to 0.12.1.
2019-12-27 21:30:25 +01:00
152a408051
gnu: r-biocparallel: Update to 1.20.1.
...
* gnu/packages/bioinformatics.scm (r-biocparallel): Update to 1.20.1.
2019-12-27 21:30:25 +01:00
827d0fa846
gnu: r-shortread: Update to 1.44.1.
...
* gnu/packages/bioinformatics.scm (r-shortread): Update to 1.44.1.
2019-12-27 21:30:21 +01:00
5bc95d2bcd
gnu: python-bbknn: Update to 1.3.6.
...
* gnu/packages/bioinformatics.scm (python-bbknn): Update to 1.3.6.
[arguments]: Disable tests until migration to python-scikit-learn.
[propgated-inputs]: Remove python-faiss, python-scanpy.
[propgated-inputs]: Add python-scipy, python-umap-learn.
2019-12-23 17:31:06 -06:00
3bedd9f40f
gnu: tophat: Build with GCC 5
...
* gnu/packages/python-xyz.scm (tophat)[native-inputs]: Add gcc-5.
(tophat)[inputs]: Reorder alphabetically the dependencies.
(tophat)[home-page]: Swapp to https.
Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2019-12-23 19:38:14 +01:00
345488d76f
gnu: fastx-toolkit: Build with GCC 6
...
* gnu/packages/bioinformatics.scm (fastx-toolkit)[native-inputs]: Add gcc-6.
Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2019-12-21 23:55:25 +01:00
61e21c0899
gnu: r-scater: Update to 1.14.6.
...
* gnu/packages/bioinformatics.scm (r-scater): Update to 1.14.6.
2019-12-20 21:26:26 +01:00
595036d9f9
gnu: Add libsbml.
...
* gnu/packages/bioinformatics.scm (libsbml): New variable.
2019-12-17 20:02:11 +01:00
f98480a975
gnu: r-seurat: Update to 3.1.2.
...
* gnu/packages/bioinformatics.scm (r-seurat): Update to 3.1.2.
2019-12-17 14:58:32 +01:00
94f9c0cdc4
gnu: python-gffutils: Update description.
...
* gnu/packages/bioinformatics.scm (python-gffutils)[description]: Reflow
paragraph and fix spelling of SQLite.
2019-12-16 23:32:55 +01:00
cfd83f3282
gnu: Add python-gffutils.
...
* gnu/packages/bioinformatics.scm (python-gffutils): New variable.
Co-authored-by: Ricardo Wurmus <rekado@elephly.net>
2019-12-16 23:27:00 +01:00
4ade2dd9d2
gnu: python-pyfaidx: Update to 0.5.7.
...
* gnu/packages/bioinformatics.scm (python-pyfaidx): Update to 0.5.7.
2019-12-16 23:22:12 +01:00
0726645eca
gnu: r-genefilter: Update to 1.68.0.
...
* gnu/packages/bioinformatics.scm (r-genefilter): Update to 1.68.0.
[propagated-inputs]: Remove r-s4vectors and add r-biocgenerics.
2019-12-15 15:39:04 +01:00
867018e138
gnu: r-deseq2: Update to 1.26.0.
...
* gnu/packages/bioinformatics.scm (r-deseq2): Update to 1.26.0.
2019-12-15 15:39:04 +01:00
ebc81e300c
gnu: r-dexseq: Update to 1.32.0.
...
* gnu/packages/bioinformatics.scm (r-dexseq): Update to 1.32.0.
2019-12-15 15:39:04 +01:00
12c4555d44
gnu: r-annotationforge: Update to 1.28.0.
...
* gnu/packages/bioinformatics.scm (r-annotationforge): Update to 1.28.0.
2019-12-15 15:39:04 +01:00
33a2acb757
gnu: r-rbgl: Update to 1.62.1.
...
* gnu/packages/bioinformatics.scm (r-rbgl): Update to 1.62.1.
2019-12-15 15:39:04 +01:00
d2661841be
gnu: r-gseabase: Update to 1.48.0.
...
* gnu/packages/bioinformatics.scm (r-gseabase): Update to 1.48.0.
2019-12-15 15:39:04 +01:00
4afcf941d2
gnu: r-category: Update to 2.52.1.
...
* gnu/packages/bioinformatics.scm (r-category): Update to 2.52.1.
2019-12-15 15:39:04 +01:00
545730891e
gnu: r-gostats: Update to 2.52.0.
...
* gnu/packages/bioinformatics.scm (r-gostats): Update to 2.52.0.
2019-12-15 15:39:04 +01:00
f29c9f0d33
gnu: r-shortread: Update to 1.44.0.
...
* gnu/packages/bioinformatics.scm (r-shortread): Update to 1.44.0.
2019-12-15 15:39:04 +01:00
58fd68b299
gnu: r-systempiper: Update to 1.20.0.
...
* gnu/packages/bioinformatics.scm (r-systempiper): Update to 1.20.0.
2019-12-15 15:39:03 +01:00
Roel Janssen
Andreas Enge
Efraim Flashner
Ricardo Wurmus
Jakub Kądziołka
Marius Bakke
Tobias Geerinckx-Rice
Ludovic Courtès
Pierre Langlois
Nicolas Goaziou
Marius Bakke
Vagrant Cascadian
Björn Höfling
Julien Lepiller
Pierre Neidhardt
Brett Gilio
Mădălin Ionel Patrașcu