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2914 Commits

Author SHA1 Message Date
Christopher Baines
6417b97c7e
Revert "gnu: Add mosaicatcher." 
mosaicatcher-unbundle-htslib.patch is missing.

This reverts commit b1ae0f30d8.
 2021-05-29 01:21:14 +01:00
Ricardo Wurmus
b1ae0f30d8
gnu: Add mosaicatcher. 
* gnu/packages/bioinformatics.scm (mosaicatcher): New variable.
 2021-05-28 23:00:47 +02:00
Roel Janssen
87c9f63fce
gnu: Add python-pyega3. 
* gnu/packages/bioinformatics.scm (python-pyega3): New variable.
 2021-05-27 23:01:35 +02:00
Roel Janssen
a30e616ccc
gnu: Add python-htsget. 
* gnu/packages/bioinformatics.scm (python-htsget): New variable.
 2021-05-27 22:50:46 +02:00
Efraim Flashner
c5f7203e3e
gnu: minimap2: Install more files. 
* gnu/packages/bioinformatics.scm (minimap2)[arguments]: Add modules.
Adjust custom 'install phase to also install library, headers and a
pkg-config file.
 2021-05-26 15:22:10 +03:00
Efraim Flashner
36a90d0637
gnu: minimap2: Update to 2.18. 
* gnu/packages/bioinformatics.scm (minimap2): Update to 2.18.
[source]: Remove patch.
* gnu/packages/patches/minimap2-aarch64-support.patch: Remove file.
* gnu/local.mk (dist_patch_DATA): Remove it.
 2021-05-26 15:22:10 +03:00
Roel Janssen
af163badb4
gnu: Add r-phantompeakqualtools. 
* gnu/packages/bioinformatics.scm (r-phantompeakqualtools): New variable.
 2021-05-26 09:34:37 +02:00
Roel Janssen
b1fee8a003
gnu: Add r-spp. 
* gnu/packages/bioinformatics.scm (r-spp): New variable.
 2021-05-26 09:29:01 +02:00
Ricardo Wurmus
7ff515aa51
gnu: r-rhdf5filters: Update to 1.2.1. 
* gnu/packages/bioinformatics.scm (r-rhdf5filters): Update to 1.2.1.
 2021-05-20 14:43:34 +02:00
Ricardo Wurmus
48b8a5e701
gnu: pigx-chipseq: Update to 0.0.52. 
* gnu/packages/bioinformatics.scm (pigx-chipseq): Update to 0.0.52.
 2021-05-17 18:45:55 +02:00
Ricardo Wurmus
848126d008
gnu: prinseq: Fix references to perl executable. 
* gnu/packages/bioinformatics.scm (prinseq)[arguments]: Embed concrete
references to the "perl" executable.
 2021-05-14 17:11:52 +02:00
Ricardo Wurmus
9b99b6d947
gnu: Add ensembl-vep. 
* gnu/packages/bioinformatics.scm (ensembl-vep): New variable.
 2021-05-07 08:52:49 +02:00
Ricardo Wurmus
ce7b202f9b
gnu: Add perl-bio-db-hts. 
* gnu/packages/bioinformatics.scm (perl-bio-db-hts): New variable.
 2021-05-06 18:56:24 +02:00
Ricardo Wurmus
da7f89c737
gnu: python-pybedtools: Update to 0.8.2. 
* gnu/packages/bioinformatics.scm (python-pybedtools): Update to 0.8.2.
[arguments]: Remove outdated substitutions; simplify check phase.
 2021-05-05 16:18:13 +02:00
Ricardo Wurmus
7694acebd1
gnu: r-summarizedexperiment: Move to (gnu packages bioconductor). 
* gnu/packages/bioinformatics.scm (r-summarizedexperiment): Move variable from here...
* gnu/packages/bioconductor.scm (r-summarizedexperiment): ...to here.
 2021-05-04 10:11:34 +02:00
Ricardo Wurmus
d4051161e7
gnu: r-ensembldb: Update to 2.14.1. 
* gnu/packages/bioinformatics.scm (r-ensembldb): Update to 2.14.1.
 2021-05-04 09:47:36 +02:00
Ricardo Wurmus
7072dc8c53
gnu: r-gage: Update to 2.40.2. 
* gnu/packages/bioinformatics.scm (r-gage): Update to 2.40.2.
 2021-05-04 09:47:36 +02:00
Ricardo Wurmus
3b002a49d4
gnu: r-annotationhub: Update to 2.22.1. 
* gnu/packages/bioinformatics.scm (r-annotationhub): Update to 2.22.1.
 2021-05-04 09:47:36 +02:00
Roel Janssen
f09e4dd8ea
gnu: Add pbgzip. 
* gnu/packages/bioinformatics.scm (pbgzip): New variable.
 2021-04-30 18:44:46 +02:00
Roel Janssen
7540f6915c
gnu: Update bedtools to 2.30.0. 
* gnu/packages/bioinformatics.scm (bedtools): Update to 2.30.0,
  [inputs]: Use latest samtools.
 2021-04-29 12:14:06 +02:00
Roel Janssen
558d11c3a8
gnu: Update samtools to 1.12. 
* gnu/packages/bioinformatics.scm (samtools): Update to 1.12.
 2021-04-29 12:14:02 +02:00
Roel Janssen
b904bb89a0
gnu: Update bcftools to 1.12. 
* gnu/packages/bioinformatics.scm (bcftools): Update to 1.12.
 2021-04-29 12:13:56 +02:00
Roel Janssen
241994230b
gnu: htslib: Update to 1.12. 
* gnu/packages/bioinformatics.scm (htslib): Update to 1.12.
 2021-04-29 12:13:46 +02:00
Ricardo Wurmus
e7707d5262
gnu: pigx-bsseq: Update to 0.1.3. 
* gnu/packages/bioinformatics.scm (pigx-bsseq): Update to 0.1.3.
[inputs]: Add r-ggbio, r-matrixstats, and r-reshape2.
 2021-04-28 21:58:05 +02:00
Ricardo Wurmus
01e33a031e
gnu: Add lofreq. 
* gnu/packages/bioinformatics.scm (lofreq): New variable.
 2021-04-28 17:41:47 +02:00
Ricardo Wurmus
f01b3cd063
gnu: kraken2: Replace references to rsync. 
* gnu/packages/bioinformatics.scm (kraken2)[inputs]: Add rsync.
[arguments]: Replace references to rsync; use WITH-DIRECTORY-EXCURSION to
avoid repeating "scripts".
 2021-04-28 14:50:50 +02:00
Ricardo Wurmus
5ea5ea6066
gnu: Add python-pyliftover. 
* gnu/packages/bioinformatics.scm (python-pyliftover): New variable.
 2021-04-28 10:52:12 +02:00
Vinicius Monego
76fb1a5cf2
gnu: Add python-louvain 0.15. 
* gnu/packages/graph.scm (python-louvain): Rename variable to
python-louvain-0.6.
(python-louvain): New variable.
* gnu/packages/bioinformatics.scm (python-scanpy)[propagated-inputs]: Use
python-louvain-0.6.

