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Author SHA1 Message Date
Mark H Weaver 6cbee49d66
gnu: All snippets report errors using exceptions, else return #t. 
* gnu/packages/admin.scm, gnu/packages/algebra.scm, gnu/packages/audio.scm,
gnu/packages/backup.scm, gnu/packages/base.scm,
gnu/packages/bioinformatics.scm, gnu/packages/cdrom.scm,
gnu/packages/chez.scm, gnu/packages/code.scm, gnu/packages/compression.scm,
gnu/packages/cross-base.scm, gnu/packages/crypto.scm, gnu/packages/cups.scm,
gnu/packages/databases.scm, gnu/packages/dns.scm, gnu/packages/emacs.scm,
gnu/packages/emulators.scm, gnu/packages/engineering.scm,
gnu/packages/enlightenment.scm, gnu/packages/fpga.scm,
gnu/packages/freedesktop.scm, gnu/packages/ftp.scm, gnu/packages/games.scm,
gnu/packages/gcc.scm, gnu/packages/geo.scm, gnu/packages/ghostscript.scm,
gnu/packages/gl.scm, gnu/packages/glib.scm, gnu/packages/gnome.scm,
gnu/packages/gnuzilla.scm, gnu/packages/graphics.scm, gnu/packages/gtk.scm,
gnu/packages/guile.scm, gnu/packages/irc.scm, gnu/packages/java.scm,
gnu/packages/kerberos.scm, gnu/packages/linux.scm, gnu/packages/lisp.scm,
gnu/packages/lxde.scm, gnu/packages/machine-learning.scm,
gnu/packages/mail.scm, gnu/packages/maths.scm, gnu/packages/messaging.scm,
gnu/packages/monitoring.scm, gnu/packages/mp3.scm, gnu/packages/music.scm,
gnu/packages/netpbm.scm, gnu/packages/networking.scm, gnu/packages/node.scm,
gnu/packages/nvi.scm, gnu/packages/ocaml.scm, gnu/packages/pdf.scm,
gnu/packages/perl.scm, gnu/packages/php.scm, gnu/packages/plotutils.scm,
gnu/packages/pretty-print.scm, gnu/packages/profiling.scm,
gnu/packages/pulseaudio.scm, gnu/packages/python-crypto.scm,
gnu/packages/python.scm, gnu/packages/qt.scm, gnu/packages/robotics.scm,
gnu/packages/sawfish.scm, gnu/packages/scanner.scm, gnu/packages/scheme.scm,
gnu/packages/scribus.scm, gnu/packages/sdl.scm,
gnu/packages/serialization.scm, gnu/packages/shells.scm,
gnu/packages/slang.scm, gnu/packages/smalltalk.scm, gnu/packages/ssh.scm,
gnu/packages/sync.scm, gnu/packages/syncthing.scm, gnu/packages/tbb.scm,
gnu/packages/terminals.scm, gnu/packages/texinfo.scm,
gnu/packages/text-editors.scm, gnu/packages/textutils.scm,
gnu/packages/tls.scm, gnu/packages/unrtf.scm,
gnu/packages/version-control.scm, gnu/packages/video.scm,
gnu/packages/vpn.scm, gnu/packages/web.scm, gnu/packages/wm.scm,
gnu/packages/wxwidgets.scm, gnu/packages/xdisorg.scm, gnu/packages/xorg.scm:
In all snippets, report errors using exceptions, or else return #t.
 2018-03-16 09:08:31 -04:00
Ricardo Wurmus 46264c73a6
gnu: Add pigx-scrnaseq. 
* gnu/packages/bioinformatics.scm (pigx-scrnaseq): New variable.
 2018-03-16 11:15:04 +01:00
Ricardo Wurmus b44437c549
gnu: kentutils: Build with mariadb. 
* gnu/packages/bioinformatics.scm (kentutils)[inputs]: Replace mysql with
mariadb.
 2018-03-16 10:01:07 +01:00
Ricardo Wurmus 80420f114c
gnu: kentutils: Build with mariadb. 
* gnu/packages/bioinformatics.scm (kentutils)[inputs]: Replace mysql with
mariadb.
 2018-03-16 10:00:31 +01:00
Leo Famulari 32cbbac11a
gnu: Add Diversitree. 
* gnu/packages/bioinformatics.scm (r-diversitree): New variable.
 2018-03-15 10:57:51 -04:00
Ricardo Wurmus 8c72ed923d
Merge branch 'master' into core-updates 2018-03-14 17:37:20 +01:00
Ludovic Courtès 189be331ac
build-system/gnu: Add 'bootstrap' phase. 
This factorizes what has become a widespread idiom.

* guix/build/gnu-build-system.scm (%bootstrap-scripts): New variable.
(bootstrap): New procedure.
(%standard-phases): Add it after 'unpack'.
* guix/build/ant-build-system.scm (%standard-phases): Delete 'bootstrap.
* guix/build/asdf-build-system.scm (%standard-phases/source)
(%standard-phases): Likewise.
* guix/build/cargo-build-system.scm (%standard-phases): Likewise.
* guix/build/cmake-build-system.scm (%standard-phases): Likewise.
* guix/build/dub-build-system.scm (%standard-phases): Likewise.
* guix/build/emacs-build-system.scm (%standard-phases): Likewise.
* guix/build/font-build-system.scm (%standard-phases): Likewise.
* guix/build/go-build-system.scm (%standard-phases): Likewise.
* guix/build/haskell-build-system.scm (%standard-phases): Likewise.
* guix/build/minify-build-system.scm (%standard-phases): Likewise.
* guix/build/ocaml-build-system.scm (%standard-phases): Likewise.
* guix/build/perl-build-system.scm (%standard-phases): Likewise.
* guix/build/python-build-system.scm (%standard-phases): Likewise.
* guix/build/r-build-system.scm (%standard-phases): Likewise.
* guix/build/ruby-build-system.scm (%standard-phases): Likewise.
* guix/build/scons-build-system.scm (%standard-phases): Likewise.
* guix/build/texlive-build-system.scm (%standard-phases): Likewise.
* guix/build/waf-build-system.scm (%standard-phases): Likewise.
* gnu/packages/audio.scm (faad2)[arguments]: Replace 'bootstrap.
(soundtouch, cuetools, bluez-alsa): Remove 'arguments'.
(cava)[arguments]: Replace 'bootstrap.
* gnu/packages/backup.scm (rdup): Remove 'bootstrap.
* gnu/packages/bioinformatics.scm (seek)[arguments]: Replace
'bootstrap.
* gnu/packages/bioinformatics.scm (htslib-for-sambamba): Remove
'arguments'.
* gnu/packages/ci.scm (hydra, cuirass): Remove 'bootstrap'.
* gnu/packages/crypto.scm (libb2): Remove #:phases.
* gnu/packages/databases.scm (guile-wiredtiger): Likewise.
* gnu/packages/debug.scm (stress-make): Remove 'bootstrap'.
* gnu/packages/documentation.scm (asciidoc): Likewise.
* gnu/packages/fontutils.scm (libuninameslist): Remove 'arguments'.
* gnu/packages/ftp.scm (weex): Remove 'arguments'.
* gnu/packages/game-development.scm (ois): Remove 'arguments'.
* gnu/packages/games.scm (pioneer): Remove 'bootstrap.
* gnu/packages/gnome.scm (vte-ng, byzanz): Replace 'bootstrap.
(arc-theme): Remove 'arguments'.
(faba-icon-theme): Remove 'bootstrap.
(arc-icon-theme): Remove 'arguments'.
* gnu/packages/gnunet.scm (guile-gnunet): Likewise.
* gnu/packages/gtk.scm (guile-rsvg): Likewise.
* gnu/packages/guile.scm (mcron2): Remove 'bootstrap.
(guile-bash): Remove #:phases.
(guile-git): Remove 'bootstrap.
(guile-syntax-highlight): Remove 'arguments'.
(guile-sjson): Likewise.
* gnu/packages/java.scm (classpath-devel): Remove 'bootstrap.
* gnu/packages/kodi.scm (libdvdnav/kodi)
(libdvdread/kodi, libdvdcss/kodi): Likewise.
* gnu/packages/libreoffice.scm (hunspell): Remove 'arguments'.
* gnu/packages/libusb.scm (hidapi): Likewise.
* gnu/packages/linux.scm (bridge-utils): Rename 'bootstrap' to
'patch-stuff'; move it before 'bootstrap', without autoreconf
invocation.
(eudev): Rename 'bootstrap' to 'patch-file-names', without 'autogen.sh'
invocation; move it before 'bootstrap.
(gpm): Replace 'bootstrap'.
(f2fs-tools): Remove 'arguments'.
(rng-tools): Remove #:phases.
* gnu/packages/messaging.scm (hexchat): Rename 'bootstrap' to
'copy-intltool-makefile'; remove "autoreconf" invocation and move before
'bootstrap'.
(libmesode): Remove 'arguments'.
(libstrophe): Likewise.
* gnu/packages/microcom.scm (microcom): Likewise.
* gnu/packages/networking.scm (libnet): Remove 'bootstrap.
* gnu/packages/onc-rpc.scm (libnsl): Remove 'arguments'.
* gnu/packages/package-management.scm (guix): Replace 'bootstrap.
