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2019-01-15gnu: Move Python compression packages to new module.Ricardo Wurmus
* 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.
2019-01-15gnu: Separate Python core packages from the rest.Ricardo Wurmus
* 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.
2019-01-13gnu: r-biocgenerics: Move to bioconductor.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-biocgenerics): Move from here... * gnu/packages/bioconductor.scm (r-biocgenerics): ...to here.
2019-01-13gnu: r-annotate: Move to bioconductor.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-annotate): Move from here... * gnu/packages/bioconductor.scm (r-annotate): ...to here.
2019-01-13gnu: r-vegan: Move from bioinformatics to cran.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-vegan): Move from here... * gnu/packages/cran.scm (r-vegan): ...to here.
2019-01-12gnu: r-rtracklayer: Update to 1.42.1.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-rtracklayer): Update to 1.42.1.
2019-01-12gnu: r-scater: Update to 1.10.1.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-scater): Update to 1.10.1.
2019-01-12gnu: r-singlecellexperiment: Update to 1.4.1.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-singlecellexperiment): Update to 1.4.1.
2019-01-12gnu: r-rhdf5lib: Update to 1.4.2.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-rhdf5lib): Update to 1.4.2.
2019-01-12gnu: r-hdf5array: Update to 1.10.1.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-hdf5array): Update to 1.10.1.
2019-01-12gnu: r-qvalue: Update to 2.14.1.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-qvalue): Update to 2.14.1.
2019-01-12gnu: r-gviz: Update to 1.26.4.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-gviz): Update to 1.26.4.
2019-01-12gnu: r-biovizbase: Update to 1.30.1.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-biovizbase): Update to 1.30.1.
2019-01-12gnu: r-ensembldb: Update to 2.6.3.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-ensembldb): Update to 2.6.3.
2019-01-12gnu: r-dirichletmultinomial: Update to 1.24.1.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-dirichletmultinomial): Update to 1.24.1.
2019-01-12gnu: r-gage: Update to 2.32.1.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-gage): Update to 2.32.1.
2019-01-12gnu: r-annotationhub: Update to 2.14.2.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-annotationhub): Update to 2.14.2.
2019-01-12gnu: r-edaseq: Update to 2.16.3.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-edaseq): Update to 2.16.3. [propagated-inputs]: Add r-biocmanager.
2019-01-12gnu: r-deseq: Update to 1.34.1.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-deseq): Update to 1.34.1.
2019-01-12gnu: r-msnid: Update to 1.16.1.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-msnid): Update to 1.16.1.
2019-01-12gnu: r-msnbase: Update to 2.8.3.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-msnbase): Update to 2.8.3.
2019-01-12gnu: r-mzid: Update to 1.20.1.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-mzid): Update to 1.20.1.
2019-01-12gnu: r-mzr: Update to 2.16.1.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-mzr): Update to 2.16.1.
2019-01-12gnu: r-sva: Update to 3.30.1.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-sva): Update to 3.30.1.
2019-01-12gnu: r-methylkit: Update to 1.8.1.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-methylkit): Update to 1.8.1.
2019-01-12gnu: r-copywriter: Update to 2.14.1.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-copywriter): Update to 2.14.1.
2019-01-12gnu: r-rhdf5: Update to 2.26.2.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-rhdf5): Update to 2.26.2.
2019-01-12gnu: r-tximport: Update to 1.10.1.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-tximport): Update to 1.10.1.
2019-01-12gnu: r-genomicalignments: Update to 1.18.1.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-genomicalignments): Update to 1.18.1.
2019-01-12gnu: r-biostrings: Update to 2.50.2.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-biostrings): Update to 2.50.2.
2019-01-12gnu: r-biocparallel: Update to 1.16.5.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-biocparallel): Update to 1.16.5.
2019-01-12gnu: r-limma: Update to 3.38.3.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-limma): Update to 3.38.3.
2019-01-12gnu: r-variantannotation: Update to 1.28.8.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-variantannotation): Update to 1.28.8.
2019-01-12gnu: r-edger: Update to 3.24.3.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-edger): Update to 3.24.3.
2019-01-12gnu: r-biocviews: Update to 1.50.10.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-biocviews): Update to 1.50.10.
2019-01-12gnu: r-systempiper: Update to 1.16.1.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-systempiper): Update to 1.16.1.
2019-01-12gnu: r-rbgl: Update to 1.58.1.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-rbgl): Update to 1.58.1.
2019-01-12gnu: r-dexseq: Update to 1.28.1.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-dexseq): Update to 1.28.1.
2019-01-12gnu: r-deseq2: Update to 1.22.2.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-deseq2): Update to 1.22.2.
2019-01-12gnu: r-scran: Update to 1.10.2.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-scran): Update to 1.10.2.
2019-01-12gnu: r-seqminer: Update to 7.1.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-seqminer): Update to 7.1.
2019-01-12gnu: r-bookdown: Update to 0.9.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-bookdown): Update to 0.9.
2019-01-12gnu: Move Java compression packages to new module.Ricardo Wurmus
* 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.
2019-01-11gnu: jamm: Remove broken "build" phase.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (jamm)[arguments]: Remove "build" phase.
2019-01-07gnu: mantis: Limit to x86_64-linux.Efraim Flashner
* gnu/packages/bioinformatics.scm (mantis)[supported-systems]: New field.
2019-01-07gnu: Add mantis.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (mantis): New variable.
2018-12-20gnu: discrover: Comment on attempt of minimal texlive-union.Pierre Neidhardt
* gnu/packages/bioinformatics.scm (discrover): Comment on attempt of minimal texlive-union.
2018-12-17gnu: gess: Don't hardcode python version.Efraim Flashner
* gnu/packages/bioinformatics.scm (gess)[arguments]: Replace hardcoded python version with parameterized one.
2018-12-05gnu: mash: Use C++ 14.Christopher Baines
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.
2018-12-04gnu: pigx-rnaseq: Update to 0.0.5.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (pigx-rnaseq): Update to 0.0.5. [inputs]: Replace snakemake-4 with snakemake.
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