Commit Graph

1726 Commits

Author SHA1 Message Date
Ricardo Wurmus
4fec042b54
gnu: Move Python compression packages to new module.
* 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.
2019-01-15 17:45:33 +01:00
Ricardo Wurmus
44d10b1f72
gnu: Separate Python core packages from the rest.
* 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.
2019-01-15 14:46:44 +01:00
Ricardo Wurmus
14bba460ab
gnu: r-biocgenerics: Move to bioconductor.
* gnu/packages/bioinformatics.scm (r-biocgenerics): Move from here...
* gnu/packages/bioconductor.scm (r-biocgenerics): ...to here.
2019-01-13 13:04:18 +01:00
Ricardo Wurmus
7097c7009d
gnu: r-annotate: Move to bioconductor.
* gnu/packages/bioinformatics.scm (r-annotate): Move from here...
* gnu/packages/bioconductor.scm (r-annotate): ...to here.
2019-01-13 13:04:18 +01:00
Ricardo Wurmus
c80fb90f4a
gnu: r-vegan: Move from bioinformatics to cran.
* gnu/packages/bioinformatics.scm (r-vegan): Move from here...
* gnu/packages/cran.scm (r-vegan): ...to here.
2019-01-13 13:04:18 +01:00
Ricardo Wurmus
c476edc2cd
gnu: r-rtracklayer: Update to 1.42.1.
* gnu/packages/bioinformatics.scm (r-rtracklayer): Update to 1.42.1.
2019-01-12 23:35:18 +01:00
Ricardo Wurmus
1e107b0960
gnu: r-scater: Update to 1.10.1.
* gnu/packages/bioinformatics.scm (r-scater): Update to 1.10.1.
2019-01-12 23:35:18 +01:00
Ricardo Wurmus
0f268bb275
gnu: r-singlecellexperiment: Update to 1.4.1.
* gnu/packages/bioinformatics.scm (r-singlecellexperiment): Update to 1.4.1.
2019-01-12 23:35:18 +01:00
Ricardo Wurmus
a0224bd4f6
gnu: r-rhdf5lib: Update to 1.4.2.
* gnu/packages/bioinformatics.scm (r-rhdf5lib): Update to 1.4.2.
2019-01-12 23:35:18 +01:00
Ricardo Wurmus
40561d0249
gnu: r-hdf5array: Update to 1.10.1.
* gnu/packages/bioinformatics.scm (r-hdf5array): Update to 1.10.1.
2019-01-12 23:35:18 +01:00
Ricardo Wurmus
ad10b3979d
gnu: r-qvalue: Update to 2.14.1.
* gnu/packages/bioinformatics.scm (r-qvalue): Update to 2.14.1.
2019-01-12 23:35:18 +01:00
Ricardo Wurmus
19cacb5a2d
gnu: r-gviz: Update to 1.26.4.
* gnu/packages/bioinformatics.scm (r-gviz): Update to 1.26.4.
2019-01-12 23:35:18 +01:00
Ricardo Wurmus
c80595935d
gnu: r-biovizbase: Update to 1.30.1.
* gnu/packages/bioinformatics.scm (r-biovizbase): Update to 1.30.1.
2019-01-12 23:35:18 +01:00
Ricardo Wurmus
27194effd7
gnu: r-ensembldb: Update to 2.6.3.
* gnu/packages/bioinformatics.scm (r-ensembldb): Update to 2.6.3.
2019-01-12 23:35:18 +01:00
Ricardo Wurmus
43931ff72f
gnu: r-dirichletmultinomial: Update to 1.24.1.
* gnu/packages/bioinformatics.scm (r-dirichletmultinomial): Update to 1.24.1.
2019-01-12 23:35:18 +01:00
Ricardo Wurmus
15d89fe9f8
gnu: r-gage: Update to 2.32.1.
* gnu/packages/bioinformatics.scm (r-gage): Update to 2.32.1.