* gnu/packages/sawfish.scm (librep): Remove 'arguments'.
* gnu/packages/version-control.scm (findnewest): Likewise.
* gnu/packages/video.scm (liba52, handbrake, motion): Replace
'bootstrap.
* gnu/packages/web.scm (fcgiwrap): Remove #:phases.
(tidy): Replace 'bootstrap.
(gumbo-parser): Remove #:phases.
* gnu/packages/wget.scm (wget2): Replace 'bootstrap.
* gnu/packages/wm.scm (i3lock-color): Remove #:phases.
* gnu/packages/xdisorg.scm (xclip): Likewise.
* gnu/packages/xml.scm (libxls): Replace 'bootstrap'.
* gnu/packages/xorg.scm (xf86-video-freedreno)
(xf86-video-intel): Remove #:phases.
* gnu/packages/zile.scm (zile-on-guile): Replace 'bootstrap.
 2018-03-11 22:04:40 +01:00
Ricardo Wurmus fb94174fc3
gnu: Add pigx-bsseq. 
* gnu/packages/bioinformatics.scm (pigx-bsseq): New variable.
 2018-03-11 20:01:53 +01:00
Ricardo Wurmus 531afc8a89
gnu: Add pigx-chipseq. 
* gnu/packages/bioinformatics.scm (pigx-chipseq): New variable.
 2018-03-11 20:01:53 +01:00
Ricardo Wurmus a539ad867d
gnu: r-rhdf5lib: Make build reproducible. 
* gnu/packages/bioinformatics.scm (r-rhdf5lib)[arguments]: Remove timestamp
and host system kernel version.
 2018-03-09 11:40:59 +01:00
Ricardo Wurmus 22a0c65969
gnu: Add r-phangorn. 
* gnu/packages/bioinformatics.scm (r-phangorn): New variable.
 2018-03-08 23:31:56 +01:00
Ricardo Wurmus 53cc59a1d8
gnu: r-ape: Move to (gnu packages cran). 
* gnu/packages/bioinformatics.scm (r-ape): Move from here...
* gnu/packages/cran.scm (r-ape): ...to here.
 2018-03-08 23:31:55 +01:00
Ricardo Wurmus 84c195e505
gnu: r-dropbead: Update to 0-2.d746c6f. 
* gnu/packages/bioinformatics.scm (r-dropbead): Update to 0-2.d746c6f.
 2018-03-08 18:53:49 +01:00
Ricardo Wurmus 0bdd5b8ab7
gnu: Add pigx-rnaseq. 
* gnu/packages/bioinformatics.scm (pigx-rnaseq): New variable.
 2018-03-07 23:25:36 +01:00
Ricardo Wurmus c072cf57b9
gnu: samtools: Update to 1.7. 
* gnu/packages/bioinformatics.scm (samtools): Update to 1.7.
 2018-03-06 16:03:04 +01:00
Ricardo Wurmus 727d847980
gnu: htslib: Update to 1.7. 
* gnu/packages/bioinformatics.scm (htslib): Update to 1.7.
[arguments]: Remove field.
 2018-03-06 16:03:04 +01:00
Ricardo Wurmus e325c89076
gnu: r-rhdf5: Make build reproducible. 
* gnu/packages/bioinformatics.scm (r-rhdf5)[arguments]: Remove timestamp and
host system information from settings file.
 2018-03-06 16:03:04 +01:00
Efraim Flashner da49d13710
gnu: piranha: Declare a source file-name. 
* gnu/packages/bioinformatics.scm (piranha)[source]: Declare a source
file-name.
 2018-03-04 12:05:13 +02:00
Efraim Flashner d9a069c2d9
gnu: libdivsufsort: Declare a source file-name. 
* gnu/packages/bioinformatics.scm (libdivsufsort)[source]: Declare a
source file-name.
 2018-03-04 12:05:13 +02:00
Efraim Flashner 5110672474
gnu: seek: Declare a source file-name. 
* gnu/packages/bioinformatics.scm (seek)[source]: Declare a source
file-name.
 2018-03-04 12:05:13 +02:00
Efraim Flashner b1d4026dfb
gnu: r-dropbead: Declare a source file-name. 
* gnu/packages/bioinformatics.scm (r-dropbead)[source]: Declare a source
file-name.
 2018-03-04 12:05:10 +02:00
Ricardo Wurmus 1adeef3194
gnu: Add dropseq-tools. 
* gnu/packages/bioinformatics.scm (dropseq-tools): New variable.
 2018-03-03 21:28:05 +01:00
Ricardo Wurmus 72299db9fe
gnu: Add java-picard-2.10.3. 
* gnu/packages/bioinformatics.scm (java-picard-2.10.3): New variable.
 2018-03-03 21:28:02 +01:00
Ricardo Wurmus 719fa958f3
gnu: Add java-htsjdk-2.10.1. 
* gnu/packages/bioinformatics.scm (java-htsjdk-2.10.1): New variable.
 2018-03-03 21:27:59 +01:00
Ricardo Wurmus 9a599c17b7
gnu: Add java-htsjdk-latest. 
* gnu/packages/bioinformatics.scm (java-htsjdk-latest): New variable.
 2018-03-03 21:27:57 +01:00
Ricardo Wurmus 9ac7db1830
gnu: Add java-biojava-alignment-4.0. 
* gnu/packages/bioinformatics.scm (java-biojava-alignment-4.0): New variable.
 2018-03-03 21:27:56 +01:00
Ricardo Wurmus 5528f9e8f0
gnu: Add java-biojava-phylo-4.0. 
* gnu/packages/bioinformatics.scm (java-biojava-phylo-4.0): New variable.
 2018-03-03 21:27:53 +01:00
Ricardo Wurmus e44da58c16
gnu: Add java-biojava-core-4.0. 
* gnu/packages/bioinformatics.scm (java-biojava-core-4.0): New variable.
 2018-03-03 21:27:51 +01:00
Ricardo Wurmus 22c09c335b
gnu: Add java-biojava-alignment. 
* gnu/packages/bioinformatics.scm (java-biojava-alignment): New variable.
 2018-03-03 21:27:48 +01:00
Ricardo Wurmus b28c803708
gnu: Add java-biojava-phylo. 
* gnu/packages/bioinformatics.scm (java-biojava-phylo): New variable.
 2018-03-03 21:27:46 +01:00
Ricardo Wurmus 10645b9212
gnu: Add java-forester-1.005. 
* gnu/packages/bioinformatics.scm (java-forester-1.005): New variable.
 2018-03-03 21:27:44 +01:00
Ricardo Wurmus f09d16e594
gnu: Add java-forester. 
* gnu/packages/bioinformatics.scm (java-forester): New variable.
 2018-03-03 21:27:41 +01:00
Ricardo Wurmus 5fef15e506
gnu: Add java-biojava-core. 
* gnu/packages/bioinformatics.scm (java-biojava-core): New variable.
 2018-03-03 21:27:36 +01:00
Ricardo Wurmus bd975831c6
gnu: Add fastqc. 
* gnu/packages/bioinformatics.scm (fastqc): New variable.
 2018-03-03 21:21:48 +01:00
Ricardo Wurmus 3ede1550e8
gnu: cutadapt: Update to 1.16. 
* gnu/packages/bioinformatics.scm (cutadapt): Update to 1.16.
[source]: Fetch via git.
[arguments]: Remove.
[native-inputs]: Replace python-nose with python-pytest.
 2018-03-02 23:44:16 +01:00
Ricardo Wurmus 9aaf2813e2
gnu: r-scran: Update to 1.6.8. 
* gnu/packages/bioinformatics.scm (r-scran): Update to 1.6.8.
 2018-03-01 21:28:53 +01:00
Ricardo Wurmus 6a0e13906b
gnu: r-wgcna: Update to 1.63. 
* gnu/packages/bioinformatics.scm (r-wgcna): Update to 1.63.
 2018-03-01 21:28:53 +01:00
Ricardo Wurmus 61cbd49b30
gnu: r-topgo: Update to 2.30.1. 
* gnu/packages/bioinformatics.scm (r-topgo): Update to 2.30.1.
 2018-03-01 21:28:53 +01:00
Ricardo Wurmus 535014ce60
gnu: r-genomicranges: Update to 1.30.3. 
* gnu/packages/bioinformatics.scm (r-genomicranges): Update to 1.30.3.
 2018-03-01 21:28:53 +01:00
Ricardo Wurmus eb8971b742
gnu: r-limma: Update to 3.34.9. 
* gnu/packages/bioinformatics.scm (r-limma): Update to 3.34.9.
 2018-03-01 21:28:53 +01:00
Ricardo Wurmus 22d96920d3
gnu: r-edger: Update to 3.20.9. 
* gnu/packages/bioinformatics.scm (r-edger): Update to 3.20.9.
 2018-03-01 21:28:53 +01:00
Ricardo Wurmus 99e4b11d81
gnu: r-shortread: Update to 1.36.1. 
* gnu/packages/bioinformatics.scm (r-shortread): Update to 1.36.1.
 2018-03-01 21:28:53 +01:00
Ricardo Wurmus b180893289
gnu: r-dexseq: Update to 1.24.3. 
* gnu/packages/bioinformatics.scm (r-dexseq): Update to 1.24.3.
