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* gnu: Use PACKAGE/INHERIT in more places.Mark H Weaver2021-03-17
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | * 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.
* gnu: hisat2: Update to 2.2.1.Ricardo Wurmus2021-03-16
| | | | | | | | | * 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.
* Revert some commits that caused `guix pull` to fail.Leo Famulari2021-03-15
| | | | | | | | | | | | | 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))
* gnu: r-delayedarray: Move to (gnu packages bioconductor).zimoun2021-03-15
| | | | | * gnu/packages/bioinformatics.scm (r-delayedarray): Move from here... * gnu/packages/bioconductor.scm (r-delayedarray): ...to here.
* gnu: r-rsamtools: Move to (gnu packages bioconductor).zimoun2021-03-15
| | | | | * gnu/packages/bioinformatics.scm (r-rsamtools): Move from here... * gnu/packages/bioconductor.scm (r-rsamtools): ...to here.
* gnu: r-biostrings: Move to (gnu packages bioconductor).zimoun2021-03-15
| | | | | * gnu/packages/bioinformatics.scm (r-biostrings): Move from here... * gnu/packages/bioconductor.scm (r-biostrings): ...to here.
* gnu: r-biocparallel: Move to (gnu packages bioconductor).zimoun2021-03-15
| | | | | * gnu/packages/bioinformatics.scm (r-biocparallel): Move from here... * gnu/packages/bioconductor.scm (r-biocparallel): ...to here.
* gnu: r-biomart: Move to (gnu packages bioconductor).zimoun2021-03-15
| | | | | * gnu/packages/bioinformatics.scm (r-biomart): Move from here... * gnu/packages/bioconductor.scm (r-biomart): ...to here.
* gnu: r-annotationdbi: Move to (gnu packages bioconductor).zimoun2021-03-15
| | | | | * gnu/packages/bioinformatics.scm (r-annotationdbi): Move from here... * gnu/packages/bioconductor.scm (r-annotationdbi): ...to here.
* gnu: r-biobase: Move to (gnu packages bioconductor).zimoun2021-03-15
| | | | | * gnu/packages/bioinformatics.scm (r-biobase): Move from here... * gnu/packages/bioconductor.scm (r-biobase): ...to here.
* gnu: r-genomicranges: Move to (gnu packages bioconductor).zimoun2021-03-15
| | | | | * gnu/packages/bioinformatics.scm (r-genomicranges): Move from here... * gnu/packages/bioconductor.scm (r-genomicranges): ...to here.
* gnu: r-xvector: Move to (gnu packages bioconductor).zimoun2021-03-15
| | | | | * gnu/packages/bioinformatics.scm (r-xvector): Move from here... * gnu/packages/bioconductor.scm (r-xvector): ...to here.
* gnu: r-limma: Move to (gnu packages bioconductor).zimoun2021-03-15
| | | | | * gnu/packages/bioinformatics.scm (r-limma): Move from here... * gnu/packages/bioconductor.scm (r-limma): ...to here.
* gnu: r-genomicfeatures: Update to 1.42.2.Ricardo Wurmus2021-03-15
| | | | * gnu/packages/bioinformatics.scm (r-genomicfeatures): Update to 1.42.2.
* gnu: r-delayedarray: Update to 0.16.2.Ricardo Wurmus2021-03-15
| | | | * gnu/packages/bioinformatics.scm (r-delayedarray): Update to 0.16.2.
* gnu: r-variantannotation: Move to (gnu packages bioconductor).zimoun2021-03-15
| | | | | * gnu/packages/bioinformatics.scm (r-variantannotation): Move from here... * gnu/packages/bioconductor.scm (r-variantannotation): ...to here.
* gnu: r-edger: Move to (gnu packages bioconductor).zimoun2021-03-15
| | | | | * gnu/packages/bioinformatics.scm (r-edger): Move from here... * gnu/packages/bioconductor.scm (r-edger): ...to here.
