| Age | Commit message (Expand) | Author |
|---|
| 2021-05-29 | gnu: Add mosaicatcher....* gnu/packages/patches/mosaicatcher-unbundle-htslib.patch: New file.
* gnu/local.mk (dist_patch_DATA): Add it.
* gnu/packages/bioinformatics.scm (mosaicatcher): New variable.
| Ricardo Wurmus |
| 2021-05-29 | Revert "gnu: Add mosaicatcher."...mosaicatcher-unbundle-htslib.patch is missing.
This reverts commit b1ae0f30d856503fa311d380584a6d7c80559332.
| Christopher Baines |
| 2021-05-28 | gnu: Add mosaicatcher....* gnu/packages/bioinformatics.scm (mosaicatcher): New variable.
| Ricardo Wurmus |
| 2021-05-27 | gnu: Add python-pyega3....* gnu/packages/bioinformatics.scm (python-pyega3): New variable.
| Roel Janssen |
| 2021-05-27 | gnu: Add python-htsget....* gnu/packages/bioinformatics.scm (python-htsget): New variable.
| Roel Janssen |
| 2021-05-26 | 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.
| Efraim Flashner |
| 2021-05-26 | 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.
| Efraim Flashner |
| 2021-05-26 | gnu: Add r-phantompeakqualtools....* gnu/packages/bioinformatics.scm (r-phantompeakqualtools): New variable.
| Roel Janssen |
| 2021-05-26 | gnu: Add r-spp....* gnu/packages/bioinformatics.scm (r-spp): New variable.
| Roel Janssen |
| 2021-05-20 | gnu: r-rhdf5filters: Update to 1.2.1....* gnu/packages/bioinformatics.scm (r-rhdf5filters): Update to 1.2.1.
| Ricardo Wurmus |
| 2021-05-17 | gnu: pigx-chipseq: Update to 0.0.52....* gnu/packages/bioinformatics.scm (pigx-chipseq): Update to 0.0.52.
| Ricardo Wurmus |
| 2021-05-14 | gnu: prinseq: Fix references to perl executable....* gnu/packages/bioinformatics.scm (prinseq)[arguments]: Embed concrete
references to the "perl" executable.
| Ricardo Wurmus |
| 2021-05-07 | gnu: Add ensembl-vep....* gnu/packages/bioinformatics.scm (ensembl-vep): New variable.
| Ricardo Wurmus |
| 2021-05-06 | gnu: Add perl-bio-db-hts....* gnu/packages/bioinformatics.scm (perl-bio-db-hts): New variable.
| Ricardo Wurmus |
| 2021-05-05 | 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[arguments]: Remove outdated substitutions; simplify check phase.
| Ricardo Wurmus |
| 2021-05-04 | 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.
| Ricardo Wurmus |
| 2021-05-04 | gnu: r-ensembldb: Update to 2.14.1....* gnu/packages/bioinformatics.scm (r-ensembldb): Update to 2.14.1.
| Ricardo Wurmus |
| 2021-05-04 | gnu: r-gage: Update to 2.40.2....* gnu/packages/bioinformatics.scm (r-gage): Update to 2.40.2.
| Ricardo Wurmus |
| 2021-05-04 | gnu: r-annotationhub: Update to 2.22.1....* gnu/packages/bioinformatics.scm (r-annotationhub): Update to 2.22.1.
| Ricardo Wurmus |
| 2021-04-30 | gnu: Add pbgzip....* gnu/packages/bioinformatics.scm (pbgzip): New variable.
| Roel Janssen |
| 2021-04-29 | gnu: Update bedtools to 2.30.0....* gnu/packages/bioinformatics.scm (bedtools): Update to 2.30.0,
[inputs]: Use latest samtools.
| Roel Janssen |
| 2021-04-29 | gnu: Update samtools to 1.12....* gnu/packages/bioinformatics.scm (samtools): Update to 1.12.