 2018-03-01 21:28:52 +01:00
Ricardo Wurmus 65c9d25739
gnu: r-qtl: Update to 1.42-8. 
* gnu/packages/bioinformatics.scm (r-qtl): Update to 1.42-8.
 2018-02-22 11:18:03 +01:00
Ricardo Wurmus 79c6af13d0
gnu: r-delayedmatrixstats: Update to 1.0.3. 
* gnu/packages/bioinformatics.scm (r-delayedmatrixstats): Update to 1.0.3.
 2018-02-19 09:53:05 +01:00
Ricardo Wurmus 59b2864d6c
gnu: r-scater: Update to 1.6.3. 
* gnu/packages/bioinformatics.scm (r-scater): Update to 1.6.3.
 2018-02-19 09:53:05 +01:00
Ricardo Wurmus d578278e35
gnu: r-gviz: Update to 1.22.3. 
* gnu/packages/bioinformatics.scm (r-gviz): Update to 1.22.3.
 2018-02-19 09:53:05 +01:00
Ricardo Wurmus ca7855fcd2
gnu: r-gprofiler: Update to 0.6.4. 
* gnu/packages/bioinformatics.scm (r-gprofiler): Update to 0.6.4.
 2018-02-19 09:53:04 +01:00
Ricardo Wurmus 8877ab432e
gnu: r-ensembldb: Update to 2.2.2. 
* gnu/packages/bioinformatics.scm (r-ensembldb): Update to 2.2.2.
 2018-02-19 09:53:04 +01:00
Ricardo Wurmus ebec98ae1d
gnu: r-seurat: Update to 2.2.1. 
* gnu/packages/bioinformatics.scm (r-seurat): Update to 2.2.1.
[propagated-inputs]: Remove r-nmf; add r-metap.
 2018-02-19 09:53:04 +01:00
Ricardo Wurmus 3118b28644
gnu: r-qtl: Update to 1.42-7. 
* gnu/packages/bioinformatics.scm (r-qtl): Update to 1.42-7.
 2018-02-19 09:53:04 +01:00
Ricardo Wurmus 824c200475
gnu: r-genomicranges: Update to 1.30.2. 
* gnu/packages/bioinformatics.scm (r-genomicranges): Update to 1.30.2.
 2018-02-19 09:53:04 +01:00
Ricardo Wurmus e8484711c6
gnu: r-getopt: Update to 1.20.2. 
* gnu/packages/bioinformatics.scm (r-getopt): Update to 1.20.2.
 2018-02-19 09:53:04 +01:00
Ricardo Wurmus 9800f7d9e8
gnu: r-bookdown: Update to 0.7. 
* gnu/packages/bioinformatics.scm (r-bookdown): Update to 0.7.
[propagated-inputs]: Add r-tinytex.
 2018-02-19 09:53:04 +01:00
Ricardo Wurmus ff9d1a2f0c
Merge branch 'master' into core-updates 2018-02-18 00:39:25 +01:00
Ben Woodcroft 369eee8763
gnu: vsearch: Update to 2.7.1. 
* gnu/packages/bioinformatics.scm (vsearch): Update to 2.7.1.
 2018-02-17 12:44:29 +10:00
Mark H Weaver 150062f190
Merge branch 'master' into core-updates 2018-02-16 13:14:26 -05:00
Ben Woodcroft 5ebc8e7f41
gnu: diamond: Update to 0.9.18. 
* gnu/packages/bioinformatics.scm (diamond): Update to 0.9.18.
 2018-02-16 08:13:24 +10:00
Ricardo Wurmus 152d30c346
gnu: Add python-loompy. 
* gnu/packages/bioinformatics.scm (python-loompy): New variable.
 2018-02-15 17:19:00 +01:00
Ricardo Wurmus 3082de04c2
gnu: Add r-dropbead. 
* gnu/packages/bioinformatics.scm (r-dropbead): New variable.
 2018-02-15 17:18:54 +01:00
Ricardo Wurmus 05f7296012
gnu: Add r-delayedmatrixstats. 
* gnu/packages/bioinformatics.scm (r-delayedmatrixstats): New variable.
 2018-02-15 17:18:52 +01:00
Mark H Weaver 932c98326d
Merge branch 'master' into core-updates 2018-02-14 03:40:08 -05:00
Ben Woodcroft 119c09c219
gnu: vsearch: Update to 2.7.0. 
* gnu/packages/bioinformatics.scm (vsearch): Update to 2.7.0.
 2018-02-14 07:43:19 +10:00
Mark H Weaver 288b8fd5e9
Merge branch 'master' into core-updates 2018-02-13 13:17:15 -05:00
Ricardo Wurmus 97bf74076c
gnu: r-gprofiler: Update to 0.6.3. 
* gnu/packages/bioinformatics.scm (r-gprofiler): Update to 0.6.3.
 2018-02-13 16:18:43 +01:00
Ricardo Wurmus 169942368f
gnu: r-ensembldb: Update to 2.2.1. 
* gnu/packages/bioinformatics.scm (r-ensembldb): Update to 2.2.1.
 2018-02-13 16:18:43 +01:00
Ricardo Wurmus 34d077b8bc
gnu: r-gage: Update to 2.28.2. 
* gnu/packages/bioinformatics.scm (r-gage): Update to 2.28.2.
 2018-02-13 16:18:43 +01:00
Ricardo Wurmus f5f9442703
gnu: r-keggrest: Update to 1.18.1. 
* gnu/packages/bioinformatics.scm (r-keggrest): Update to 1.18.1.
 2018-02-13 16:18:43 +01:00
Ricardo Wurmus 26e3e28cc9
gnu: r-seurat: Update to 2.2.0. 
* gnu/packages/bioinformatics.scm (r-seurat): Update to 2.2.0.
[propagated-inputs]: Remove r-ggjoy; add r-rcppeigen and r-ggridges.
 2018-02-13 16:18:42 +01:00
Ricardo Wurmus 53f0dea9d7
gnu: r-msnbase: Update to 2.4.2. 
* gnu/packages/bioinformatics.scm (r-msnbase): Update to 2.4.2.
 2018-02-13 16:18:42 +01:00
Ricardo Wurmus b1f2753627
gnu: r-methylkit: Update to 1.4.1. 
* gnu/packages/bioinformatics.scm (r-methylkit): Update to 1.4.1.
 2018-02-13 16:18:42 +01:00
Ricardo Wurmus 5ef76bc28c
gnu: r-gkmsvm: Update to 0.79.0. 
* gnu/packages/bioinformatics.scm (r-gkmsvm): Update to 0.79.0.
 2018-02-13 16:18:42 +01:00
Ricardo Wurmus 0b24dc95b5
gnu: r-wgcna: Update to 1.62. 
* gnu/packages/bioinformatics.scm (r-wgcna): Update to 1.62.
 2018-02-13 16:18:42 +01:00
Ricardo Wurmus e1129446ec
gnu: r-genomation: Update to 1.11.3. 
* gnu/packages/bioinformatics.scm (r-genomation): Update to 1.11.3.
 2018-02-13 16:18:42 +01:00
Ricardo Wurmus 0b18856532
gnu: r-genomicfeatures: Update to 1.30.3. 
* gnu/packages/bioinformatics.scm (r-genomicfeatures): Update to 1.30.3.
 2018-02-13 16:18:42 +01:00
Ricardo Wurmus 99b3236e65
gnu: r-rtracklayer: Update to 1.38.3. 
* gnu/packages/bioinformatics.scm (r-rtracklayer): Update to 1.38.3.
 2018-02-13 16:18:42 +01:00
Ricardo Wurmus c37b361e44
gnu: r-summarizedexperiment: Update to 1.8.1. 
* gnu/packages/bioinformatics.scm (r-summarizedexperiment): Update to 1.8.1.
 2018-02-13 16:18:42 +01:00
Ricardo Wurmus 373430672d
gnu: r-biomart: Update to 2.34.2. 
* gnu/packages/bioinformatics.scm (r-biomart): Update to 2.34.2.
 2018-02-13 16:18:42 +01:00
Ricardo Wurmus 024f19c68b
gnu: r-genomicranges: Update to 1.30.1. 
* gnu/packages/bioinformatics.scm (r-genomicranges): Update to 1.30.1.
 2018-02-13 16:18:42 +01:00
Ricardo Wurmus 0674657908
gnu: r-limma: Update to 3.34.8. 
* gnu/packages/bioinformatics.scm (r-limma): Update to 3.34.8.
 2018-02-13 16:18:42 +01:00
Ricardo Wurmus 5fb1fee67b
gnu: r-variantannotation: Update to 1.24.5. 
* gnu/packages/bioinformatics.scm (r-variantannotation): Update to 1.24.5.
 2018-02-13 16:18:42 +01:00
Ricardo Wurmus d22abe1e5d
gnu: r-edger: Update to 3.20.8. 
* gnu/packages/bioinformatics.scm (r-edger): Update to 3.20.8.
 2018-02-13 16:18:42 +01:00
Ricardo Wurmus 66ae706c24
gnu: r-bookdown: Update to 0.6. 
* gnu/packages/bioinformatics.scm (r-bookdown): Update to 0.6.
[propagated-inputs]: Add r-xfun and ghc-pandoc.