* gnu: r-genomeinfodb: Move to (gnu packages bioconductor).zimoun2021-03-15
| | | | | * gnu/packages/bioinformatics.scm (r-genomeinfodb): Move from here... * gnu/packages/bioconductor.scm (r-genomeinfodb): ...to here.
* gnu: r-genomeinfodbdata: Move to (gnu packages bioconductor).zimoun2021-03-15
| | | | | | * gnu/packages/bioinformatics.scm (r-genomeinfodbdata): Move from here... * gnu/packages/bioconductor.scm (r-genomeinfodbdata): ...to here. [source]: Use 'bioconductor-uri'.
* gnu: r-iranges: Move to (gnu packages bioconductor).zimoun2021-03-15
| | | | | * gnu/packages/bioinformatics.scm (r-iranges): Move from here... * gnu/packages/bioconductor.scm (r-iranges): ...to here.
* gnu: r-s4vectors: Move to (gnu packages bioconductor).zimoun2021-03-15
| | | | | * gnu/packages/bioinformatics.scm (r-s4vectors): Move from here... * gnu/packages/bioconductor.scm (r-s4vectors): ...to here.
* gnu: r-bioccheck: Move to (gnu packages bioconductor).zimoun2021-03-15
| | | | | * gnu/packages/bioinformatics.scm (r-bioccheck): Move from here... * gnu/packages/bioconductor.scm (r-bioccheck): ...to here.
* gnu: r-grohmm: Move to (gnu packages bioconductor).zimoun2021-03-15
| | | | | * gnu/packages/bioinformatics.scm (r-grohmm): Move from here... * gnu/packages/bioconductor.scm (r-grohmm): ...to here.
* gnu: r-biocstyle: Move to (gnu packages bioconductor).zimoun2021-03-15
| | | | | * gnu/packages/bioinformatics.scm (r-biocstyle): Move from here... * gnu/packages/bioconductor.scm (r-biocstyle): ...to here.
* gnu: r-biocviews: Move to (gnu packages bioconductor).zimoun2021-03-15
| | | | | * gnu/packages/bioinformatics.scm (r-biocviews): Move from here... * gnu/packages/bioconductor.scm (r-biocviews): ...to here.
* gnu: Add instrain.Ricardo Wurmus2021-03-15
| | | | * gnu/packages/bioinformatics.scm (instrain): New variable.
* gnu: Add python-drep.Ricardo Wurmus2021-03-15
| | | | * gnu/packages/bioinformatics.scm (python-drep): New variable.
* gnu: r-systempiper: Move to (gnu packages bioconductor).zimoun2021-03-12
| | | | | * gnu/packages/bioinformatics.scm (r-systempiper): Move from here... * gnu/packages/bioconductor.scm (r-systempiper): ...to here.
* gnu: r-shortread: Move to (gnu packages bioconductor).zimoun2021-03-12
| | | | | * gnu/packages/bioinformatics.scm (r-shortread): Move from here... * gnu/packages/bioconductor.scm (r-shortread): ...to here.
* gnu: r-gostats: Move to (gnu packages bioconductor).zimoun2021-03-12
| | | | | * gnu/packages/bioinformatics.scm (r-gostats): Move from here... * gnu/packages/bioconductor.scm (r-gostats): ...to here.
* gnu: r-category: Move to (gnu packages bioconductor).zimoun2021-03-12
| | | | | * gnu/packages/bioinformatics.scm (r-category): Move from here... * gnu/packages/bioconductor.scm (r-category): ...to here.
* gnu: r-gseabase: Move to (gnu packages bioconductor).zimoun2021-03-12
| | | | | * gnu/packages/bioinformatics.scm (r-gseabase): Move from here... * gnu/packages/bioconductor.scm (r-gseabase): ...to here.
* gnu: r-rbgl: Move to (gnu packages bioconductor).zimoun2021-03-12
| | | | | * gnu/packages/bioinformatics.scm (r-rbgl): Move from here... * gnu/packages/bioconductor.scm (r-rbgl): ...to here.