Co-authored-by: Leo Famulari <leo@famulari.name>
 2021-04-25 14:49:57 -04:00
Ricardo Wurmus
f1f17c7bba
gnu: Add shorah. 
* gnu/packages/bioinformatics.scm (shorah): New variable.
 2021-04-23 15:53:51 +02:00
Ricardo Wurmus
c9371b698d
gnu: Add r-shinycell. 
* gnu/packages/bioinformatics.scm (r-shinycell): New variable.
 2021-04-23 15:53:51 +02:00
Ricardo Wurmus
92032d8081
gnu: Add kraken2. 
* gnu/packages/bioinformatics.scm (kraken2): New variable.
 2021-04-22 08:31:17 +02:00
Roel Janssen
c3926120ba
gnu: Update blast+ to 2.11.0. 
* gnu/packages/bioinformatics.scm (blast+): Update to 2.11.0.
 2021-04-16 20:56:43 +02:00
Arun Isaac
563e4bd884
gnu: cwltool: Update to 3.0.20210319143721. 
* gnu/packages/bioinformatics.scm (cwltool): Update to 3.0.20210319143721.
[arguments]: In the loosen-version-restrictions phase, relax pytest version
restriction. In the modify-tests phase, delete file tests/test_content_type.py
since it contains tests that require network access.
 2021-04-14 22:39:54 +05:30
Arun Isaac
12e210d907
gnu: python-schema-salad: Update to 7.1.20210316164414. 
* gnu/packages/bioinformatics.scm (python-schema-salad): Update to
7.1.20210316164414.
[arguments]: Add skip-failing-tests phase.
 2021-04-14 22:39:54 +05:30
Tobias Geerinckx-Rice
e5852655b8
gnu: sortmerna: Mark up description. 
* gnu/packages/bioinformatics.scm (sortmerna)[description]: Use @acronym{}.
 2021-04-10 14:11:26 +02:00
Ricardo Wurmus
5f0c3535aa
gnu: r-genomicfeatures: Update to 1.42.3. 
* gnu/packages/bioinformatics.scm (r-genomicfeatures): Update to 1.42.3.
 2021-04-08 13:28:24 +02:00
zimoun
23686ba3eb
Revert "Revert some commits that caused guix pull to fail." 
This reverts commit 8ec0ca8faf.
 2021-03-31 21:23:45 +02:00
Efraim Flashner
04ba7a196a
gnu: plink-ng: Build prettify binary. 
* gnu/packages/bioinformatics.scm (plink-ng)[arguments]: Adjust
make-flags to also build prettify.
 2021-03-31 14:33:42 +03:00
Efraim Flashner
5f3f2a7cc8
gnu: plink-ng: Remove custom install phase. 
* gnu/packages/bioinformatics.scm (plink-ng)[arguments]: Adjust
make-flags and remove custom 'install phase.
 2021-03-31 14:33:34 +03:00
Efraim Flashner
977ea2c0a3
gnu: plink-ng: Sort inputs alphabetically. 
* gnu/packages/bioinformatics.scm (plink-ng)[inputs]: Sort
alphabetically.
 2021-03-31 14:32:43 +03:00
Efraim Flashner
58e9e0e142
gnu: plink-ng: Update to 2.00a2.3. 
* gnu/packages/bioinformatics.scm (plink-ng): Update to 2.00a2.3.
[arguments]: Adjust make-flags.
 2021-03-31 14:32:43 +03:00
Hong Li
ee4fc3b662
gnu: Add r-signac. 
* gnu/packages/bioinformatics.scm (r-signac): New variable.

Co-authored-by: Ricardo Wurmus <rekado@elephly.net>
 2021-03-22 14:27:17 +01:00
Mark H Weaver
1a265842e6
gnu: Use PACKAGE/INHERIT in more places. 
* gnu/packages/algebra.scm (fftwf, fftw-openmpi),
gnu/packages/audio.scm (ztoolkit-rsvg),
gnu/packages/bioinformatics.scm (python2-dendropy),
gnu/packages/boost.scm (boost-with-python2),
gnu/packages/check.scm (python2-mock, python2-pytest-mock),
gnu/packages/cups.scm (hplip-minimal),
gnu/packages/freedesktop.scm (libinput-minimal),
gnu/packages/gettext.scm (gnu-gettext),
gnu/packages/glib.scm (python2-pygobject),
gnu/packages/gnome.scm (gdl-minimal, libsoup-minimal, python2-pyatspi),
gnu/packages/groff.scm (groff-minimal),
gnu/packages/jami.scm (ffmpeg-jami),
gnu/packages/libcanberra.scm (libcanberra/gtk+-2),
gnu/packages/lirc.scm (python2-lirc),
gnu/packages/llvm.scm (clang-runtime-3.5),
gnu/packages/mpi.scm (java-openmpi, openmpi-thread-multiple),
gnu/packages/node.scm (libnode),
gnu/packages/onc-rpc.scm (libtirpc/hurd),
gnu/packages/python-compression.scm (bitshuffle-for-snappy),
gnu/packages/python-crypto.scm (python2-pycrypto, python2-cryptography)
(python2-cryptography, python2-m2crypto),
gnu/packages/python-web.scm (python2-html2text, python2-tornado)
(python2-terminado, python2-ndg-httpsclient, python2-websocket-client)
(python2-rauth, python2-url, python2-s3transfer),
gnu/packages/python-xyz.scm (python2-psutil, python2-serpent)
(python2-humanfriendly, python2-empy, python2-parse-type, python2-polib)
(python2-jsonschema, python2-pystache, python2-cython, python2-numpydoc)
(python2-ipyparallel, python2-traitlets, python2-dbus)
(python2-beautifulsoup4, python2-pep517, python2-flake8, python2-llfuse)
(python2-tlsh, python-file, python2-notebook, python-jupyter-console-minimal)
(python2-contextlib2, python2-promise, python2-anyjson, python2-amqp)
(python2-kombu, python2-billiard, python2-celery, python2-whoosh)
(python2-jellyfish, python-rope, ptpython-2, python2-binaryornot)
(python2-setproctitle, python2-argcomplete, python2-xopen, python2-isort)
(python2-radon, python2-rfc6555, python2-activepapers, python2-send2trash)
(python2-cloudpickle, python2-reparser),
gnu/packages/python.scm (python2-called-python),
gnu/packages/qt.scm (python2-sip, python-pyqt-without-qtwebkit, python2-pyqt)
(python-qscintilla, python-pyqt+qscintilla),
gnu/packages/scanner.scm (sane-backends),
gnu/packages/sdl.scm (guile3.0-sdl2),
gnu/packages/selinux.scm (checkpolicy, libselinux, libsemanage, secilc)
(python-sepolgen, policycoreutils),
gnu/packages/serialization.scm (lua5.1-libmpack, lua5.2-libmpack),
gnu/packages/simulation.scm (fenics),
gnu/packages/statistics.scm (python2-statsmodels),
gnu/packages/texinfo.scm (info-reader),
gnu/packages/wxwidgets.scm (wxwidgets-gtk2, wxwidgets-gtk2-3.1),
gnu/packages/xml.scm (xmlsec-nss),
gnu/packages/xorg.scm (uim-gtk, uim-qt),
guix/build-system/python.scm (package-with-explicit-python)
(strip-python2-variant): Use PACKAGE/INHERIT.
 2021-03-17 03:58:10 -04:00
Ricardo Wurmus
fcf8c6c565
gnu: hisat2: Update to 2.2.1. 
* gnu/packages/bioinformatics.scm (hisat2): Update to 2.2.1.
[source]: Fetch from git repository on Github.
[arguments]: Add phase to build manual; remove trailing #t from other phases.
[native-inputs]: Remove unzip.
[home-page]: Update.
[inputs]: Add python-wrapper.
 2021-03-16 11:12:01 +01:00
Leo Famulari
8ec0ca8faf
Revert some commits that caused guix pull to fail. 
This reverts commits 821e643921 through
8f9fd9b70c.

