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2021-05-07gnu: Add ensembl-vep....* gnu/packages/bioinformatics.scm (ensembl-vep): New variable. Ricardo Wurmus
2021-05-06gnu: Add perl-bio-db-hts....* gnu/packages/bioinformatics.scm (perl-bio-db-hts): New variable. Ricardo Wurmus
2021-05-05gnu: 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 [arguments]: Remove outdated substitutions; simplify check phase.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
2021-05-04gnu: 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
2021-05-04gnu: r-ensembldb: Update to 2.14.1....* gnu/packages/bioinformatics.scm (r-ensembldb): Update to 2.14.1. Ricardo Wurmus
2021-05-04gnu: r-gage: Update to 2.40.2....* gnu/packages/bioinformatics.scm (r-gage): Update to 2.40.2. Ricardo Wurmus
2021-05-04gnu: r-annotationhub: Update to 2.22.1....* gnu/packages/bioinformatics.scm (r-annotationhub): Update to 2.22.1. Ricardo Wurmus
2021-04-30gnu: Add pbgzip....* gnu/packages/bioinformatics.scm (pbgzip): New variable. Roel Janssen
2021-04-29gnu: Update bedtools to 2.30.0....* gnu/packages/bioinformatics.scm (bedtools): Update to 2.30.0, [inputs]: Use latest samtools. Roel Janssen
2021-04-29gnu: Update samtools to 1.12....* gnu/packages/bioinformatics.scm (samtools): Update to 1.12. Roel Janssen
2021-04-29gnu: Update bcftools to 1.12....* gnu/packages/bioinformatics.scm (bcftools): Update to 1.12. Roel Janssen
2021-04-29gnu: htslib: Update to 1.12....* gnu/packages/bioinformatics.scm (htslib): Update to 1.12. Roel Janssen
2021-04-28gnu: 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
2021-04-28gnu: Add lofreq....* gnu/packages/bioinformatics.scm (lofreq): New variable. Ricardo Wurmus
2021-04-28gnu: 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
2021-04-28gnu: Add python-pyliftover....* gnu/packages/bioinformatics.scm (python-pyliftover): New variable. Ricardo Wurmus
2021-04-25gnu: 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
2021-04-23gnu: Add shorah....* gnu/packages/bioinformatics.scm (shorah): New variable. Ricardo Wurmus
2021-04-23gnu: Add r-shinycell....* gnu/packages/bioinformatics.scm (r-shinycell): New variable. Ricardo Wurmus
2021-04-22gnu: Add kraken2....* gnu/packages/bioinformatics.scm (kraken2): New variable. Ricardo Wurmus
2021-04-16gnu: Update blast+ to 2.11.0....* gnu/packages/bioinformatics.scm (blast+): Update to 2.11.0. Roel Janssen
2021-04-14gnu: 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
2021-04-14gnu: 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
2021-04-10gnu: sortmerna: Mark up description....* gnu/packages/bioinformatics.scm (sortmerna)[description]: Use @acronym{}. Tobias Geerinckx-Rice
2021-04-08gnu: r-genomicfeatures: Update to 1.42.3....* gnu/packages/bioinformatics.scm (r-genomicfeatures): Update to 1.42.3. Ricardo Wurmus
2021-03-31Revert "Revert some commits that caused `guix pull` to fail."...This reverts commit 8ec0ca8faff62f19426f22aeb1bd59a8950ca05a. zimoun
2021-03-31gnu: plink-ng: Build prettify binary....* gnu/packages/bioinformatics.scm (plink-ng)[arguments]: Adjust make-flags to also build prettify. Efraim Flashner
2021-03-31gnu: plink-ng: Remove custom install phase....* gnu/packages/bioinformatics.scm (plink-ng)[arguments]: Adjust make-flags and remove custom 'install phase. Efraim Flashner
2021-03-31gnu: plink-ng: Sort inputs alphabetically....* gnu/packages/bioinformatics.scm (plink-ng)[inputs]: Sort alphabetically. Efraim Flashner
2021-03-31gnu: plink-ng: Update to 2.00a2.3....* gnu/packages/bioinformatics.scm (plink-ng): Update to 2.00a2.3. [arguments]: Adjust make-flags. Efraim Flashner
2021-03-22gnu: Add r-signac....* gnu/packages/bioinformatics.scm (r-signac): New variable. Co-authored-by: Ricardo Wurmus <rekado@elephly.net> Hong Li
2021-03-17gnu: 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
2021-03-16gnu: 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
2021-03-15Revert 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
2021-03-15gnu: 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
2021-03-15gnu: 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
2021-03-15gnu: 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
2021-03-15gnu: 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
2021-03-15gnu: r-biomart: Move to (gnu packages bioconductor)....* gnu/packages/bioinformatics.scm (r-biomart): Move from here... * gnu/packages/bioconductor.scm (r-biomart): ...to here. zimoun
2021-03-15gnu: r-annotationdbi: Move to (gnu packages bioconductor)....* gnu/packages/bioinformatics.scm (r-annotationdbi): Move from here... * gnu/packages/bioconductor.scm (r-annotationdbi): ...to here. zimoun
2021-03-15gnu: r-biobase: Move to (gnu packages bioconductor)....* gnu/packages/bioinformatics.scm (r-biobase): Move from here... * gnu/packages/bioconductor.scm (r-biobase): ...to here. zimoun
2021-03-15gnu: r-genomicranges: Move to (gnu packages bioconductor)....* gnu/packages/bioinformatics.scm (r-genomicranges): Move from here... * gnu/packages/bioconductor.scm (r-genomicranges): ...to here. zimoun
2021-03-15gnu: r-xvector: Move to (gnu packages bioconductor)....* gnu/packages/bioinformatics.scm (r-xvector): Move from here... * gnu/packages/bioconductor.scm (r-xvector): ...to here. zimoun
2021-03-15gnu: r-limma: Move to (gnu packages bioconductor)....* gnu/packages/bioinformatics.scm (r-limma): Move from here... * gnu/packages/bioconductor.scm (r-limma): ...to here. zimoun
2021-03-15gnu: r-genomicfeatures: Update to 1.42.2....* gnu/packages/bioinformatics.scm (r-genomicfeatures): Update to 1.42.2. Ricardo Wurmus
2021-03-15gnu: r-delayedarray: Update to 0.16.2....* gnu/packages/bioinformatics.scm (r-delayedarray): Update to 0.16.2. Ricardo Wurmus
2021-03-15gnu: r-variantannotation: Move to (gnu packages bioconductor)....* gnu/packages/bioinformatics.scm (r-variantannotation): Move from here... * gnu/packages/bioconductor.scm (r-variantannotation): ...to here. zimoun
2021-03-15gnu: r-edger: Move to (gnu packages bioconductor)....* gnu/packages/bioinformatics.scm (r-edger): Move from here... * gnu/packages/bioconductor.scm (r-edger): ...to here. zimoun
2021-03-15gnu: r-genomeinfodb: Move to (gnu packages bioconductor)....* gnu/packages/bioinformatics.scm (r-genomeinfodb): Move from here... * gnu/packages/bioconductor.scm (r-genomeinfodb): ...to here. zimoun
2021-03-15gnu: 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'. zimoun
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