* gnu: r-annotationforge: Move to (gnu packages bioconductor).zimoun2021-03-12
| | | | | * gnu/packages/bioinformatics.scm (r-annotationforge): Move from here... * gnu/packages/bioconductor.scm (r-annotationforge): ...to here.
* gnu: r-dexseq: Move to (gnu packages bioconductor).zimoun2021-03-12
| | | | | * gnu/packages/bioinformatics.scm (r-dexseq): Move from here... * gnu/packages/bioconductor.scm (r-dexseq): ...to here.
* gnu: r-deseq2: Move to (gnu packages bioconductor).zimoun2021-03-12
| | | | | * gnu/packages/bioinformatics.scm (r-deseq2): Move from here... * gnu/packages/bioconductor.scm (r-deseq2): ...to here.
* gnu: r-genefilter: Move to (gnu packages bioconductor).zimoun2021-03-12
| | | | | * gnu/packages/bioinformatics.scm (r-genefilter): Move from here... * gnu/packages/bioconductor.scm (r-genefilter): ...to here.
* gnu: Add bandage.Efraim Flashner2021-03-11
| | | | * gnu/packages/bioinformatics.scm (bandage): New variable.
* gnu: trim-galore: Update to 0.6.6.Ricardo Wurmus2021-03-09
| | | | * gnu/packages/bioinformatics.scm (trim-galore): Update to 0.6.6.
* gnu: bbmap: Update to 38.90.Ricardo Wurmus2021-03-09
| | | | * gnu/packages/bioinformatics.scm (bbmap): Update to 38.90.
* gnu: seqan-1: Use HTTPS source URI.Nicolas Goaziou2021-03-06
| | | | * gnu/packages/bioinformatics.scm (seqan-1)[source]: Use HTTPS URI.
* gnu: seqan: Use HTTPS home page URI.Nicolas Goaziou2021-03-06
| | | | * gnu/packages/bioinformatics.scm (seqan)[home-page]: Use HTTPS URI.
* gnu: Add r-cellchat.Ricardo Wurmus2021-03-05
| | | | * gnu/packages/bioinformatics.scm (r-cellchat): New variable.
* gnu: infernal: Update to 1.1.4.Tim Howes2021-03-03
| | | | | | * gnu/packages/bioinformatics.scm (infernal): Update to 1.1.4. Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
* gnu: hmmer: Update to 3.3.2.Tim Howes2021-03-03
| | | | | | * gnu/packages/bioinformatics.scm (hmmer): Update to 3.3.2. Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
* gnu: kallisto: Update to 0.46.2.Ricardo Wurmus2021-03-02
| | | | | * gnu/packages/bioinformatics.scm (kallisto): Update to 0.46.2. [source]: Remove bundled htslib sources.
* gnu: kallisto: Use older htslib.Ricardo Wurmus2021-03-02
| | | | | * gnu/packages/bioinformatics.scm (kallisto)[inputs]: Use htslib-1.9 instead of the latest.
* gnu: f-seq: Use HTTPS home page URI.Nicolas Goaziou2021-02-28
| | | | * gnu/packages/bioinformatics.scm (f-seq)[home-page]: Use HTTPS URI.
* gnu: Add star-for-pigx.Ricardo Wurmus2021-02-23
| | | | | | | This is a follow-up to commit f1f6e49190a11f926af3bef0d45541cabf47c742. * gnu/packages/bioinformatics.scm (star-for-pigx): New variable. (pigx-rnaseq, pigx-scrnaseq)[inputs]: Replace star with star-for-pigx.
* gnu: star: Update to 2.7.8a.Ricardo Wurmus2021-02-22
| | | | * gnu/packages/bioinformatics.scm (star): Update to 2.7.8a.
generated by cgit v1.2.3 (git 2.45.0) at 2025-01-18 05:47:17 +0000