Specifically, these commits caused the build failure of
guix-package-cache.drv like this:

------
(repl-version 0 1 1)
Generating package cache for '/gnu/store/vyz7q26kxxd4z70m24rkkqqhaizdla7g-profile'...
(exception unbound-variable (value #f) (value "Unbound variable: ~S") (value (r-biobase)) (value #f))
 2021-03-15 19:52:34 -04:00
zimoun
d99a18252c
gnu: r-delayedarray: Move to (gnu packages bioconductor). 
* gnu/packages/bioinformatics.scm (r-delayedarray): Move from here...
* gnu/packages/bioconductor.scm (r-delayedarray): ...to here.
 2021-03-15 23:30:26 +01:00
zimoun
adf45daae9
gnu: r-rsamtools: Move to (gnu packages bioconductor). 
* gnu/packages/bioinformatics.scm (r-rsamtools): Move from here...
* gnu/packages/bioconductor.scm (r-rsamtools): ...to here.
 2021-03-15 23:30:26 +01:00
zimoun
b1a19ab6e2
gnu: r-biostrings: Move to (gnu packages bioconductor). 
* gnu/packages/bioinformatics.scm (r-biostrings): Move from here...
* gnu/packages/bioconductor.scm (r-biostrings): ...to here.
 2021-03-15 23:30:26 +01:00
zimoun
eab9807fb3
gnu: r-biocparallel: Move to (gnu packages bioconductor). 
* gnu/packages/bioinformatics.scm (r-biocparallel): Move from here...
* gnu/packages/bioconductor.scm (r-biocparallel): ...to here.
 2021-03-15 23:30:26 +01:00
zimoun
c11b541fba
gnu: r-biomart: Move to (gnu packages bioconductor). 
* gnu/packages/bioinformatics.scm (r-biomart): Move from here...
* gnu/packages/bioconductor.scm (r-biomart): ...to here.
 2021-03-15 23:30:26 +01:00
zimoun
16c7e79ebb
gnu: r-annotationdbi: Move to (gnu packages bioconductor). 
* gnu/packages/bioinformatics.scm (r-annotationdbi): Move from here...
* gnu/packages/bioconductor.scm (r-annotationdbi): ...to here.
 2021-03-15 23:30:26 +01:00
zimoun
457de7f401
gnu: r-biobase: Move to (gnu packages bioconductor). 
* gnu/packages/bioinformatics.scm (r-biobase): Move from here...
* gnu/packages/bioconductor.scm (r-biobase): ...to here.
 2021-03-15 23:30:26 +01:00
zimoun
f3f09b99cd
gnu: r-genomicranges: Move to (gnu packages bioconductor). 
* gnu/packages/bioinformatics.scm (r-genomicranges): Move from here...
* gnu/packages/bioconductor.scm (r-genomicranges): ...to here.
 2021-03-15 23:30:26 +01:00
zimoun
e56b3db82e
gnu: r-xvector: Move to (gnu packages bioconductor). 
* gnu/packages/bioinformatics.scm (r-xvector): Move from here...
* gnu/packages/bioconductor.scm (r-xvector): ...to here.
 2021-03-15 23:30:26 +01:00
zimoun
821e643921
gnu: r-limma: Move to (gnu packages bioconductor). 
* gnu/packages/bioinformatics.scm (r-limma): Move from here...
* gnu/packages/bioconductor.scm (r-limma): ...to here.
 2021-03-15 23:30:26 +01:00
Ricardo Wurmus
14204d696c
gnu: r-genomicfeatures: Update to 1.42.2. 
* gnu/packages/bioinformatics.scm (r-genomicfeatures): Update to 1.42.2.
 2021-03-15 15:03:08 +01:00
Ricardo Wurmus
f10f2745eb
gnu: r-delayedarray: Update to 0.16.2. 
* gnu/packages/bioinformatics.scm (r-delayedarray): Update to 0.16.2.
 2021-03-15 15:03:08 +01:00
zimoun
bf612ead76
gnu: r-variantannotation: Move to (gnu packages bioconductor). 
* gnu/packages/bioinformatics.scm (r-variantannotation): Move from here...
* gnu/packages/bioconductor.scm (r-variantannotation): ...to here.
 2021-03-15 14:06:24 +01:00
zimoun
082f3c5433
gnu: r-edger: Move to (gnu packages bioconductor). 
* gnu/packages/bioinformatics.scm (r-edger): Move from here...
* gnu/packages/bioconductor.scm (r-edger): ...to here.
 2021-03-15 14:06:16 +01:00
zimoun
35b62c044e
gnu: r-genomeinfodb: Move to (gnu packages bioconductor). 
* gnu/packages/bioinformatics.scm (r-genomeinfodb): Move from here...
* gnu/packages/bioconductor.scm (r-genomeinfodb): ...to here.
 2021-03-15 14:05:56 +01:00
zimoun
8d6d75ff39
gnu: r-genomeinfodbdata: Move to (gnu packages bioconductor). 
* gnu/packages/bioinformatics.scm (r-genomeinfodbdata): Move from here...
* gnu/packages/bioconductor.scm (r-genomeinfodbdata): ...to here.
[source]: Use 'bioconductor-uri'.
 2021-03-15 14:05:47 +01:00
zimoun
9949f459bf
gnu: r-iranges: Move to (gnu packages bioconductor). 
* gnu/packages/bioinformatics.scm (r-iranges): Move from here...
* gnu/packages/bioconductor.scm (r-iranges): ...to here.
 2021-03-15 14:05:37 +01:00
zimoun
d64e3a487b
gnu: r-s4vectors: Move to (gnu packages bioconductor). 
* gnu/packages/bioinformatics.scm (r-s4vectors): Move from here...
* gnu/packages/bioconductor.scm (r-s4vectors): ...to here.
 2021-03-15 14:05:27 +01:00
zimoun
852fa82d4c
gnu: r-bioccheck: Move to (gnu packages bioconductor). 
* gnu/packages/bioinformatics.scm (r-bioccheck): Move from here...
* gnu/packages/bioconductor.scm (r-bioccheck): ...to here.
 2021-03-15 14:05:22 +01:00
zimoun
d5576b6eb7
gnu: r-grohmm: Move to (gnu packages bioconductor). 
* gnu/packages/bioinformatics.scm (r-grohmm): Move from here...
* gnu/packages/bioconductor.scm (r-grohmm): ...to here.
 2021-03-15 14:04:26 +01:00
zimoun
5ac55aea8b
gnu: r-biocstyle: Move to (gnu packages bioconductor). 
* gnu/packages/bioinformatics.scm (r-biocstyle): Move from here...
* gnu/packages/bioconductor.scm (r-biocstyle): ...to here.
 2021-03-15 14:03:21 +01:00
zimoun
134404b437
gnu: r-biocviews: Move to (gnu packages bioconductor). 
* gnu/packages/bioinformatics.scm (r-biocviews): Move from here...
* gnu/packages/bioconductor.scm (r-biocviews): ...to here.
 2021-03-15 14:03:18 +01:00
Ricardo Wurmus
6e0ed09e68
gnu: Add instrain. 
* gnu/packages/bioinformatics.scm (instrain): New variable.
 2021-03-15 11:43:20 +01:00
Ricardo Wurmus
ad34eb222c
gnu: Add python-drep. 
* gnu/packages/bioinformatics.scm (python-drep): New variable.
 2021-03-15 11:43:20 +01:00
zimoun
df6b3c25bb
gnu: r-systempiper: Move to (gnu packages bioconductor). 
* gnu/packages/bioinformatics.scm (r-systempiper): Move from here...
* gnu/packages/bioconductor.scm (r-systempiper): ...to here.
 2021-03-12 14:45:55 +01:00
zimoun
8957efa8ef
gnu: r-shortread: Move to (gnu packages bioconductor). 
* gnu/packages/bioinformatics.scm (r-shortread): Move from here...
* gnu/packages/bioconductor.scm (r-shortread): ...to here.
 2021-03-12 14:45:54 +01:00
zimoun
2a97057688
gnu: r-gostats: Move to (gnu packages bioconductor). 
* gnu/packages/bioinformatics.scm (r-gostats): Move from here...
* gnu/packages/bioconductor.scm (r-gostats): ...to here.
 2021-03-12 14:45:54 +01:00
zimoun
4e7cf96c9f
gnu: r-category: Move to (gnu packages bioconductor). 
* gnu/packages/bioinformatics.scm (r-category): Move from here...
* gnu/packages/bioconductor.scm (r-category): ...to here.
 2021-03-12 14:45:54 +01:00
zimoun
031fdda47a
gnu: r-gseabase: Move to (gnu packages bioconductor). 
* gnu/packages/bioinformatics.scm (r-gseabase): Move from here...
* gnu/packages/bioconductor.scm (r-gseabase): ...to here.
 2021-03-12 14:45:54 +01:00
zimoun
f44079bc21
gnu: r-rbgl: Move to (gnu packages bioconductor). 
* gnu/packages/bioinformatics.scm (r-rbgl): Move from here...
* gnu/packages/bioconductor.scm (r-rbgl): ...to here.
 2021-03-12 14:45:54 +01:00
zimoun
ff92c2873c
gnu: r-annotationforge: Move to (gnu packages bioconductor). 
* gnu/packages/bioinformatics.scm (r-annotationforge): Move from here...
* gnu/packages/bioconductor.scm (r-annotationforge): ...to here.
 2021-03-12 14:45:53 +01:00
zimoun
d769b10714
gnu: r-dexseq: Move to (gnu packages bioconductor). 
* gnu/packages/bioinformatics.scm (r-dexseq): Move from here...
* gnu/packages/bioconductor.scm (r-dexseq): ...to here.
 2021-03-12 14:45:53 +01:00
zimoun
373545855d
gnu: r-deseq2: Move to (gnu packages bioconductor). 
* gnu/packages/bioinformatics.scm (r-deseq2): Move from here...
* gnu/packages/bioconductor.scm (r-deseq2): ...to here.
 2021-03-12 14:45:53 +01:00
zimoun
a35ea5fed9
gnu: r-genefilter: Move to (gnu packages bioconductor). 
* gnu/packages/bioinformatics.scm (r-genefilter): Move from here...
* gnu/packages/bioconductor.scm (r-genefilter): ...to here.
 2021-03-12 14:45:53 +01:00
Efraim Flashner
5ae7414860
gnu: Add bandage. 
* gnu/packages/bioinformatics.scm (bandage): New variable.
 2021-03-11 16:54:38 +02:00
Ricardo Wurmus
133a918923
gnu: trim-galore: Update to 0.6.6. 
* gnu/packages/bioinformatics.scm (trim-galore): Update to 0.6.6.
 2021-03-09 11:54:59 +01:00
Ricardo Wurmus
49d85b3f11
gnu: bbmap: Update to 38.90. 
* gnu/packages/bioinformatics.scm (bbmap): Update to 38.90.
 2021-03-09 11:54:59 +01:00
Nicolas Goaziou
ea8e89292c
gnu: seqan-1: Use HTTPS source URI. 
* gnu/packages/bioinformatics.scm (seqan-1)[source]: Use HTTPS URI.
 2021-03-06 16:05:44 +01:00
Nicolas Goaziou
e062572812
gnu: seqan: Use HTTPS home page URI. 
* gnu/packages/bioinformatics.scm (seqan)[home-page]: Use HTTPS URI.
 2021-03-06 16:01:24 +01:00
Ricardo Wurmus
f5c3e8e2ec
gnu: Add r-cellchat. 
* gnu/packages/bioinformatics.scm (r-cellchat): New variable.
 2021-03-05 15:04:15 +01:00
Tim Howes
dcee10506c
gnu: infernal: Update to 1.1.4. 
* gnu/packages/bioinformatics.scm (infernal): Update to 1.1.4.

Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
 2021-03-03 10:11:51 +02:00
Tim Howes
9f4ffc249f
gnu: hmmer: Update to 3.3.2. 
* gnu/packages/bioinformatics.scm (hmmer): Update to 3.3.2.

Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
 2021-03-03 10:11:51 +02:00
Ricardo Wurmus
f21c711a0f
gnu: kallisto: Update to 0.46.2. 
* gnu/packages/bioinformatics.scm (kallisto): Update to 0.46.2.
[source]: Remove bundled htslib sources.
 2021-03-02 17:06:58 +01:00
Ricardo Wurmus
cc39e9dbdc
gnu: kallisto: Use older htslib. 
* gnu/packages/bioinformatics.scm (kallisto)[inputs]: Use htslib-1.9 instead
of the latest.
 2021-03-02 17:06:58 +01:00
Nicolas Goaziou
3759df574d
gnu: f-seq: Use HTTPS home page URI. 
* gnu/packages/bioinformatics.scm (f-seq)[home-page]: Use HTTPS URI.
 2021-02-28 11:03:56 +01:00
Ricardo Wurmus
5d5bbd6fcc
gnu: Add star-for-pigx. 
This is a follow-up to commit f1f6e49190.

* gnu/packages/bioinformatics.scm (star-for-pigx): New variable.
(pigx-rnaseq, pigx-scrnaseq)[inputs]: Replace star with star-for-pigx.
 2021-02-23 19:40:59 +01:00
Ricardo Wurmus
f1f6e49190
gnu: star: Update to 2.7.8a. 
* gnu/packages/bioinformatics.scm (star): Update to 2.7.8a.
 2021-02-22 21:16:19 +01:00
Ricardo Wurmus
f310b06685
gnu: nanopolish: Fix script wrapping. 
* gnu/packages/bioinformatics.scm (nanopolish)[arguments]: Fix wrap-programs
phase.
[inputs]: Add Guile for wrap-script; add bioperl and perl-getopt-long for Perl
scripts.
 2021-02-19 23:35:04 +01:00
Ricardo Wurmus
15c0cc4aa2
gnu: Add prinseq. 
* gnu/packages/bioinformatics.scm (prinseq): New variable.
 2021-02-19 23:14:59 +01:00
Ricardo Wurmus
80d3150c94
gnu: Add ngshmmalign. 
* gnu/packages/bioinformatics.scm (ngshmmalign): New variable.
 2021-02-19 17:24:52 +01:00
Ricardo Wurmus
8360705948
gnu: Add r-archr. 
* gnu/packages/bioinformatics.scm (r-archr): New variable.
 2021-02-18 16:11:38 +01:00
Ricardo Wurmus
9904a15a4c
gnu: Add indelfixer. 
* gnu/packages/bioinformatics.scm (indelfixer): New variable.
 2021-02-15 13:51:58 +01:00
Mădălin Ionel Patrașcu
160e4a95e7
gnu: bowtie1: Update to 1.3.0. 
* gnu/packages/bioinformatics.scm (bowtie1): Update to 1.3.0.
[arguments]: Set CC in make flags.

Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
 2021-02-11 22:29:37 +01:00
Ricardo Wurmus
0e3e26ca60
gnu: r-gage: Update to 2.40.1. 
* gnu/packages/bioinformatics.scm (r-gage): Update to 2.40.1.
 2021-02-11 21:33:38 +01:00
Ricardo Wurmus
5103da059a
gnu: r-msnbase: Update to 2.16.1. 
* gnu/packages/bioinformatics.scm (r-msnbase): Update to 2.16.1.
 2021-02-11 21:33:38 +01:00
Ricardo Wurmus
2596200514
gnu: r-methylkit: Update to 1.16.1. 
* gnu/packages/bioinformatics.scm (r-methylkit): Update to 1.16.1.
 2021-02-11 21:33:38 +01:00
Ricardo Wurmus
3f7e96acc7
gnu: r-delayedarray: Update to 0.16.1. 
* gnu/packages/bioinformatics.scm (r-delayedarray): Update to 0.16.1.
 2021-02-11 21:33:38 +01:00
Ricardo Wurmus
9b66b8017d
gnu: r-biomart: Update to 2.46.3. 
* gnu/packages/bioinformatics.scm (r-biomart): Update to 2.46.3.
 2021-02-11 21:33:38 +01:00
Ricardo Wurmus
8e25b1acf9
gnu: r-edger: Update to 3.32.1. 
* gnu/packages/bioinformatics.scm (r-edger): Update to 3.32.1.
 2021-02-11 21:33:38 +01:00
Ricardo Wurmus
809f725977
gnu: r-iranges: Update to 2.24.1. 
* gnu/packages/bioinformatics.scm (r-iranges): Update to 2.24.1.
 2021-02-11 21:33:37 +01:00
Ricardo Wurmus
88fd569ddf
gnu: r-s4vectors: Update to 0.28.1. 
* gnu/packages/bioinformatics.scm (r-s4vectors): Update to 0.28.1.
 2021-02-11 21:33:37 +01:00
Ricardo Wurmus
babb2dce34
gnu: r-systempiper: Update to 1.24.3. 
* gnu/packages/bioinformatics.scm (r-systempiper): Update to 1.24.3.
 2021-02-11 21:33:37 +01:00
Ricardo Wurmus
d3ac91dd9d
gnu: r-gseabase: Update to 1.52.1. 
* gnu/packages/bioinformatics.scm (r-gseabase): Update to 1.52.1.
 2021-02-11 21:33:37 +01:00
Ricardo Wurmus
074d142ab6
gnu: r-genefilter: Update to 1.72.1. 
* gnu/packages/bioinformatics.scm (r-genefilter): Update to 1.72.1.
 2021-02-11 21:33:37 +01:00
Ricardo Wurmus
8d61539883
gnu: rsem: Link with shared libhts library. 
* gnu/packages/bioinformatics.scm (rsem)[arguments]: Link with libhts.so
instead of libhts.a.
 2021-02-05 23:30:43 +01:00
Efraim Flashner
877ab0266c
gnu: vcflib: Fix generated pkg-config file. 
* gnu/packages/bioinformatics.scm (vcflib)[arguments]: In custom
generated pkg-config file, link with all needed libraries and
fix linker library.
* gnu/packages/patches/freebayes-devendor-deps.patch: Adjust accordingly.
 2021-02-01 19:02:14 +02:00
Maxim Cournoyer
23a5dcce1d
gnu: grocsvs: Remove package. 
This package depends on Python 2 and doesn't build anymore.  Upstream doesn't
seem active, but if they ever port it to Python 3, they should let people know
here: https://github.com/grocsvs/grocsvs/issues/6.

* gnu/packages/bioinformatics.scm (grocsvs): Delete.
 2021-01-29 10:58:25 -05:00
Ricardo Wurmus
c4a2cbeb06
gnu: Add r-demultiplex. 
* gnu/packages/bioinformatics.scm (r-demultiplex): New variable.
 2021-01-28 22:24:51 +01:00
Ricardo Wurmus
04b1a1f6bd
gnu: Add repeat-masker. 
* gnu/packages/bioinformatics.scm (repeat-masker): New variable.
 2021-01-28 15:07:55 +01:00
Ricardo Wurmus
6d3cafa086
gnu: Add trf. 
* gnu/packages/bioinformatics.scm (trf): New variable.
 2021-01-28 15:07:55 +01:00
Efraim Flashner
b3e39a475f
gnu: freebayes: Update source, home-page URIs. 
* gnu/packages/bioinformatics.scm (freebayes)[source]: Update to new
upstream URI.
[home-page]: Same.
 2021-01-19 11:48:38 +02:00
Efraim Flashner
99043adf46
gnu: freebayes: Don't include vcflib sources. 
* gnu/packages/bioinformatics.scm (freebayes)[native-inputs]: Remove
vcflib-source, intervaltree-source. Move vcflib ...
[inputs]: ... to here.
[arguments]: Adjust 'patch-source and 'unpack-submodule-sources for
changes in vendored code.
* gnu/packages/patches/freebayes-devendor-deps.patch: Update patch.
 2021-01-19 11:41:07 +02:00
Efraim Flashner
1bbfe1789d
gnu: vcflib: Add pkg-config file. 
* gnu/packages/bioinformatics.scm (vcflib)[arguments]: Add phase to
create pkg-config file.
 2021-01-19 11:36:01 +02:00
Efraim Flashner
d6a8148c8d
gnu: vcflib: Build a shared library. 
* gnu/packages/bioinformatics.scm (vcflib)[arguments]: Add phase to
build a shared library instead of a static one.
 2021-01-19 10:43:06 +02:00
Efraim Flashner
797585746b
gnu: freebayes: Extend test timeout on slower architectures. 
* gnu/packages/bioinformatics.scm (freebayes)[arguments]: Use custom
'check phase  on aarch64-linux and armhf-linux to extend the test timeout.
 2021-01-19 10:33:19 +02:00
Mădălin Ionel Patrașcu
c0afd8044f
gnu: Add r-snapatac. 
* gnu/packages/bioinformatics.scm (r-snapatac): New variable.
 2021-01-18 23:26:53 +01:00
Mădălin Ionel Patrașcu
2d9c6542c8
gnu: mafft: Update to 7.475. 
* gnu/packages/bioinformatics.scm (mafft): Update to 7.475.

Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
 2021-01-18 11:57:28 +02:00
Efraim Flashner
6cb86e23a9
gnu: ruby-bio-vcf: Rename to bio-vcf. 
This package is widely known in select circles specifically as 'bio-vcf'.