2019-01-12 23:35:18 +01:00
Ricardo Wurmus
4615cf9f1a
gnu: r-annotationhub: Update to 2.14.2.
* gnu/packages/bioinformatics.scm (r-annotationhub): Update to 2.14.2.
2019-01-12 23:35:18 +01:00
Ricardo Wurmus
ab4a862ab8
gnu: r-edaseq: Update to 2.16.3.
* gnu/packages/bioinformatics.scm (r-edaseq): Update to 2.16.3.
[propagated-inputs]: Add r-biocmanager.
2019-01-12 23:35:18 +01:00
Ricardo Wurmus
3bdc41b352
gnu: r-deseq: Update to 1.34.1.
* gnu/packages/bioinformatics.scm (r-deseq): Update to 1.34.1.
2019-01-12 23:35:18 +01:00
Ricardo Wurmus
9abf344f8b
gnu: r-msnid: Update to 1.16.1.
* gnu/packages/bioinformatics.scm (r-msnid): Update to 1.16.1.
2019-01-12 23:35:17 +01:00
Ricardo Wurmus
880ed11e9f
gnu: r-msnbase: Update to 2.8.3.
* gnu/packages/bioinformatics.scm (r-msnbase): Update to 2.8.3.
2019-01-12 23:35:17 +01:00
Ricardo Wurmus
6451af78e1
gnu: r-mzid: Update to 1.20.1.
* gnu/packages/bioinformatics.scm (r-mzid): Update to 1.20.1.
2019-01-12 23:35:17 +01:00
Ricardo Wurmus
a4f038dc97
gnu: r-mzr: Update to 2.16.1.
* gnu/packages/bioinformatics.scm (r-mzr): Update to 2.16.1.
2019-01-12 23:35:17 +01:00
Ricardo Wurmus
46508c3a92
gnu: r-sva: Update to 3.30.1.
* gnu/packages/bioinformatics.scm (r-sva): Update to 3.30.1.
2019-01-12 23:35:17 +01:00
Ricardo Wurmus
c20426ec5c
gnu: r-methylkit: Update to 1.8.1.
* gnu/packages/bioinformatics.scm (r-methylkit): Update to 1.8.1.
2019-01-12 23:35:17 +01:00
Ricardo Wurmus
5c72ebafeb
gnu: r-copywriter: Update to 2.14.1.
* gnu/packages/bioinformatics.scm (r-copywriter): Update to 2.14.1.
2019-01-12 23:35:17 +01:00
Ricardo Wurmus
86162c767e
gnu: r-rhdf5: Update to 2.26.2.
* gnu/packages/bioinformatics.scm (r-rhdf5): Update to 2.26.2.
2019-01-12 23:35:17 +01:00
Ricardo Wurmus
4c7b9222dd
gnu: r-tximport: Update to 1.10.1.
* gnu/packages/bioinformatics.scm (r-tximport): Update to 1.10.1.
2019-01-12 23:35:17 +01:00
Ricardo Wurmus
4bfde52178
gnu: r-genomicalignments: Update to 1.18.1.
* gnu/packages/bioinformatics.scm (r-genomicalignments): Update to 1.18.1.
2019-01-12 23:35:17 +01:00
Ricardo Wurmus
1fa12b2f06
gnu: r-biostrings: Update to 2.50.2.
* gnu/packages/bioinformatics.scm (r-biostrings): Update to 2.50.2.
2019-01-12 23:35:17 +01:00
Ricardo Wurmus
d4fc834cf7
gnu: r-biocparallel: Update to 1.16.5.
* gnu/packages/bioinformatics.scm (r-biocparallel): Update to 1.16.5.
2019-01-12 23:35:17 +01:00
Ricardo Wurmus
52c977a05b
gnu: r-limma: Update to 3.38.3.
* gnu/packages/bioinformatics.scm (r-limma): Update to 3.38.3.
2019-01-12 23:35:17 +01:00
Ricardo Wurmus
3fd48846eb
gnu: r-variantannotation: Update to 1.28.8.