 2018-02-13 16:18:42 +01:00
Ricardo Wurmus 2e9da3390c
gnu: r-vegan: Update to 2.4-6. 
* gnu/packages/bioinformatics.scm (r-vegan): Update to 2.4-6.
 2018-02-13 16:18:41 +01:00
Ricardo Wurmus 7f1d9bef50
gnu: Add r-scran. 
* gnu/packages/bioinformatics.scm (r-scran): New variable.
 2018-02-12 15:29:44 +01:00
Ricardo Wurmus 658ab21d2e
gnu: Add r-scater. 
* gnu/packages/bioinformatics.scm (r-scater): New variable.

Co-authored-by: Raoul Jean Pierre Bonnal <ilpuccio.febo@gmail.com>
 2018-02-12 15:29:43 +01:00
Ricardo Wurmus 6fb1dc17a3
gnu: Add r-singlecellexperiment. 
* gnu/packages/bioinformatics.scm (r-singlecellexperiment): New variable.
 2018-02-12 15:29:43 +01:00
Ricardo Wurmus 9ec0898824
gnu: Add r-beachmat. 
* gnu/packages/bioinformatics.scm (r-beachmat): New variable.
 2018-02-12 15:29:43 +01:00
Ricardo Wurmus 748e9f163a
gnu: Add r-rhdf5lib. 
* gnu/packages/bioinformatics.scm (r-rhdf5lib): New variable.
 2018-02-12 15:29:43 +01:00
Ricardo Wurmus aba3e482b9
gnu: Add r-hdf5array. 
* gnu/packages/bioinformatics.scm (r-hdf5array): New variable.
 2018-02-11 11:42:09 +01:00
Marius Bakke 9e94d063ab
gnu: multiqc: Update to 1.4. 
* gnu/packages/bioinformatics.scm (multiqc): Update to 1.4.
[propagated-inputs]: Remove PYTHON-ENUM34.
 2018-02-07 15:34:08 +01:00
Mark H Weaver e7ca634912
Merge branch 'master' into core-updates 2018-02-03 22:46:07 -05:00
Ben Woodcroft 7502badb81
gnu: diamond: Update to 0.9.17. 
* gnu/packages/bioinformatics.scm (diamond): Update to 0.9.17.
 2018-02-02 23:04:46 +10:00
Marius Bakke bee7bb315c
Merge branch 'master' into core-updates 2018-02-01 13:18:47 +01:00
Ben Woodcroft ae8522d265
gnu: diamond: Update to 0.9.16. 
* gnu/packages/bioinformatics.scm (diamond): Update to 0.9.16.
 2018-01-27 10:21:06 +10:00
Mark H Weaver b89d8a4271
Merge branch 'master' into core-updates 2018-01-26 00:15:26 -05:00
Ben Woodcroft a81f7eb858
gnu: diamond: Update to 0.9.15. 
* gnu/packages/bioinformatics.scm (diamond): Update to 0.9.15.
 2018-01-26 12:47:02 +10:00
Tobias Geerinckx-Rice cd70f9bdb0
gnu: deeptools: Update URI. 
* gnu/packages/bioinformatics.scm (deeptools)[source, home-page]: Update
URI.
 2018-01-26 00:09:19 +01:00
Mark H Weaver a102d359a6
Merge branch 'master' into core-updates 2018-01-23 17:01:07 -05:00
Ricardo Wurmus 625cdc3fde
gnu: star: Make reproducible. 
* gnu/packages/bioinformatics.scm (star)[arguments]: Add build phase
"make-reproducible".
 2018-01-22 22:49:10 +01:00
Efraim Flashner 3df57b3a97
gnu: khmer: Add aarch64-linux to supported systems. 
* gnu/packages/bioinformatics.scm (khmer)[supported-systems]: Add
aarch64-linux to the supported systems.
 2018-01-22 09:39:59 +02:00
Ricardo Wurmus 7762646d95
gnu: Add salmon. 
* gnu/packages/bioinformatics.scm (libstadenio-for-salmon,
spdlog-for-salmon, bwa-for-salmon, salmon): New variables.
 2018-01-21 14:18:09 +01:00
Ricardo Wurmus 8d77a085a7
gnu: Add sailfish. 
* gnu/packages/bioinformatics.scm (sailfish): New variable.
 2018-01-21 14:18:09 +01:00
Ricardo Wurmus 1fe0bde34d
gnu: Add libdivsufsort. 
* gnu/packages/bioinformatics.scm (libdivsufsort): New variable.
 2018-01-21 14:18:09 +01:00
Ricardo Wurmus c3b2ab9d3b
gnu: Add libgff. 
* gnu/packages/bioinformatics.scm (libgff): New variable.
 2018-01-21 14:18:09 +01:00
Leo Famulari 4adb40bffc
Merge branch 'master' into core-updates 2018-01-11 14:22:50 -08:00
Ben Woodcroft f6e2d86f8e
gnu: seqmagick: Use 'pypi-uri'. 
* gnu/packages/bioinformatics.scm (seqmagick)[source]: Use 'pypi-uri'.
 2018-01-10 20:16:36 +10:00
Ben Woodcroft 3146f22dec
gnu: mafft: Update to 7.313. 
* gnu/packages/bioinformatics.scm (mafft): Update to 7.313.
[source]: Use HTTPS URI.
 2018-01-10 20:16:36 +10:00
Ben Woodcroft 39fb853abe
gnu: seqmagick: Update to 0.7.0. 
* gnu/packages/bioinformatics.scm (seqmagick): Update to 0.7.0.  Use
python-3.
[arguments]: Remove replacement phase for check.
[inputs]: Add biopython.  Remove python2-biopython-1.66.
(python2-biopython-1.66): Remove variable.
 2018-01-09 22:39:05 +10:00
Leo Famulari 4ed41f472b
Merge branch 'master' into core-updates 2018-01-03 14:18:01 -05:00
Tobias Geerinckx-Rice 8057dee15b
gnu: htslib: Mark up description. 
* gnu/packages/bioinformatics.scm (htslib)[description]: Use @command{}.
 2018-01-02 16:13:23 +01:00
Ricardo Wurmus 7edee34427
gnu: ribotaper: Wrap executables. 
* gnu/packages/bioinformatics.scm (ribotaper)[arguments]: Add phase
"wrap-executables".
 2018-01-02 12:07:06 +01:00
Tobias Geerinckx-Rice 6856518456
gnu: python-pysam: Update to 0.13.0. 
* gnu/packages/bioinformatics.scm (python-pysam): Update to 0.13.0.
 2018-01-02 02:13:38 +01:00
Tobias Geerinckx-Rice ddf38ece8a
gnu: htslib: Update to 1.6. 
* gnu/packages/bioinformatics.scm (htslib): Update to 1.6.
 2018-01-02 01:47:42 +01:00
Efraim Flashner 23de2e1d5f
Merge remote-tracking branch 'origin/master' into core-updates 2017-12-31 14:10:25 +02:00
Ben Woodcroft f14a6586ec
gnu: vsearch: Update to 2.6.2. 
* gnu/packages/bioinformatics.scm (vsearch): Update to 2.6.2.
 2017-12-27 22:12:08 +10:00
Tobias Geerinckx-Rice e9960d8cba
gnu, doc: Use HTTPS for cran.r-project.org home pages. 
* gnu/packages/bioinformatics.scm (r-sparql, r-acsnminer, r-gkmsvm)
(r-maldiquant, r-gprofiler)[home-page]: Use HTTPS.
* gnu/packages/cran.scm (r-colorspace, r-auc, r-calibrate, r-shape)
(r-compare, r-proxy, r-sp, r-rmtstat, r-lmtest, r-inline, r-bbmle)
(r-lpsolve, r-energy, r-suppdists, r-ksamples, r-cvst, r-drr, r-prodlim)
(r-ddalpha, r-rcpproll, r-ipred, r-psych, r-truncnorm, r-rsolnp, r-laeken)
(r-vcd, r-ica, r-scatterplot3d)[home-page]: Likewise.
* gnu/packages/machine-learning.scm (r-adaptivesparsity, r-kernlab)
[home-page]: Likewise.
* gnu/packages/maths.scm (r-quadprog, r-pracma)[home-page]: Likewise.
* gnu/packages/statistics.scm (r-boot, r-cluster, r-codetools, r-foreign)
(r-kernsmooth, r-nlme, r-mgcv, r-rpart, r-dichromat, r-estimability)
(r-pheatmap, r-labeling, r-magrittr, r-munsell, r-rcolorbrewer, r-sendmailr)
(r-gdtools, r-acepack, r-formula, r-locfit, r-chron, r-coda, r-backports)
(r-brew, r-commonmark, r-rstudioapi, r-plotrix, r-gridbase, r-bitops)
(r-catools, r-xnomial, r-lambda-r, r-whoreadsthis, r-futile-options)
(r-futile-logger, r-segmented, r-snow, r-iterators, r-foreach, r-doparallel)
(r-domc, r-irlba, r-registry, r-e1071, r-bigmemory-sri, r-r-methodss3)
(r-tidyselect, r-base64, r-runit, r-sfsmisc, r-gtools, r-gdata, r-gplots)
(r-ztable, r-vipor, r-sourcetools, r-statmod, r-compquadform, r-mixtools)
(r-fastica, r-diptest, r-modeltools, r-flexmix, r-deoptimr, r-pcapp)
(r-rrcov, r-fit-models, r-robust, r-trimcluster, r-fpc, r-fnn)
(r-modelmetrics, r-nloptr, r-lme4, r-tclust, r-lubridate)[home-page]:
Likewise.