* gnu/packages/bioinformatics.scm (ruby-bio-vcf): Rename to bio-vcf.
 2021-01-18 11:19:37 +02:00
Efraim Flashner
9b6cddd32d
gnu: Add ruby-bio-vcf. 
* gnu/packages/bioinformatics.scm (ruby-bio-vcf): New variable.
 2021-01-18 10:41:46 +02:00
Efraim Flashner
fc9fd5496f
gnu: freebayes: Update to 1.3.3. 
* gnu/packages/bioinformatics.scm (freebayes): Update to 1.3.3.
[source]: Add patch. Add snippet to remove vendored library.
[build-system]: Switch to meson-build-system.
[inputs]: Remove bamtools. Add fastahack, smithwaterman, tabixpp.
[native-inputs]: Remove procps, python-2, tabixpp source, smithwaterman
source, multichoose source, fsom source, filevercmp source, fastahack
source, bash-tap source. Add bash-tap, grep, pkg-config, simde, vcflib.
[arguments]: Drop make-flags. Don't delete 'configure phase. Delete
custom 'fix-tests, 'build-tabixpp-and-vcflib, 'fix-makefiles, 'install
phases. Adjust 'unpack-submodule-sources phase to changed native-inputs.
Add new 'patch-source phase.
 2021-01-17 15:47:32 +02:00
Efraim Flashner
3ddeefe854
gnu: multichoose: Install header files. 
* gnu/packages/bioinformatics.scm (multichoose)[arguments]: Adjust
'install phase to also install header files.
 2021-01-17 15:47:32 +02:00
Efraim Flashner
976603b909
gnu: filevercmp: Install header files. 
* gnu/packages/bioinformatics.scm (filevercmp)[arguments]: Adjust
'install phase to install header files.
 2021-01-17 15:47:32 +02:00
Efraim Flashner
93309e25c7
gnu: vcflib: Update to 1.0.2. 
* gnu/packages/bioinformatics.scm (vcflib): Update to 1.0.2.
[source]: Download using git-fetch. Remove patch. Update snippet to use
packaged libraries.
[build-system]: Switch to cmake-build-system.
[inputs]: Add bzip2.
[native-inputs]: Add package-source of fsom.
[arguments]: Delete custom 'set-flags, 'install phases. Don't delete
'configure phase. Adjust 'unpack-submodule-sources phase.
* gnu/packages/patches/vcflib-use-shared-libraries.patch: Remove file.
* gnu/local.mk (dist_patch_DATA): Remove it.
 2021-01-14 20:43:31 +02:00
Efraim Flashner
db30d6eada
gnu: sambamba Update to 0.8.0. 
* gnu/packages/bioinformatics.scm (sambamba): Update to 0.8.0.
[source, home-page]: Update to new upstream URI.
[arguments]: Shorten 'fix-ldc-version phase. Remove
'place-biod-and-undead phase. Update 'unbundle-prerequisites and
'insatll phases.
[native-inputs]: Remove rdmd, biod. Move ldc ...
[inputs]: ... to here. Add zlib.
(htslib-for-sambamba): Remove variable.
 2021-01-14 20:43:31 +02:00
Efraim Flashner
2051be4f4c
gnu: gemma: Enable tests. 
* gnu/packages/bioinformatics.scm (gemma)[source]: Add snippet to remove
bundled sources.
[native-inputs]: Add catch-framework2-1, perl, shunit2, which.
[arguments]: Don't disable tests. Override 'check phase.
 2021-01-14 20:43:31 +02:00
Efraim Flashner
daf96e704d
gnu: gemma: Add Texinfo markup. 
* gnu/packages/bioinformatics.scm (gemma)[description]: Use Texinfo
markup.
 2021-01-14 20:43:30 +02:00
Efraim Flashner
a36abbe005
gnu: gemma: Update to 0.98.3. 
* gnu/packages/bioinformatics.scm (gemma): Update to 0.98.3.
[source, home-page]: Update to new upstream URI.
[inputs]: Remove eigen, gfortran, lapack.
[arguments]: Remove make-flags. Remove 'find-eigen phase. Rename
'bin-mkdir phase to 'prepare-build and substitute openblas include
directory.
 2021-01-14 20:43:30 +02:00
zimoun
610cd6a170
gnu: r-ggbio: Move to (gnu packages bioconductor). 
* gnu/packages/bioinformatics.scm (r-ggbio): Move from here...
* gnu/packages/bioconductor.scm (r-ggbio): ...to here.
 2020-12-29 17:40:28 +01:00
zimoun
81f481d6cd
gnu: r-gqtlstats: Move to (gnu packages bioconductor). 
* gnu/packages/bioinformatics.scm (r-gqtlstats): Move from here...
* gnu/packages/bioconductor.scm (r-gqtlstats): ...to here.
 2020-12-29 17:40:28 +01:00
zimoun
61ec8928c7
gnu: r-snpstats: Move to (gnu packages bioconductor). 
* gnu/packages/bioinformatics.scm (r-snpstats): Move from here...
* gnu/packages/bioconductor.scm (r-snpstats): ...to here.
 2020-12-29 17:40:28 +01:00
zimoun
a2c66d18a5
gnu: r-homo-sapiens: Move to (gnu packages bioconductor). 
* gnu/packages/bioinformatics.scm (r-homo-sapiens): Move from here...
* gnu/packages/bioconductor.scm (r-homo-sapiens): ...to here.
Replace 'string-append' by 'bioconductor-uri' with 'annotation'.
 2020-12-29 17:40:28 +01:00
zimoun
8c2b7c9a2a
gnu: r-erma: Move to (gnu packages bioconductor). 
* gnu/packages/bioinformatics.scm (r-erma): Move from here...
* gnu/packages/bioconductor.scm (r-erma): ...to here.
 2020-12-29 17:40:28 +01:00
zimoun
8f1237c350
gnu: r-ldblock: Move to (gnu packages bioconductor). 
* gnu/packages/bioinformatics.scm (r-ldblock): Move from here...
* gnu/packages/bioconductor.scm (r-ldblock): ...to here.
 2020-12-29 17:40:28 +01:00
zimoun
9534e7b706
gnu: r-gqtlstats: Move to (gnu packages bioconductor). 
* gnu/packages/bioinformatics.scm (r-gqtlstats): Move from here...
* gnu/packages/bioconductor.scm (r-gqtlstats): ...to here.
 2020-12-29 17:40:28 +01:00
zimoun
2a4322f7c3
gnu: r-gviz: Move to (gnu packages bioconductor). 
* gnu/packages/bioinformatics.scm (r-gviz): Move from here...
* gnu/packages/bioconductor.scm (r-gviz): ...to here.
 2020-12-29 17:40:28 +01:00
zimoun
69a5e066c1
gnu: r-gwascat: Move to (gnu packages bioconductor). 
* gnu/packages/bioinformatics.scm (r-gwascat): Move from here...
* gnu/packages/bioconductor.scm (r-gwascat): ...to here.
 2020-12-29 17:40:28 +01:00
zimoun
838db0de5e
gnu: r-sushi: Move to (gnu packages bioconductor). 
* gnu/packages/bioinformatics.scm (r-sushi): Move from here...
* gnu/packages/bioconductor.scm (r-sushi): ...to here.
 2020-12-29 17:40:25 +01:00
Marius Bakke
6203b8e5bd
gnu: kentutils: Build with OpenSSL 1.1. 
* gnu/packages/bioinformatics.scm (kentutils)[inputs]: Change from OPENSSL-1.0
to OPENSSL.
 2020-12-20 16:30:42 +01:00
Marius Bakke
ca27b0e528
gnu: kentutils: Add a file name for the "samtabix" input. 
* gnu/packages/bioinformatics.scm (kentutils)[native-inputs]: For "samtabix",
add a file name on the origin.
 2020-12-20 16:30:42 +01:00
Ricardo Wurmus
48f77ecbb1
gnu: r-keggrest: Update to 1.30.1. 
* gnu/packages/bioinformatics.scm (r-keggrest): Update to 1.30.1.
 2020-12-09 23:30:12 +01:00
Ricardo Wurmus
4745f0dfca
gnu: r-genomeinfodb: Update to 1.26.2. 
* gnu/packages/bioinformatics.scm (r-genomeinfodb): Update to 1.26.2.
 2020-12-09 23:30:12 +01:00
Ricardo Wurmus
baeaa02e75
gnu: r-biocstyle: Update to 2.18.1. 
* gnu/packages/bioinformatics.scm (r-biocstyle): Update to 2.18.1.
 2020-12-09 23:30:12 +01:00
Ricardo Wurmus
4617cc7fd5
gnu: r-rhtslib: Propagate zlib. 
* gnu/packages/bioinformatics.scm (r-rhtslib)[inputs]: Move zlib from here...
[propagated-inputs]: ...to here.
(r-variantannotation, r-rsamtools, r-bamsignals, r-rhdf5,
r-methylkit)[inputs]: Remove zlib.
* gnu/packages/bioconductor.scm (r-diffbind, r-quasr, r-cytolib, r-ncdfflow,
r-flowworkspace, r-seqbias)[inputs]: Remove zlib.
 2020-12-09 12:12:48 +01:00
zimoun
cde035e67f
gnu: r-gqtlstats: Update to 1.21.3. 
* gnu/packages/bioinformatics.scm (r-gqtlstats): Update to 1.21.3.
 2020-12-09 12:12:48 +01:00
zimoun
6a4818716d
gnu: r-gqtlbase: Update to 1.21.1. 
Co-authored-by: Ricardo Wurmus <rekado@elephly.net>

