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.
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* 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.
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* 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[arguments]: Remove outdated substitutions; simplify check phase.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).
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* 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.
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* 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.
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* 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.
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* 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.
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* 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.
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* 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.
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* 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.
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* gnu/packages/bioinformatics.scm (lofreq): New variable.
2021-04-28 17:41:47 +02:00
Ricardo Wurmus
f01b3cd063
gnu: kraken2: Replace references to rsync.
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* 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.
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* 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.
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* 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.
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* gnu/packages/bioinformatics.scm (shorah): New variable.
2021-04-23 15:53:51 +02:00
Ricardo Wurmus
c9371b698d
gnu: Add r-shinycell.
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* gnu/packages/bioinformatics.scm (r-shinycell): New variable.
2021-04-23 15:53:51 +02:00
Ricardo Wurmus
92032d8081
gnu: Add kraken2.
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* 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.
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* 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.
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* 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.
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* 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.
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* 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.
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* 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."
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This reverts commit 8ec0ca8faf
2021-03-31 21:23:45 +02:00
Efraim Flashner
04ba7a196a
gnu: plink-ng: Build prettify binary.
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* 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.
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* 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.
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* 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.
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* 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.
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* 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.
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* 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.
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* 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.
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This reverts commits 821e6439218f9fd9b70c
2021-03-15 19:52:34 -04:00
zimoun
d99a18252c
gnu: r-delayedarray: Move to (gnu packages bioconductor).
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* 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).
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* 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).
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* 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.
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* 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.
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* 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