* gnu/packages/web.scm (r-htmltools, r-hwriter, r-rjson, r-rook)[home-page]:
Likewise.
* doc/guix.texi (Invoking guix import, Invoking guix refresh): Likewise.
 2017-12-24 16:12:13 +01:00
Roel Janssen b9bf2b8985
gnu: Update r-mutationalpatterns to 1.4.2. 
* gnu/packages/bioinformatics.scm (r-mutationalpatterns): Update to 1.4.2.
 2017-12-22 12:23:06 +01:00
Leo Famulari f76fc96866
Merge branch 'master' into core-updates 2017-12-21 13:58:35 -05:00
Ricardo Wurmus b9e8a5c594
gnu: r-biomart: Update to 2.34.1. 
* gnu/packages/bioinformatics.scm (r-biomart): Update to 2.34.1.
[propagated-inputs]: Add r-httr.
 2017-12-19 20:35:04 +01:00
Ricardo Wurmus 11e42209a8
gnu: r-gviz: Update to 1.22.2. 
* gnu/packages/bioinformatics.scm (r-gviz): Update to 1.22.2.
 2017-12-19 20:35:04 +01:00
Ricardo Wurmus 2ccd850192
gnu: r-gqtlstats: Update to 1.10.1. 
* gnu/packages/bioinformatics.scm (r-gqtlstats): Update to 1.10.1.
 2017-12-19 20:35:04 +01:00
Ricardo Wurmus 28d25d037e
gnu: r-rtracklayer: Update to 1.38.2. 
* gnu/packages/bioinformatics.scm (r-rtracklayer): Update to 1.38.2.
 2017-12-19 20:35:04 +01:00
Ricardo Wurmus d41f678420
gnu: r-limma: Update to 3.34.4. 
* gnu/packages/bioinformatics.scm (r-limma): Update to 3.34.4.
 2017-12-19 20:35:03 +01:00
Ricardo Wurmus ab0dd8ac10
gnu: r-edger: Update to 3.20.2. 
* gnu/packages/bioinformatics.scm (r-edger): Update to 3.20.2.
 2017-12-19 20:35:03 +01:00
Ricardo Wurmus 7665fb39f5
gnu: r-biocstyle: Update to 2.6.1. 
* gnu/packages/bioinformatics.scm (r-biocstyle): Update to 2.6.1.
 2017-12-19 20:35:03 +01:00
Ricardo Wurmus 756ac7254c
gnu: r-dexseq: Update to 1.24.2. 
* gnu/packages/bioinformatics.scm (r-dexseq): Update to 1.24.2.
 2017-12-19 20:35:03 +01:00
Ricardo Wurmus 8d11ef4470
gnu: r-vegan: Update to 2.4-5. 
* gnu/packages/bioinformatics.scm (r-vegan): Update to 2.4-5.
 2017-12-19 20:35:02 +01:00
Efraim Flashner 677bc34d5b
gnu: Remove redundant cmake libdir configure flags. 
* gnu/packages/bioinformatics.scm (imp)[arguments]: Remove
CMAKE_INSTALL_LIBDIR flag.
* gnu/packages/calendar.scm (libical): Same.
* gnu/packages/engineering.scm (kicad): Same.
* gnu/packages/games.scm (openrct2, mgba): Same.
* gnu/packages/gl.scm (virtualgl): Same.
* gnu/packages/image-processing.scm (mia): Same.
* gnu/packages/linux.scm (rdma-core): Same.
* gnu/packages/machine-learning.scm (dlib): Same.
* gnu/packages/maths.scm (lapack, superlu, z3): Same.
* gnu/packages/password-utils.scm (keepassxc): Same.
* gnu/packages/photo.scm (darktable): Same.
* gnu/packages/rdesktop.scm (freerdp): Same.
 2017-12-19 19:52:01 +02:00
Ricardo Wurmus f1a2b1cb20
gnu: r-seurat: Update to 2.1.0. 
* gnu/packages/bioinformatics.scm (r-seurat): Update to 2.1.0.
[propagated-inputs]: Add r-diffusionmap, r-dtw, r-ggjoy, r-hmisc, r-ica,
r-mass, r-matrix, r-nmf, r-plotly, r-sdmtools, r-tidyr; remove r-plyr,
r-rcppeigen, r-fastica.
 2017-12-18 12:01:35 +01:00
Ricardo Wurmus 8271b8d22a
gnu: r-seurat: Fix ModularityOptimizer.jar. 
* gnu/packages/bioinformatics.scm (r-seurat)[arguments]: Include Main-Class
attribute in manifest.
 2017-12-18 12:01:34 +01:00
Ben Woodcroft 6098a386a9
gnu: bedtools: Update to 2.27.1. 
* gnu/packages/ruby.scm (bedtools): Update to 2.27.1.
 2017-12-15 13:56:51 +10:00
Ben Woodcroft 4e0b3583ea
gnu: diamond: Update to 0.9.14. 
* gnu/packages/bioinformatics.scm (diamond): Update to 0.9.14.
 2017-12-14 22:50:10 +10:00
Christopher Baines 9cf5f134d5
gnu: Switch to using the version-major procedure. 
* gnu/packages/audio.scm (ardour)[arguments]: Switch to using version-major.
  (hmmer)[source]: Switch to using version-major.
  (pidgin)[native-search-paths]: Switch to using version-major.
  (r-minimal)[source]: Switch to using version-major.
 2017-12-11 19:12:33 +00:00
Ricardo Wurmus 83b9d121a7
gnu: bedtools-2.18: Fix build. 
* gnu/packages/bioinformatics.scm (bedtools-2.18)[arguments]: Restore custom
install phase.

Reported by Mark H Weaver <mhw@netris.org>.
 2017-12-09 13:01:15 +01:00
Ricardo Wurmus 0d9824cc12
gnu: bedtools: Update to 2.27.0. 
* gnu/packages/bioinformatics.scm (bedtools): Update to 2.27.0.
[arguments]: Remove custom "install" phase; specify prefix.
 2017-12-06 19:13:35 +01:00
Ricardo Wurmus d112e5a8c2
gnu: Add kallisto. 
* gnu/packages/bioinformatics.scm (kallisto): New variable.
 2017-12-03 18:38:58 +01:00
Ricardo Wurmus 117d8cc40e
gnu: jellyfish: Update to 2.2.7. 
* gnu/packages/bioinformatics.scm (jellyfish): Update to 2.2.7.
[native-inputs]: Add pkg-config.
[inputs]: Add htslib.
 2017-11-30 17:38:36 +01:00
Ricardo Wurmus 9b8d02011f
gnu: r-annotationhub: Update to 2.10.1. 
* gnu/packages/bioinformatics.scm (r-annotationhub): Update to 2.10.1.
 2017-11-30 17:28:24 +01:00
Ricardo Wurmus 87e91a9fff
gnu: r-msnid: Update to 1.12.1. 
* gnu/packages/bioinformatics.scm (r-msnid): Update to 1.12.1.
 2017-11-30 17:28:23 +01:00
Ricardo Wurmus 439492654b
gnu: r-maldiquant: Update to 1.17. 
* gnu/packages/bioinformatics.scm (r-maldiquant): Update to 1.17.
 2017-11-30 17:28:23 +01:00
Ricardo Wurmus 06e8e0fc6c
gnu: r-genomicalignments: Update to 1.14.1. 
* gnu/packages/bioinformatics.scm (r-genomicalignments): Update to 1.14.1.
 2017-11-30 17:28:22 +01:00
Ricardo Wurmus 1ce5d32b49
gnu: r-limma: Update to 3.34.2. 
* gnu/packages/bioinformatics.scm (r-limma): Update to 3.34.2.
 2017-11-30 17:28:22 +01:00
Ricardo Wurmus 8131cf4162
gnu: r-variantannotation: Update to 1.24.2. 
* gnu/packages/bioinformatics.scm (r-variantannotation): Update to 1.24.2.
 2017-11-30 17:28:21 +01:00
Ricardo Wurmus d2081a17ed
gnu: r-getopt: Update to 1.20.1. 
* gnu/packages/bioinformatics.scm (r-getopt): Update to 1.20.1.
 2017-11-30 17:28:20 +01:00
Ricardo Wurmus 4220ab0c81
gnu: r-gseabase: Update to 1.40.1. 
* gnu/packages/bioinformatics.scm (r-gseabase): Update to 1.40.1.
 2017-11-30 17:28:20 +01:00
Ricardo Wurmus d259932ca8
gnu: r-dexseq: Update to 1.24.1. 
* gnu/packages/bioinformatics.scm (r-dexseq): Update to 1.24.1.
 2017-11-30 17:28:19 +01:00
Ricardo Wurmus 058644c0f2
gnu: r-deseq2: Update to 1.18.1. 
* gnu/packages/bioinformatics.scm (r-deseq2): Update to 1.18.1.