* gnu/packages/bioinformatics.scm (r-gqtlbase): Update to 1.21.1.
[arguments]: Add phase to patch broken NAMESPACE file.
 2020-12-09 12:12:48 +01:00
zimoun
970984237a
gnu: r-biocviews: Update to 1.58.1. 
* gnu/packages/bioinformatics.scm (r-biocviews): Update to 1.58.1.

Co-authored-by: Ricardo Wurmus <reka@elephly.net>.
 2020-12-09 12:12:47 +01:00
zimoun
53affb349a
gnu: r-rhdf5: Update to 2.34.0. 
* gnu/packages/bioinformatics.scm (r-rhdf5): Update to 2.34.0.
[propagated-inputs]: Add r-rhdf5filters.
[arguments]: Avoid to have a plain directory on the list of libraries to
link.

Co-authored-by: Ricardo Wurmus <reka@elephly.net>.
 2020-12-09 12:12:46 +01:00
Ricardo Wurmus
86fcceeae1
gnu: Add r-rhdf5filters. 
* gnu/packages/bioinformatics.scm (r-rhdf5filters): New variable.
 2020-12-09 12:12:46 +01:00
zimoun
60ad3c7b3b
gnu: r-genomationdata: Update to 1.22.0. 
* gnu/packages/bioinformatics.scm (r-genomationdata): Update to 1.22.0.
 2020-12-09 12:12:46 +01:00
zimoun
e707820442
gnu: r-sushi: Update to 1.28.0. 
* gnu/packages/bioinformatics.scm (r-sushi): Update to 1.28.0.
 2020-12-09 12:12:45 +01:00
zimoun
83129edfb7
gnu: r-gwascat: Update to 2.22.0. 
* gnu/packages/bioinformatics.scm (r-gwascat): Update to 2.22.0.
[propagated-inputs]: Add r-biocfilecache, r-readr, r-snpstats, and
r-variantannotation; remove r-biocgenerics, r-ggplot2, r-rsamtools, and
r-rtracklayer.
 2020-12-09 12:12:45 +01:00
zimoun
717e53fdc0
gnu: r-gviz: Update to 1.34.0. 
* gnu/packages/bioinformatics.scm (r-gviz): Update to 1.34.0.
 2020-12-09 12:12:45 +01:00
zimoun
0a8d08e887
gnu: r-ldblock: Update to 1.20.0. 
* gnu/packages/bioinformatics.scm (r-ldblock): Update to 1.20.0.
 2020-12-09 12:12:45 +01:00
zimoun
494010ad3e
gnu: r-erma: Update to 1.6.0. 
* gnu/packages/bioinformatics.scm (r-erma): Update to 1.6.0.
 2020-12-09 12:12:45 +01:00
zimoun
6e338901bf
gnu: r-snpstats: Update to 1.40.0. 
* gnu/packages/bioinformatics.scm (r-snpstats): Update to 1.40.0.
 2020-12-09 12:12:45 +01:00
zimoun
74a11b21be
gnu: r-ggbio: Update to 1.38.0. 
* gnu/packages/bioinformatics.scm (r-ggbio): Update to 1.38.0.
 2020-12-09 12:12:45 +01:00
zimoun
3c6eecdeed
gnu: r-biovizbase: Update to 1.38.0. 
* gnu/packages/bioinformatics.scm (r-biovizbase): Update to 1.38.0.
 2020-12-09 12:12:45 +01:00
zimoun
6e182c237a
gnu: r-organismdbi: Update to 1.32.0. 
* gnu/packages/bioinformatics.scm (r-organismdbi): Update to 1.32.0.
 2020-12-09 12:12:44 +01:00
zimoun
06fe3b7a53
gnu: r-ensembldb: Update to 2.14.0. 
* gnu/packages/bioinformatics.scm (r-ensembldb): Update to 2.14.0.
 2020-12-09 12:12:44 +01:00
zimoun
8962a13afe
gnu: r-dirichletmultinomial: Update to 1.32.0. 
* gnu/packages/bioinformatics.scm (r-dirichletmultinomial): Update to 1.32.0.
 2020-12-09 12:12:44 +01:00
Roel Janssen
4ef1e375b4
gnu: r-complexheatmap: Update to 2.6.2. 
* gnu/packages/bioinformatics.scm (r-complexheatmap): Update to 2.6.2;
[propagated-inputs]: Add r-cairo, r-digest, r-iranges, r-matrixstats, and
r-s4vectors.
 2020-12-09 12:12:44 +01:00
zimoun
0fde2f9ad2
gnu: r-genomicfiles: Update to 1.26.0. 
* gnu/packages/bioinformatics.scm (r-genomicfiles): Update to 1.26.0.
[propagated-inputs]: Add r-matrixgenerics.
 2020-12-09 12:12:44 +01:00
zimoun
78cadd0fef
gnu: r-gage: Update to 2.40.0. 
* gnu/packages/bioinformatics.scm (r-gage): Update to 2.40.0.
 2020-12-09 12:12:44 +01:00
zimoun
143437c623
gnu: r-keggrest: Update to 1.30.0. 
* gnu/packages/bioinformatics.scm (r-keggrest): Update to 1.30.0.
 2020-12-09 12:12:44 +01:00
zimoun
b6dd0722c8
gnu: r-fastseg: Update to 1.36.0. 
* gnu/packages/bioinformatics.scm (r-fastseg): Update to 1.36.0.
 2020-12-09 12:12:44 +01:00
zimoun
a9dc755e67
gnu: r-annotationhub: Update to 2.22.0. 
* gnu/packages/bioinformatics.scm (r-annotationhub): Update to 2.22.0.
 2020-12-09 12:12:43 +01:00
zimoun
3becce3ff3
gnu: r-interactivedisplaybase: Update to 1.28.0. 
* gnu/packages/bioinformatics.scm (r-interactivedisplaybase): Update to 1.28.0.
 2020-12-09 12:12:43 +01:00
zimoun
8e55b9f502
gnu: r-edaseq: Update to 2.24.0. 
* gnu/packages/bioinformatics.scm (r-edaseq): Update to 2.24.0.
 2020-12-09 12:12:43 +01:00
zimoun
8db8a683b9
gnu: r-aroma-light: Update to 3.20.0. 
* gnu/packages/bioinformatics.scm (r-aroma-light): Update to 3.20.0.
 2020-12-09 12:12:43 +01:00
zimoun
