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* gnu: Move Python compression packages to new module.Ricardo Wurmus2019-01-15
| | | | | | | | | | | * gnu/packages/compression.scm (python-lzo, python2-lzo, python-lz4, python2-lz4, python-lzstring, python2-lzstring, bitshuffle, bitshuffle-for-snappy): Move variables from here... * gnu/packages/python-compression.scm: ...to this new module. * gnu/local.mk (GNU_SYSTEM_MODULES): Add it. * gnu/packages/bioinformatics.scm, gnu/packages/java-compression.scm, gnu/packages/xorg.scm: Adjust module references.
* gnu: Separate Python core packages from the rest.Ricardo Wurmus2019-01-15
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | * gnu/packages/python.scm: Move hundreds of package definitions from here... * gnu/packages/python-xyz.scm: ...to this new module. * gnu/local.mk (GNU_SYSTEM_MODULES): Add it. * gnu/packages/ada.scm, gnu/packages/admin.scm, gnu/packages/android.scm, gnu/packages/audio.scm, gnu/packages/backup.scm, gnu/packages/benchmark.scm, gnu/packages/bioinformatics.scm, gnu/packages/bittorrent.scm, gnu/packages/calendar.scm, gnu/packages/check.scm, gnu/packages/chemistry.scm, gnu/packages/cluster.scm, gnu/packages/compression.scm, gnu/packages/connman.scm, gnu/packages/crypto.scm, gnu/packages/cups.scm, gnu/packages/databases.scm, gnu/packages/dav.scm, gnu/packages/direct-connect.scm, gnu/packages/disk.scm, gnu/packages/django.scm, gnu/packages/dlang.scm, gnu/packages/docker.scm, gnu/packages/ebook.scm, gnu/packages/elf.scm, gnu/packages/emacs.scm, gnu/packages/emulators.scm, gnu/packages/engineering.scm, gnu/packages/enlightenment.scm, gnu/packages/finance.scm, gnu/packages/fltk.scm, gnu/packages/fontutils.scm, gnu/packages/freedesktop.scm, gnu/packages/game-development.scm, gnu/packages/games.scm, gnu/packages/geo.scm, gnu/packages/gl.scm, gnu/packages/glib.scm, gnu/packages/gnome.scm, gnu/packages/gnupg.scm, gnu/packages/gnuzilla.scm, gnu/packages/graph.scm, gnu/packages/graphics.scm, gnu/packages/graphviz.scm, gnu/packages/gtk.scm, gnu/packages/ham-radio.scm, gnu/packages/image-processing.scm, gnu/packages/image-viewers.scm, gnu/packages/image.scm, gnu/packages/irc.scm, gnu/packages/jrnl.scm, gnu/packages/julia.scm, gnu/packages/kde-frameworks.scm, gnu/packages/key-mon.scm, gnu/packages/libffi.scm, gnu/packages/libreoffice.scm, gnu/packages/libusb.scm, gnu/packages/lirc.scm, gnu/packages/logging.scm, gnu/packages/machine-learning.scm, gnu/packages/mail.scm, gnu/packages/mate.scm, gnu/packages/maths.scm, gnu/packages/medical.scm, gnu/packages/messaging.scm, gnu/packages/monitoring.scm, gnu/packages/mp3.scm, gnu/packages/mpd.scm, gnu/packages/music.scm, gnu/packages/networking.scm, gnu/packages/nutrition.scm, gnu/packages/openldap.scm, gnu/packages/openstack.scm, gnu/packages/package-management.scm, gnu/packages/password-utils.scm, gnu/packages/patchutils.scm, gnu/packages/pdf.scm, gnu/packages/photo.scm, gnu/packages/polkit.scm, gnu/packages/protobuf.scm, gnu/packages/python-crypto.scm, gnu/packages/python-web.scm, gnu/packages/qt.scm, gnu/packages/rdf.scm, gnu/packages/ruby.scm, gnu/packages/search.scm, gnu/packages/selinux.scm, gnu/packages/serialization.scm, gnu/packages/shells.scm, gnu/packages/simulation.scm, gnu/packages/ssh.scm, gnu/packages/statistics.scm, gnu/packages/storage.scm, gnu/packages/sync.scm, gnu/packages/terminals.scm, gnu/packages/textutils.scm, gnu/packages/time.scm, gnu/packages/tls.scm, gnu/packages/tor.scm, gnu/packages/tryton.scm, gnu/packages/version-control.scm, gnu/packages/video.scm, gnu/packages/virtualization.scm, gnu/packages/vpn.scm, gnu/packages/web-browsers.scm, gnu/packages/web.scm, gnu/packages/wicd.scm, gnu/packages/xdisorg.scm, gnu/packages/xorg.scm: Update module references.
* gnu: r-biocgenerics: Move to bioconductor.Ricardo Wurmus2019-01-13
| | | | | * gnu/packages/bioinformatics.scm (r-biocgenerics): Move from here... * gnu/packages/bioconductor.scm (r-biocgenerics): ...to here.