 2017-11-30 17:28:18 +01:00
Ricardo Wurmus 654c29aceb
gnu: r-annotate: Update to 1.56.1. 
* gnu/packages/bioinformatics.scm (r-annotate): Update to 1.56.1.
 2017-11-30 17:28:18 +01:00
Arun Isaac 9364a520ce
gnu: metabat: Use scons-build-system. 
* gnu/packages/bioinformatics.scm (metabat): Switch to scons-build-system.
 2017-11-30 18:19:32 +05:30
Roel Janssen 1fd904fb38
gnu: Update r-mutationalpatterns to 1.4.1. 
* gnu/packages/bioinformatics.scm (r-mutationalpatterns): Update to 1.4.1.
 2017-11-29 14:56:28 +01:00
Roel Janssen efa6a1ddb5
gnu: Add r-copynumber. 
* gnu/packages/bioinformatics.scm (r-copynumber): New variable.
 2017-11-29 12:46:17 +01:00
Ricardo Wurmus d7f24778de
gnu: Add java-picard-1.113. 
* gnu/packages/bioinformatics.scm (java-picard-1.113): New variable.
 2017-11-27 12:12:41 +01:00
Ricardo Wurmus d7fed31ad2
gnu: Add java-picard. 
* gnu/packages/bioinformatics.scm (java-picard): New variable.
 2017-11-27 12:12:40 +01:00
Ricardo Wurmus bd94b6f850
gnu: java-htsjdk: Update to 2.3.0. 
* gnu/packages/bioinformatics.scm (java-htsjdk): Update to 2.3.0.
[arguments]: Build with JDK 8.
[inputs]: Add java-ngs, java-snappy, java-commons-compress,
java-commons-logging-minimal, java-commons-jexl-2, and java-xz.
[native-inputs]: Add java-testng.
 2017-11-27 12:12:40 +01:00
Ricardo Wurmus 35e78aaa25
gnu: r-rhdf5: Fix build phase. 
* gnu/packages/bioinformatics.scm (r-rhdf5)[arguments]: Fix "unpack-smallhdf5"
phase.
 2017-11-27 12:11:52 +01:00
Ricardo Wurmus e6debcaf02
gnu: subread: Update to 1.6.0. 
* gnu/packages/bioinformatics.scm (subread): Update to 1.6.0.
 2017-11-23 13:16:12 +01:00
Ricardo Wurmus aa33cc29ca
gnu: idr: Update to 2.0.3. 
* gnu/packages/bioinformatics.scm (idr): Update to 2.0.3.
[source]: Add snippet to remove generated code.
 2017-11-21 23:17:43 +01:00
Ricardo Wurmus 40590caf3b
gnu: idr: Correct license. 
* gnu/packages/bioinformatics.scm (idr)[license]: Change to GPLv2+.
 2017-11-21 23:17:43 +01:00
Ricardo Wurmus 261b38a978
gnu: r-genomeinfodbdata: Update to 0.99.1. 
* gnu/packages/bioinformatics.scm (r-genomeinfodbdata): Update to 0.99.1.
 2017-11-18 11:18:41 +01:00
Ricardo Wurmus 592f4a9434
gnu: r-go-db: Update to 3.5.0. 
* gnu/packages/bioinformatics.scm (r-go-db): Update to 3.5.0.
 2017-11-18 11:18:41 +01:00
Ricardo Wurmus e4664290ce
gnu: r-org-ce-eg-db: Update to 3.5.0. 
* gnu/packages/bioinformatics.scm (r-org-ce-eg-db): Update to 3.5.0.
 2017-11-18 11:18:40 +01:00
Ricardo Wurmus 19fc299f68
gnu: r-org-dm-eg-db: Update to 3.5.0. 
* gnu/packages/bioinformatics.scm (r-org-dm-eg-db): Update to 3.5.0.
 2017-11-18 11:18:40 +01:00
Ricardo Wurmus f3569f5218
gnu: r-org-mm-eg-db: Update to 3.5.0. 
* gnu/packages/bioinformatics.scm (r-org-mm-eg-db): Update to 3.5.0.
 2017-11-18 11:18:40 +01:00
Ricardo Wurmus 57dc9b58db
gnu: r-genomationdata: Update to 1.10.0. 
* gnu/packages/bioinformatics.scm (r-genomationdata): Update to 1.10.0.
 2017-11-18 11:18:39 +01:00
Ricardo Wurmus 90dbd984f8
gnu: Remove duplicate from (gnu packages bioinformatics). 
* gnu/packages/bioinformatics.scm (r-annotationfilter): Remove duplicate.
 2017-11-18 11:18:39 +01:00
Ricardo Wurmus 676507e388
gnu: r-org-hs-eg-db: Clarify description. 
* gnu/packages/bioinformatics.scm (r-org-hs-eg-db)[description]: Clarify.
 2017-11-18 11:18:38 +01:00
Ricardo Wurmus d595fed33d
gnu: r-org-hs-eg-db: Update to 3.5.0. 
* gnu/packages/bioinformatics.scm (r-org-hs-eg-db): Update to 3.5.0.
 2017-11-18 11:18:37 +01:00
Ricardo Wurmus ccedfd3a43
gnu: r-org-hs-eg-db: Remove duplicate package definition. 
* gnu/packages/bioinformatics.scm (r-org-hs-eg-db): Remove duplicate variable.
 2017-11-18 11:18:37 +01:00
Ricardo Wurmus ac257f127a
gnu: Move testing packages from python.scm to check.scm. 
* gnu/packages/python.scm (python-behave-web-api, python2-behave-web-api,
python-mock, python2-mock, python-mock-2, python-nose, python2-nose,
python-nose2, python2-nose2, python-unittest2, python2-unittest2,
python-pytest, python2-pytest, python-pytest-3.0, python2-pytest-3.0,
python-pytest-cov, python2-pytest-cov, python-pytest-runner,
python2-pytest-runner, python-pytest-mock, python2-pytest-mock,
python-pytest-xdist, python2-pytest-xdist, python-scripttest,
python2-scripttest, python-testtools, python2-testtools, python-testscenarios,
python2-testscenarios, python-testresources, python2-testresources,
python-subunit, python2-subunit, python-fixtures, python2-fixtures,
python-testrepository, python2-testrepository, python-coverage,
python2-coverage, python-cov-core, python2-cov-core, python-testpath,
python2-testpath, python-testlib, python2-testlib, python-pytest-cache,
python2-pytest-cache, python-pytest-localserver, python-pytest-xprocess,
python-pytest-subtesthack, python2-pytest-subtesthack, python-hypothesis,
python2-hypothesis, python-lit, python2-lit, python-pytest-pep8,
python2-pytest-pep8, python-pytest-flakes, python2-pytest-flakes,
python2-coverage-test-runner, python-pylint, python2-pylint,
python-paramunittest, python2-python-paramunittest, python-pytest-warnings,
python2-pytest-warnings, python-pytest-capturelog, python2-pytest-capturelog,
python-pytest-catchlog, python2-pytest-catchlog, python-nosexcover,
python2-nosexcover, python-discover, python2-discover, behave, python-rednose,
python2-rednose, python-nose-randomly, python2-nose-randomly,
python-nose-timer, python2-nose-timer): Move from here...
* gnu/packages/check.scm: ...to here.
* gnu/packages/admin.scm,
gnu/packages/android.scm,
gnu/packages/backup.scm,
gnu/packages/bioinformatics.scm,
gnu/packages/calendar.scm,
gnu/packages/dav.scm,
gnu/packages/django.scm,
gnu/packages/freedesktop.scm,
gnu/packages/haskell.scm,
gnu/packages/image.scm,
gnu/packages/irc.scm,
gnu/packages/jrnl.scm,
gnu/packages/ldc.scm,
gnu/packages/libffi.scm,
gnu/packages/mail.scm,
gnu/packages/mpd.scm,
gnu/packages/openstack.scm,
gnu/packages/package-management.scm,
gnu/packages/password-utils.scm,
gnu/packages/python-crypto.scm,
gnu/packages/python-web.scm,
gnu/packages/rdf.scm,
gnu/packages/statistics.scm,
gnu/packages/storage.scm,
gnu/packages/time.scm,
gnu/packages/tls.scm,
gnu/packages/tor.scm,
gnu/packages/tryton.scm: Adjust accordingly.
 2017-11-17 22:36:26 +01:00
Ludovic Courtès 589e3f4e70
gnu: Move more packages from python to python-web. 
* gnu/packages/python.scm (python-requests, python2-requests)
(python-requests-2.7, python-oauthlib, python2-oauthlib)
(python-furl, python2-furl, python-wsgi-intercept)
(python-publicsuffix, python2-publicsuffix)
(python-publicsuffix2, python2-publicsuffix2): Move to...
* gnu/packages/python-web.scm: ... here.
* gnu/packages/bioinformatics.scm, gnu/packages/finance.scm:
gnu/packages/maths.scm, gnu/packages/terminals.scm,
gnu/packages/video.scm, gnu/packages/virtualization.scm: Adjust
accordingly.
 2017-11-16 08:45:15 +01:00
Ben Woodcroft a68e586097
gnu: diamond: Update to 0.9.13. 
* gnu/packages/bioinformatics.scm (diamond): Update to 0.9.13.