971f3a377c
gnu: r-msnid: Update to 1.24.0. 
* gnu/packages/bioinformatics.scm (r-msnid): Update to 1.24.0.
[propagated-inputs]: Add r-annotationdbi, r-annotationhub, r-biocgenerics,
r-biocstyle, r-biostrings, r-ggplot2, r-msmstests, r-purrr, r-rlang, r-runit,
r-stringr, r-tibble, and r-xtable.
 2020-12-09 12:12:43 +01:00
zimoun
2ed937e0aa
gnu: r-pcamethods: Update to 1.82.0. 
* gnu/packages/bioinformatics.scm (r-pcamethods): Update to 1.82.0.
 2020-12-09 12:12:43 +01:00
zimoun
b47560c1cf
gnu: r-mzid: Update to 1.28.0. 
* gnu/packages/bioinformatics.scm (r-mzid): Update to 1.28.0.
[propagated-inputs]: Remove r-rcpp.
 2020-12-09 12:12:43 +01:00
zimoun
75bdab83cc
gnu: r-vsn: Update to 3.58.0. 
* gnu/packages/bioinformatics.scm (r-vsn): Update to 3.58.0.
 2020-12-09 12:12:42 +01:00
zimoun
6a6f38b89e
gnu: r-affy: Update to 1.68.0. 
* gnu/packages/bioinformatics.scm (r-affy): Update to 1.68.0.
 2020-12-09 12:12:42 +01:00
zimoun
d6750c6587
gnu: r-affyio: Update to 1.60.0. 
* gnu/packages/bioinformatics.scm (r-affyio): Update to 1.60.0.
 2020-12-09 12:12:42 +01:00
Ricardo Wurmus
471ceb5e5e
gnu: r-mzr: Fix linking. 
* gnu/packages/bioinformatics.scm (r-mzr)[arguments]: Fix linking with rhdf5
libraries.
 2020-12-09 12:12:42 +01:00
Ricardo Wurmus
badb4678bd
gnu: r-mzr: Update to 2.24.1. 
* gnu/packages/bioinformatics.scm (r-mzr): Update to 2.24.1.
 2020-12-09 12:12:42 +01:00
zimoun
4d9e168db8
gnu: r-protgenerics: Update to 1.22.0. 
* gnu/packages/bioinformatics.scm (r-protgenerics): Update to 1.22.0.
 2020-12-09 12:12:42 +01:00
zimoun
858eb988a0
gnu: r-sva: Update to 3.38.0. 
* gnu/packages/bioinformatics.scm (r-sva): Update to 3.38.0.
 2020-12-09 12:12:42 +01:00
zimoun
99bd4f2d7c
gnu: r-methylkit: Update to 1.16.0. 
* gnu/packages/bioinformatics.scm (r-methylkit): Update to 1.16.0.
 2020-12-09 12:12:42 +01:00
zimoun
2ed79a0a42
gnu: r-copywriter: Update to 2.22.0. 
* gnu/packages/bioinformatics.scm (r-copywriter): Update to 2.22.0.
 2020-12-09 12:12:41 +01:00
zimoun
36fd725b6f
gnu: r-chipseq: Update to 1.40.0. 
* gnu/packages/bioinformatics.scm (r-chipseq): Update to 1.40.0.
 2020-12-09 12:12:41 +01:00
zimoun
cad3eb4eb4
gnu: r-annotationfilter: Update to 1.14.0. 
* gnu/packages/bioinformatics.scm (r-annotationfilter): Update to 1.14.0.
 2020-12-09 12:12:41 +01:00
zimoun
ec0050c0a9
gnu: r-tximport: Update to 1.18.0. 
* gnu/packages/bioinformatics.scm (r-tximport): Update to 1.18.0.
 2020-12-09 12:12:41 +01:00
Roel Janssen
6d5a4dd0a7
gnu: r-mutationalpatterns: Update to 3.0.1. 
* gnu/packages/bioinformatics.scm (r-mutationalpatterns): Update to 3.0.1.
[native-inputs]: Add r-knitr.
[propagated-inputs]: Add r-bsgenome, r-dplyr, r-ggalluvial,
r-magrittr, r-purrr, r-stringr, r-tibble, and r-tidyr; remove
r-reshape2 and r-summarizedexperiment.
 2020-12-09 12:12:41 +01:00
zimoun
a823a74525
gnu: r-rcas: Update to 1.16.0. 
* gnu/packages/bioinformatics.scm (r-rcas): Update to 1.16.0.
 2020-12-09 12:12:41 +01:00
zimoun
2c15a1c502
gnu: r-bamsignals: Update to 1.22.0. 
* gnu/packages/bioinformatics.scm (r-bamsignals): Update to 1.22.0.
 2020-12-09 12:12:41 +01:00
zimoun
728369634f
gnu: r-rhtslib: Update to 1.22.0. 
* gnu/packages/bioinformatics.scm (r-rhtslib): Update to 1.22.0.
 2020-12-09 12:12:41 +01:00
zimoun
b0d85e36f1
gnu: r-zlibbioc: Update to 1.36.0. 
* gnu/packages/bioinformatics.scm (r-zlibbioc): Update to 1.36.0.
 2020-12-09 12:12:40 +01:00
zimoun
329879b70c
gnu: r-seqlogo: Update to 1.56.0. 
* gnu/packages/bioinformatics.scm (r-seqlogo): Update to 1.56.0.
 2020-12-09 12:12:40 +01:00
zimoun
2a70c96e3d
gnu: r-genomation: Update to 1.22.0. 
* gnu/packages/bioinformatics.scm (r-genomation): Update to 1.22.0.
 2020-12-09 12:12:40 +01:00
zimoun
44bf116f03
gnu: r-seqpattern: Update to 1.22.0. 
* gnu/packages/bioinformatics.scm (r-seqpattern): Update to 1.22.0.
 2020-12-09 12:12:40 +01:00
zimoun
a180744b37
gnu: r-impute: Update to 1.64.0. 
* gnu/packages/bioinformatics.scm (r-impute): Update to 1.64.0.
 2020-12-09 12:12:40 +01:00
zimoun
e2e11f095f
gnu: r-bsgenome: Update to 1.58.0. 
* gnu/packages/bioinformatics.scm (r-bsgenome): Update to 1.58.0.
 2020-12-09 12:12:40 +01:00
Roel Janssen
6a7de43a58
gnu: r-topgo: Update to 2.42.0. 
* gnu/packages/bioinformatics.scm (r-topgo): Update to 2.42.0.
 2020-12-09 12:12:40 +01:00