| Roel Janssen |
| 2021-04-29 | gnu: Update bcftools to 1.12....* gnu/packages/bioinformatics.scm (bcftools): Update to 1.12.
| Roel Janssen |
| 2021-04-29 | gnu: htslib: Update to 1.12....* gnu/packages/bioinformatics.scm (htslib): Update to 1.12.
| Roel Janssen |
| 2021-04-28 | 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.
| Ricardo Wurmus |
| 2021-04-28 | gnu: Add lofreq....* gnu/packages/bioinformatics.scm (lofreq): New variable.
| Ricardo Wurmus |
| 2021-04-28 | 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".
| Ricardo Wurmus |
| 2021-04-28 | gnu: Add python-pyliftover....* gnu/packages/bioinformatics.scm (python-pyliftover): New variable.
| Ricardo Wurmus |
| 2021-04-25 | 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>
| Vinicius Monego |
| 2021-04-23 | gnu: Add shorah....* gnu/packages/bioinformatics.scm (shorah): New variable.
| Ricardo Wurmus |
| 2021-04-23 | gnu: Add r-shinycell....* gnu/packages/bioinformatics.scm (r-shinycell): New variable.
| Ricardo Wurmus |
| 2021-04-22 | gnu: Add kraken2....* gnu/packages/bioinformatics.scm (kraken2): New variable.
| Ricardo Wurmus |
| 2021-04-16 | gnu: Update blast+ to 2.11.0....* gnu/packages/bioinformatics.scm (blast+): Update to 2.11.0.
| Roel Janssen |
| 2021-04-14 | 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.
| Arun Isaac |
| 2021-04-14 | 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.
| Arun Isaac |
| 2021-04-10 | gnu: sortmerna: Mark up description....* gnu/packages/bioinformatics.scm (sortmerna)[description]: Use @acronym{}.
| Tobias Geerinckx-Rice |
| 2021-04-08 | gnu: r-genomicfeatures: Update to 1.42.3....* gnu/packages/bioinformatics.scm (r-genomicfeatures): Update to 1.42.3.
| Ricardo Wurmus |
| 2021-03-31 | Revert "Revert some commits that caused `guix pull` to fail."...This reverts commit 8ec0ca8faff62f19426f22aeb1bd59a8950ca05a.
| zimoun |
| 2021-03-31 | gnu: plink-ng: Build prettify binary....* gnu/packages/bioinformatics.scm (plink-ng)[arguments]: Adjust
make-flags to also build prettify.
| Efraim Flashner |
| 2021-03-31 | gnu: plink-ng: Remove custom install phase....* gnu/packages/bioinformatics.scm (plink-ng)[arguments]: Adjust
make-flags and remove custom 'install phase.
| Efraim Flashner |
| 2021-03-31 | gnu: plink-ng: Sort inputs alphabetically....* gnu/packages/bioinformatics.scm (plink-ng)[inputs]: Sort
alphabetically.
| Efraim Flashner |
| 2021-03-31 | gnu: plink-ng: Update to 2.00a2.3....* gnu/packages/bioinformatics.scm (plink-ng): Update to 2.00a2.3.
[arguments]: Adjust make-flags.
| Efraim Flashner |
| 2021-03-22 | gnu: Add r-signac....* gnu/packages/bioinformatics.scm (r-signac): New variable.
Co-authored-by: Ricardo Wurmus <rekado@elephly.net>
| Hong Li |
| 2021-03-17 | 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.
| Mark H Weaver |
| 2021-03-16 | 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.
| Ricardo Wurmus |
| 2021-03-15 | Revert some commits that caused `guix pull` to fail....This reverts commits 821e6439212f8e94580674eaaff2ce6752cd3b18 through
8f9fd9b70c7bf166d96a4b1dc8b427f8cdf040b5.
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))
| Leo Famulari |
| 2021-03-15 | 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.
| zimoun |
| 2021-03-15 | 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.
| zimoun |
| 2021-03-15 | 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.
| zimoun |
| 2021-03-15 | 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.
| zimoun |