 2017-11-14 08:25:43 +10:00
Ricardo Wurmus 5ccde2079e
gnu: Move test packages from perl to perl-check. 
* gnu/packages/perl.scm (perl-test2-bundle-extended,
perl-test2-plugin-nowarnings, perl-test-base, perl-test-class,
perl-test-class-most, perl-test-cleannamespaces, perl-test-command,
perl-test-cpan-meta, perl-test-cpan-meta-json, perl-test-deep,
perl-test-differences, perl-test-directory, perl-test-eol,
perl-test-exception, perl-test-fatal, perl-test-file-sharedir-dist,
perl-test-files, perl-test-harness, perl-test-leaktrace,
perl-test-longstring, perl-test-manifest, perl-test-memory-cycle,
perl-test-mockobject, perl-test-mocktime, perl-test-most, perl-test-needs,
perl-test-notabs, perl-test-nowarnings, perl-test-number-delta,
perl-test-output, perl-test-pod, perl-test-pod-coverage, perl-test-requires,
perl-test-script, perl-test-sharedfork, perl-test-simple, perl-test-taint,
perl-test-tester, perl-test-trap, perl-test-utf8, perl-test-warn,
perl-test-warnings, perl-test-without-module, perl-test-writevariants,
perl-test-yaml, perl-test-trailingspace): Move variables to ...
* gnu/packages/perl-check.scm: ... this new file.
* gnu/local.mk (GNU_SYSTEM_MODULES): Add it.
* gnu/packages/admin.scm,
gnu/packages/bioinformatics.scm,
gnu/packages/crypto.scm,
gnu/packages/databases.scm,
gnu/packages/glib.scm,
gnu/packages/gnupg.scm,
gnu/packages/image-viewers.scm,
gnu/packages/language.scm,
gnu/packages/networking.scm,
gnu/packages/package-management.scm,
gnu/packages/perl.scm,
gnu/packages/terminals.scm,
gnu/packages/tex.scm,
gnu/packages/version-control.scm,
gnu/packages/web.scm,
gnu/packages/xml.scm,
gnu/packages/xorg.scm: Use perl-check module.
 2017-11-13 23:03:01 +01:00
Ricardo Wurmus d4735e8c65
gnu: cd-hit: Update source tarball hash. 
* gnu/packages/bioinformatics.scm (cd-hit)[source]: Update hash.
 2017-11-13 16:02:35 +01:00
Tobias Geerinckx-Rice 11ed4108fb
gnu: methylkit: Use new home page. 
* gnu/packages/bioinformatics.scm (methylkit)[home-page]: Update.
 2017-11-11 05:17:58 +01:00
Ben Woodcroft 7c087150ec
gnu: vsearch: Update to 2.6.0. 
* gnu/packages/bioinformatics.scm (vsearch): Update to 2.6.0.
 2017-11-11 09:33:16 +10:00
Ricardo Wurmus 0af4df7e61
gnu: cutadapt: Update to 1.14. 
* gnu/packages/bioinformatics.scm (cutadapt): Update to 1.14.
 2017-11-10 15:32:42 +01:00
Ben Woodcroft da4a707c88
gnu: roary: Update to 3.11.0. 
* gnu/packages/bioinformatics.scm (roary): Update to 3.11.0.
[inputs]: Add perl-digest-md5-file.
 2017-11-09 18:12:32 +10:00
Ricardo Wurmus 34260a10d7
gnu: miso: Use pypi-uri. 
* gnu/packages/bioinformatics.scm (miso)[source]: Use pypi-uri.
 2017-11-08 17:41:08 +01:00
Ricardo Wurmus c49102ecca
gnu: Add r-hitc. 
* gnu/packages/bioinformatics.scm (r-hitc): New variable.
 2017-11-07 23:32:45 +01:00
Ricardo Wurmus 30eb4e37c8
gnu: Add r-fithic. 
* gnu/packages/bioinformatics.scm (r-fithic): New variable.
 2017-11-07 23:32:45 +01:00
Ricardo Wurmus fbf5440637
gnu: Add r-sushi. 
* gnu/packages/bioinformatics.scm (r-sushi): New variable.
 2017-11-07 23:32:45 +01:00
Ricardo Wurmus 2e4ce60e7c
gnu: Add r-gwascat. 
* gnu/packages/bioinformatics.scm (r-gwascat): New variable.
 2017-11-07 23:32:44 +01:00
Ricardo Wurmus 4272000661
gnu: Add r-gviz. 
* gnu/packages/bioinformatics.scm (r-gviz): New variable.
 2017-11-07 23:32:44 +01:00
Ricardo Wurmus 794ff347a9
gnu: Add r-gqtlstats. 
* gnu/packages/bioinformatics.scm (r-gqtlstats): New variable.
 2017-11-07 23:32:44 +01:00
Ricardo Wurmus 66c39102e5
gnu: Add r-ldblock. 
* gnu/packages/bioinformatics.scm (r-ldblock): New variable.
 2017-11-07 23:32:44 +01:00
Ricardo Wurmus 15f98b0d23
gnu: Add r-erma. 
* gnu/packages/bioinformatics.scm (r-erma): New variable.
 2017-11-07 23:32:43 +01:00
Ricardo Wurmus 421c68e3f7
gnu: Add r-homo-sapiens. 
* gnu/packages/bioinformatics.scm (r-homo-sapiens): New variable.
 2017-11-07 23:32:43 +01:00
Ricardo Wurmus b52a866d14
gnu: Add r-org-hs-eg-db. 
* gnu/packages/bioinformatics.scm (r-org-hs-eg-db): New variable.
 2017-11-07 23:32:43 +01:00
Ricardo Wurmus dd5fc8b78e
gnu: Add r-snpstats. 
* gnu/packages/bioinformatics.scm (r-snpstats): New variable.
 2017-11-07 23:32:43 +01:00
Ricardo Wurmus e2b927993e
gnu: Add r-gqtlbase. 
* gnu/packages/bioinformatics.scm (r-gqtlbase): New variable.
 2017-11-07 23:32:43 +01:00
Ricardo Wurmus 96a392a0b2
gnu: Add r-gprofiler. 
* gnu/packages/bioinformatics.scm (r-gprofiler): New variable.
 2017-11-07 23:32:42 +01:00
Ricardo Wurmus 60faf94597
gnu: Add r-ggbio. 
* gnu/packages/bioinformatics.scm (r-ggbio): New variable.
 2017-11-07 23:32:42 +01:00
Ricardo Wurmus 7af1f40373
gnu: Add r-biovizbase. 
* gnu/packages/bioinformatics.scm (r-biovizbase): New variable.
 2017-11-07 23:32:42 +01:00
Ricardo Wurmus 2f6f61fd8e
gnu: Add r-organismdbi. 
* gnu/packages/bioinformatics.scm (r-organismdbi): New variable.
 2017-11-07 23:32:42 +01:00
Ricardo Wurmus aa30ab5aee
gnu: Add r-ensembldb. 
* gnu/packages/bioinformatics.scm (r-ensembldb): New variable.
 2017-11-07 23:32:42 +01:00
Ricardo Wurmus 763e98103a
gnu: Add r-annotationfilter. 
* gnu/packages/bioinformatics.scm (r-annotationfilter): New variable.
 2017-11-07 23:32:42 +01:00
Ricardo Wurmus 04e2a2e969
gnu: Add r-dirichletmultinomial. 
* gnu/packages/bioinformatics.scm (r-dirichletmultinomial): New variable.
 2017-11-07 23:32:41 +01:00
Ricardo Wurmus 3af149f524
gnu: Add r-complexheatmap. 
* gnu/packages/bioinformatics.scm (r-complexheatmap): New variable.
 2017-11-07 23:32:41 +01:00
Ricardo Wurmus 902fb15d92
gnu: Add r-genomicfiles. 
* gnu/packages/bioinformatics.scm (r-genomicfiles): New variable.
 2017-11-07 23:32:41 +01:00
Ricardo Wurmus e160aa1f81
gnu: Add r-gage. 
* gnu/packages/bioinformatics.scm (r-gage): New variable.
 2017-11-07 12:39:51 +01:00
Ricardo Wurmus 3121814ef1
gnu: Add r-keggrest. 
* gnu/packages/bioinformatics.scm (r-keggrest): New variable.
 2017-11-07 12:39:51 +01:00
Ricardo Wurmus baa00ee90d
gnu: r-msnbase: Update to 2.4.0. 
* gnu/packages/bioinformatics.scm (r-msnbase): Update to 2.4.0.
[propagated-inputs]: Add r-lattice; remove r-reshape2.
 2017-11-07 08:15:44 +01:00
Ricardo Wurmus 39d9098def
gnu: r-mutationalpatterns: Update to 1.4.0. 
* gnu/packages/bioinformatics.scm (r-mutationalpatterns): Update to 1.4.0.
[propagated-inputs]: Add r-cowplot, r-ggdendro, and r-s4vectors.
 2017-11-07 08:15:44 +01:00
Ricardo Wurmus 14b3c71911
gnu: r-annotationhub: Update to 2.10.0. 
* gnu/packages/bioinformatics.scm (r-annotationhub): Update to 2.10.0.
[propagated-inputs]: Add r-curl.