* gnu: r-annotate: Move to bioconductor.Ricardo Wurmus2019-01-13
| | | | | * gnu/packages/bioinformatics.scm (r-annotate): Move from here... * gnu/packages/bioconductor.scm (r-annotate): ...to here.
* gnu: r-vegan: Move from bioinformatics to cran.Ricardo Wurmus2019-01-13
| | | | | * gnu/packages/bioinformatics.scm (r-vegan): Move from here... * gnu/packages/cran.scm (r-vegan): ...to here.
* gnu: r-rtracklayer: Update to 1.42.1.Ricardo Wurmus2019-01-12
| | | | * gnu/packages/bioinformatics.scm (r-rtracklayer): Update to 1.42.1.
* gnu: r-scater: Update to 1.10.1.Ricardo Wurmus2019-01-12
| | | | * gnu/packages/bioinformatics.scm (r-scater): Update to 1.10.1.
* gnu: r-singlecellexperiment: Update to 1.4.1.Ricardo Wurmus2019-01-12
| | | | * gnu/packages/bioinformatics.scm (r-singlecellexperiment): Update to 1.4.1.
* gnu: r-rhdf5lib: Update to 1.4.2.Ricardo Wurmus2019-01-12
| | | | * gnu/packages/bioinformatics.scm (r-rhdf5lib): Update to 1.4.2.
* gnu: r-hdf5array: Update to 1.10.1.Ricardo Wurmus2019-01-12
| | | | * gnu/packages/bioinformatics.scm (r-hdf5array): Update to 1.10.1.
* gnu: r-qvalue: Update to 2.14.1.Ricardo Wurmus2019-01-12
| | | | * gnu/packages/bioinformatics.scm (r-qvalue): Update to 2.14.1.
* gnu: r-gviz: Update to 1.26.4.Ricardo Wurmus2019-01-12
| | | | * gnu/packages/bioinformatics.scm (r-gviz): Update to 1.26.4.
* gnu: r-biovizbase: Update to 1.30.1.Ricardo Wurmus2019-01-12
| | | | * gnu/packages/bioinformatics.scm (r-biovizbase): Update to 1.30.1.
* gnu: r-ensembldb: Update to 2.6.3.Ricardo Wurmus2019-01-12
| | | | * gnu/packages/bioinformatics.scm (r-ensembldb): Update to 2.6.3.
* gnu: r-dirichletmultinomial: Update to 1.24.1.Ricardo Wurmus2019-01-12
| | | | * gnu/packages/bioinformatics.scm (r-dirichletmultinomial): Update to 1.24.1.
* gnu: r-gage: Update to 2.32.1.Ricardo Wurmus2019-01-12
| | | | * gnu/packages/bioinformatics.scm (r-gage): Update to 2.32.1.
* gnu: r-annotationhub: Update to 2.14.2.Ricardo Wurmus2019-01-12
| | | | * gnu/packages/bioinformatics.scm (r-annotationhub): Update to 2.14.2.
* gnu: r-edaseq: Update to 2.16.3.Ricardo Wurmus2019-01-12
| | | | | * gnu/packages/bioinformatics.scm (r-edaseq): Update to 2.16.3. [propagated-inputs]: Add r-biocmanager.
* gnu: r-deseq: Update to 1.34.1.Ricardo Wurmus2019-01-12
| | | | * gnu/packages/bioinformatics.scm (r-deseq): Update to 1.34.1.
* gnu: r-msnid: Update to 1.16.1.Ricardo Wurmus2019-01-12
| | | | * gnu/packages/bioinformatics.scm (r-msnid): Update to 1.16.1.
* gnu: r-msnbase: Update to 2.8.3.Ricardo Wurmus2019-01-12
| | | | * gnu/packages/bioinformatics.scm (r-msnbase): Update to 2.8.3.
* gnu: r-mzid: Update to 1.20.1.Ricardo Wurmus2019-01-12
| | | | * gnu/packages/bioinformatics.scm (r-mzid): Update to 1.20.1.
* gnu: r-mzr: Update to 2.16.1.Ricardo Wurmus2019-01-12
| | | | * gnu/packages/bioinformatics.scm (r-mzr): Update to 2.16.1.
* gnu: r-sva: Update to 3.30.1.Ricardo Wurmus2019-01-12
| | | | * gnu/packages/bioinformatics.scm (r-sva): Update to 3.30.1.
* gnu: r-methylkit: Update to 1.8.1.Ricardo Wurmus2019-01-12
| | | | * gnu/packages/bioinformatics.scm (r-methylkit): Update to 1.8.1.
* gnu: r-copywriter: Update to 2.14.1.Ricardo Wurmus2019-01-12
| | | | * gnu/packages/bioinformatics.scm (r-copywriter): Update to 2.14.1.
* gnu: r-rhdf5: Update to 2.26.2.Ricardo Wurmus2019-01-12
| | | | * gnu/packages/bioinformatics.scm (r-rhdf5): Update to 2.26.2.
* gnu: r-tximport: Update to 1.10.1.Ricardo Wurmus2019-01-12
| | | | * gnu/packages/bioinformatics.scm (r-tximport): Update to 1.10.1.
