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1736 Commits

Author SHA1 Message Date
Ricardo Wurmus 307182d4f7
gnu: rcas-web: Update to 0.1.0. 
* gnu/packages/bioinformatics.scm (rcas-web): Update to 0.1.0.
[inputs]: Replace guile2.2-redis with guile-redis.
 2019-02-08 22:45:12 +01:00
Ricardo Wurmus 6df215f8c8
gnu: star: Update to 2.7.0b. 
* gnu/packages/bioinformatics.scm (star): Update to 2.7.0b.
[arguments]: Add "add-missing-header" build phase.
 2019-02-06 21:32:16 +01:00
Ricardo Wurmus ba123b6dda
gnu: star: Update to 2.7.0a. 
* gnu/packages/bioinformatics.scm (star): Update to 2.7.0a.
 2019-01-30 15:44:47 +01:00
Ricardo Wurmus 1d1e3676ba
gnu: r-genomicfeatures: Update to 1.34.2. 
* gnu/packages/bioinformatics.scm (r-genomicfeatures): Update to 1.34.2.
 2019-01-28 16:27:35 +01:00
Ricardo Wurmus ea0eaf537a
gnu: r-variantannotation: Update to 1.28.10. 
* gnu/packages/bioinformatics.scm (r-variantannotation): Update to 1.28.10.
 2019-01-28 16:27:35 +01:00
Ricardo Wurmus 5d9b140b29
gnu: r-qtl: Update to 1.44-9. 
* gnu/packages/bioinformatics.scm (r-qtl): Update to 1.44-9.
 2019-01-28 16:27:34 +01:00
Ricardo Wurmus 439d821a3b
gnu: r-optparse: Update to 1.6.1. 
* gnu/packages/bioinformatics.scm (r-optparse): Update to 1.6.1.
 2019-01-28 16:27:33 +01:00
Ricardo Wurmus 0791437f97
gnu: Move most packages from guile.scm to new module. 
* gnu/packages/guile.scm (artanis, guildhall, guile-aspell, guile-bash,
guile-8sync, guile-daemon, guile-dsv, guile-fibers, guile-syntax-highlight,
guile-sjson, guile-colorized, guile-pfds, guile-aa-tree, guile-simple-zmq,
jupyter-guile-kernel, guile-sparql, guile-debbugs, guile-email,
guile-debbugs-next, guile-newt, guile-mastodon, guile-parted, guile-xosd,
guile-dbi, guile-dbd-sqlite3, guile-config, guile-hall, guile-ics, guile-wisp,
guile-sly, g-wrap, guile-miniadapton, guile-reader, guile2.2-reader,
guile-ncurses, guile-ncurses/gpm, guile-lib, guile2.0-lib, guile2.2-lib,
guile-minikanren, guile2.0-minikanren, guile2.2-minikanren, guile-irregex,
guile2.0-irregex, guile2.2-irregex, haunt, guile2.0-haunt, guile2.2-haunt,
guile-redis, guile2.0-redis, guile2.2-redis, guile-commonmark,
guile2.0-commonmark, guile2.2-commonmark, mcron, mcron2): Move these variables
from here...
* gnu/packages/guile-xyz.scm: ...to this new file.
* gnu/local.mk (GNU_SYSTEM_MODULES): Add it.
* gnu/installer.scm,
gnu/packages/bioinformatics.scm,
gnu/packages/ci.scm,
gnu/packages/gtk.scm,
gnu/packages/guile.scm,
gnu/packages/mail.scm,
gnu/packages/package-management.scm,
gnu/packages/skribilo.scm,
gnu/packages/web.scm,
gnu/services/mcron.scm: Update module references.
 2019-01-28 14:57:10 +01:00
Ricardo Wurmus fdb0b40b0e
gnu: pepr: Use PYPI-URI. 
* gnu/packages/bioinformatics.scm (pepr)[source]: Use PYPI-URI.
 2019-01-25 23:27:25 +01:00
Ricardo Wurmus 4cd7c58cf1
gnu: python2-warpedlmm: Use PYPI-URI. 
* gnu/packages/bioinformatics.scm (python2-warpedlmm)[source]: Use PYPI-URI.
 2019-01-25 23:26:50 +01:00
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