* gnu/packages/bioinformatics.scm (r-variantannotation): Update to 1.28.8.
2019-01-12 23:35:17 +01:00
Ricardo Wurmus
a619850930
gnu: r-edger: Update to 3.24.3.
* gnu/packages/bioinformatics.scm (r-edger): Update to 3.24.3.
2019-01-12 23:35:17 +01:00
Ricardo Wurmus
00f105fe20
gnu: r-biocviews: Update to 1.50.10.
* gnu/packages/bioinformatics.scm (r-biocviews): Update to 1.50.10.
2019-01-12 23:35:16 +01:00
Ricardo Wurmus
9c1b2b2ae0
gnu: r-systempiper: Update to 1.16.1.
* gnu/packages/bioinformatics.scm (r-systempiper): Update to 1.16.1.
2019-01-12 23:35:16 +01:00
Ricardo Wurmus
3b8c884285
gnu: r-rbgl: Update to 1.58.1.
* gnu/packages/bioinformatics.scm (r-rbgl): Update to 1.58.1.
2019-01-12 23:35:16 +01:00
Ricardo Wurmus
ffe16ef33c
gnu: r-dexseq: Update to 1.28.1.
* gnu/packages/bioinformatics.scm (r-dexseq): Update to 1.28.1.
2019-01-12 23:35:16 +01:00
Ricardo Wurmus
f7e95c50b8
gnu: r-deseq2: Update to 1.22.2.
* gnu/packages/bioinformatics.scm (r-deseq2): Update to 1.22.2.
2019-01-12 23:35:16 +01:00
Ricardo Wurmus
feb561f721
gnu: r-scran: Update to 1.10.2.
* gnu/packages/bioinformatics.scm (r-scran): Update to 1.10.2.
2019-01-12 23:35:16 +01:00
Ricardo Wurmus
80c4e75b87
gnu: r-seqminer: Update to 7.1.
* gnu/packages/bioinformatics.scm (r-seqminer): Update to 7.1.
2019-01-12 23:35:16 +01:00
Ricardo Wurmus
3bc0667f3c
gnu: r-bookdown: Update to 0.9.
* gnu/packages/bioinformatics.scm (r-bookdown): Update to 0.9.
2019-01-12 23:35:16 +01:00
Ricardo Wurmus
24155bf40d
gnu: Move Java compression packages to new module.
* 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.
2019-01-12 12:14:28 +01:00
Ricardo Wurmus
e7c6bc45ed
gnu: jamm: Remove broken "build" phase.
* gnu/packages/bioinformatics.scm (jamm)[arguments]: Remove "build" phase.
2019-01-11 06:08:43 +01:00
Efraim Flashner
6fd2ed23ac
gnu: mantis: Limit to x86_64-linux.
* gnu/packages/bioinformatics.scm (mantis)[supported-systems]: New field.
2019-01-07 15:47:34 +02:00
Ricardo Wurmus
e942813aac
gnu: Add mantis.
* gnu/packages/bioinformatics.scm (mantis): New variable.
2019-01-07 11:56:18 +01:00
Pierre Neidhardt
8894668cd2
gnu: discrover: Comment on attempt of minimal texlive-union.
* gnu/packages/bioinformatics.scm (discrover): Comment on attempt of minimal
  texlive-union.
2018-12-20 12:07:40 +01:00
Efraim Flashner
2f3977b9a7
gnu: gess: Don't hardcode python version.
* gnu/packages/bioinformatics.scm (gess)[arguments]: Replace hardcoded
python version with parameterized one.
2018-12-17 12:08:05 +02:00
Christopher Baines
9718265eec
gnu: mash: Use C++ 14.
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.
2018-12-05 20:29:12 +00:00
Ricardo Wurmus
42c3e00c20
gnu: pigx-rnaseq: Update to 0.0.5.
* gnu/packages/bioinformatics.scm (pigx-rnaseq): Update to 0.0.5.
[inputs]: Replace snakemake-4 with snakemake.
2018-12-04 16:21:50 +01:00