* gnu: r-genomicalignments: Update to 1.18.1.Ricardo Wurmus2019-01-12
| | | | * gnu/packages/bioinformatics.scm (r-genomicalignments): Update to 1.18.1.
* gnu: r-biostrings: Update to 2.50.2.Ricardo Wurmus2019-01-12
| | | | * gnu/packages/bioinformatics.scm (r-biostrings): Update to 2.50.2.
* gnu: r-biocparallel: Update to 1.16.5.Ricardo Wurmus2019-01-12
| | | | * gnu/packages/bioinformatics.scm (r-biocparallel): Update to 1.16.5.
* gnu: r-limma: Update to 3.38.3.Ricardo Wurmus2019-01-12
| | | | * gnu/packages/bioinformatics.scm (r-limma): Update to 3.38.3.
* gnu: r-variantannotation: Update to 1.28.8.Ricardo Wurmus2019-01-12
| | | | * gnu/packages/bioinformatics.scm (r-variantannotation): Update to 1.28.8.
* gnu: r-edger: Update to 3.24.3.Ricardo Wurmus2019-01-12
| | | | * gnu/packages/bioinformatics.scm (r-edger): Update to 3.24.3.
* gnu: r-biocviews: Update to 1.50.10.Ricardo Wurmus2019-01-12
| | | | * gnu/packages/bioinformatics.scm (r-biocviews): Update to 1.50.10.
* gnu: r-systempiper: Update to 1.16.1.Ricardo Wurmus2019-01-12
| | | | * gnu/packages/bioinformatics.scm (r-systempiper): Update to 1.16.1.
* gnu: r-rbgl: Update to 1.58.1.Ricardo Wurmus2019-01-12
| | | | * gnu/packages/bioinformatics.scm (r-rbgl): Update to 1.58.1.
* gnu: r-dexseq: Update to 1.28.1.Ricardo Wurmus2019-01-12
| | | | * gnu/packages/bioinformatics.scm (r-dexseq): Update to 1.28.1.
* gnu: r-deseq2: Update to 1.22.2.Ricardo Wurmus2019-01-12
| | | | * gnu/packages/bioinformatics.scm (r-deseq2): Update to 1.22.2.
* gnu: r-scran: Update to 1.10.2.Ricardo Wurmus2019-01-12
| | | | * gnu/packages/bioinformatics.scm (r-scran): Update to 1.10.2.
* gnu: r-seqminer: Update to 7.1.Ricardo Wurmus2019-01-12
| | | | * gnu/packages/bioinformatics.scm (r-seqminer): Update to 7.1.
* gnu: r-bookdown: Update to 0.9.Ricardo Wurmus2019-01-12
| | | | * gnu/packages/bioinformatics.scm (r-bookdown): Update to 0.9.
* gnu: Move Java compression packages to new module.Ricardo Wurmus2019-01-12
| | | | | | | | | | * gnu/packages/compression.scm (bitshuffle-for-snappy): Export variable. (java-snappy, java-snappy-1, java-iq80-snappy, java-jbzip2, java-tukaani-xz): Move these variables from here... * gnu/packages/java-compression.scm: ...to this new file. * gnu/local.mk (GNU_SYSTEM_MODULES): Add it. * gnu/packages/java.scm, gnu/packages/bioinformatics.scm: Adjust module references.
* gnu: jamm: Remove broken "build" phase.Ricardo Wurmus2019-01-11
| | | | * gnu/packages/bioinformatics.scm (jamm)[arguments]: Remove "build" phase.
* gnu: mantis: Limit to x86_64-linux.Efraim Flashner2019-01-07
| | | | * gnu/packages/bioinformatics.scm (mantis)[supported-systems]: New field.
* gnu: Add mantis.Ricardo Wurmus2019-01-07
| | | | * gnu/packages/bioinformatics.scm (mantis): New variable.
* gnu: discrover: Comment on attempt of minimal texlive-union.Pierre Neidhardt2018-12-20
| | | | | * gnu/packages/bioinformatics.scm (discrover): Comment on attempt of minimal texlive-union.
* gnu: gess: Don't hardcode python version.Efraim Flashner2018-12-17
| | | | | * gnu/packages/bioinformatics.scm (gess)[arguments]: Replace hardcoded python version with parameterized one.
* gnu: mash: Use C++ 14.Christopher Baines2018-12-05
| | | | | | | | | | | I'm looking to upgrade capnproto, and mash fails to build with 0.7. Therefore, tweak the compilation to allow it to build with 0.7. The package also builds with the current version of capnproto. I got the idea of changing the c++ version from here [1]. 1: https://github.com/marbl/Mash/issues/98 * gnu/packages/bioinformatics.scm (mash)[arguments]: Add new use-c++14 phase.
* gnu: pigx-rnaseq: Update to 0.0.5.Ricardo Wurmus2018-12-04
| | | | | * gnu/packages/bioinformatics.scm (pigx-rnaseq): Update to 0.0.5. [inputs]: Replace snakemake-4 with snakemake.
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