 2017-11-07 08:15:44 +01:00
Ricardo Wurmus 15ca195979
gnu: r-mzr: Remove bundled copy of boost. 
* gnu/packages/bioinformatics.scm (r-mzr)[source]: Remove boost source.
[arguments]: Add build phase "use-system-boost" to link with our boost
package and avoid building the bundled sources.
 2017-11-07 08:15:44 +01:00
Ricardo Wurmus 34b9675449
gnu: r-mzr: Update to 2.12.0. 
* gnu/packages/bioinformatics.scm (r-mzr): Update to 2.12.0.
 2017-11-07 08:15:43 +01:00
Ricardo Wurmus b500dbcdef
gnu: r-mzid: Update to 1.16.0. 
* gnu/packages/bioinformatics.scm (r-mzid): Update to 1.16.0.
 2017-11-07 08:15:43 +01:00
Ricardo Wurmus eeaa6967f9
gnu: r-chipseq: Update to 1.28.0. 
* gnu/packages/bioinformatics.scm (r-chipseq): Update to 1.28.0.
[propagated-inputs]: Add r-lattice.
 2017-11-07 08:15:43 +01:00
Ricardo Wurmus 158b6743dc
gnu: r-genomicfeatures: Update to 1.30.0. 
* gnu/packages/bioinformatics.scm (r-genomicfeatures): Update to 1.30.0.
[propagated-inputs]: Add r-rmysql.
 2017-11-07 08:15:43 +01:00
Ricardo Wurmus 4dd469ef6d
gnu: r-rtracklayer: Update to 1.38.0. 
* gnu/packages/bioinformatics.scm (r-rtracklayer): Update to 1.38.0.
[arguments]: Adjust patch to use system zlib.
 2017-11-07 08:15:42 +01:00
Ricardo Wurmus a044c7f4c4
gnu: r-biocparallel: Update to 1.12.0. 
* gnu/packages/bioinformatics.scm (r-biocparallel): Update to 1.12.0.
[propagated-inputs]: Add r-bh.
 2017-11-07 08:15:42 +01:00
Ricardo Wurmus 42e11d3301
gnu: r-biomart: Update to 2.34.0. 
* gnu/packages/bioinformatics.scm (r-biomart): Update to 2.34.0.
[propagated-inputs]: Add r-progress and r-stringr.
 2017-11-07 08:15:42 +01:00
Ricardo Wurmus 010ab2ffd2
gnu: r-edger: Update to 3.20.1. 
* gnu/packages/bioinformatics.scm (r-edger): Update to 3.20.1.
[propagated-inputs]: Add r-rcpp.
 2017-11-07 08:15:42 +01:00
Ricardo Wurmus eb3f5cc76a
gnu: r-gostats: Update to 2.44.0. 
* gnu/packages/bioinformatics.scm (r-gostats): Update to 2.44.0.
[propagated-inputs]: Add r-rgraphviz.
 2017-11-07 08:15:41 +01:00
Ricardo Wurmus 2404cc4283
gnu: r-category: Update to 2.44.0. 
* gnu/packages/bioinformatics.scm (r-category): Update to 2.44.0.
[propagated-inputs]: Remove r-rsqlite; add r-dbi.
 2017-11-07 08:15:41 +01:00
Ricardo Wurmus 1be0f53664
gnu: r-vsn: Update to 3.46.0. 
* gnu/packages/bioinformatics.scm (r-vsn): Update to 3.46.0.
[propagated-inputs]: Remove r-hexbin.
 2017-11-07 08:15:40 +01:00
Ricardo Wurmus 007424b5a5
gnu: r-motifrg: Rename input label. 
* gnu/packages/bioinformatics.scm (r-motifrg)[propagated-inputs]:
Rename label of r-bsgenome-hsapiens-ucsc-hg19.
 2017-11-07 08:15:40 +01:00
Ricardo Wurmus ce59d62519
gnu: r-motifrg: Update to 1.22.0. 
* gnu/packages/bioinformatics.scm (r-motifrg): Update to 1.22.0.
 2017-11-07 08:15:40 +01:00
Ricardo Wurmus 98791c25c8
gnu: r-qvalue: Update to 2.10.0. 
* gnu/packages/bioinformatics.scm (r-qvalue): Update to 2.10.0.
 2017-11-07 08:15:39 +01:00
Ricardo Wurmus 87fa5aface
gnu: r-fastseq: Update to 1.24.0. 
* gnu/packages/bioinformatics.scm (r-fastseq): Update to 1.24.0.
 2017-11-07 08:15:39 +01:00
Ricardo Wurmus 1567c8d91b
gnu: r-interactivedisplaybase: Update to 1.16.0. 
* gnu/packages/bioinformatics.scm (r-interactivedisplaybase): Update to
1.16.0.
 2017-11-07 08:15:39 +01:00
Ricardo Wurmus 0096127974
gnu: r-edaseq: Update to 2.12.0. 
* gnu/packages/bioinformatics.scm (r-edaseq): Update to 2.12.0.
 2017-11-07 08:15:39 +01:00
Ricardo Wurmus 22752bef3b
gnu: r-msnid: Update to 1.11.0. 
* gnu/packages/bioinformatics.scm (r-msnid): Update to 1.11.0.
 2017-11-07 08:15:38 +01:00
Ricardo Wurmus 8140f680ad
gnu: r-deseq: Update to 1.30.0. 
* gnu/packages/bioinformatics.scm (r-deseq): Update to 1.30.0.
 2017-11-07 08:15:38 +01:00
Ricardo Wurmus 531e80903f
gnu: r-aroma-light: Update to 3.8.0. 
* gnu/packages/bioinformatics.scm (r-aroma-light): Update to 3.8.0.
 2017-11-07 08:15:38 +01:00
Ricardo Wurmus a998c9a464
gnu: r-pcamethods: Update to 1.70.0. 
* gnu/packages/bioinformatics.scm (r-pcamethods): Update to 1.70.0.
 2017-11-07 08:15:38 +01:00
Ricardo Wurmus 8a8138d248
gnu: r-affyio: Update to 1.48.0. 
* gnu/packages/bioinformatics.scm (r-affyio): Update to 1.48.0.
 2017-11-07 08:15:38 +01:00
Ricardo Wurmus dad5f83817
gnu: r-affy: Update to 1.56.0. 
* gnu/packages/bioinformatics.scm (r-affy): Update to 1.56.0.
 2017-11-07 08:15:37 +01:00
Ricardo Wurmus 9a665dfb6f
gnu: r-protgenerics: Update to 1.10.0. 
* gnu/packages/bioinformatics.scm (r-protgenerics): Update to 1.10.0.
 2017-11-07 08:15:37 +01:00
Ricardo Wurmus 617700895b
gnu: r-seqlogo: Update to 1.44.0. 
* gnu/packages/bioinformatics.scm (r-seqlogo): Update to 1.44.0.
 2017-11-07 08:15:37 +01:00
Ricardo Wurmus e127c918f8
gnu: r-genomation: Update to 1.10.0. 
* gnu/packages/bioinformatics.scm (r-genomation): Update to 1.10.0.
[propagated-inputs]: Remove r-rhtslib.
[inputs]: Remove zlib.
 2017-11-07 08:15:37 +01:00
Ricardo Wurmus e6ce4bf00d
gnu: r-impute: Update to 1.52.0. 
* gnu/packages/bioinformatics.scm (r-impute): Update to 1.52.0.
 2017-11-07 08:15:37 +01:00
Ricardo Wurmus 0f948b116b
gnu: r-seqpattern: Update to 1.10.0. 
* gnu/packages/bioinformatics.scm (r-seqpattern): Update to 1.10.0.
 2017-11-07 08:15:36 +01:00
Ricardo Wurmus e67850b40d
gnu: r-bsgenome: Update to 1.46.0. 
* gnu/packages/bioinformatics.scm (r-bsgenome): Update to 1.46.0.
 2017-11-07 08:15:36 +01:00
Ricardo Wurmus d13a3fea7e
gnu: r-topgo: Update to 2.30.0. 
* gnu/packages/bioinformatics.scm (r-topgo): Update to 2.30.0.
 2017-11-07 08:15:36 +01:00
Ricardo Wurmus aeb73879f6
gnu: r-graph: Update to 1.56.0. 
* gnu/packages/bioinformatics.scm (r-graph): Update to 1.56.0.
 2017-11-07 08:15:36 +01:00
Ricardo Wurmus 96fb465174
gnu: r-genomicalignments: Update to 1.14.0. 
* gnu/packages/bioinformatics.scm (r-genomicalignments): Update to 1.14.0.
 2017-11-07 08:15:35 +01:00
Ricardo Wurmus 6fcbed7329
gnu: r-summarizedexperiment: Update to 1.8.0. 
* gnu/packages/bioinformatics.scm (r-summarizedexperiment): Update to 1.8.0.
 2017-11-07 08:15:35 +01:00
Ricardo Wurmus cb0a9a7493
gnu: r-delayedarray: Update to 0.4.1. 
* gnu/packages/bioinformatics.scm (r-delayedarray): Update to 0.4.1.
 2017-11-07 08:15:35 +01:00
Ricardo Wurmus f8068419a6
gnu: r-rsamtools: Update to 1.30.0. 
* gnu/packages/bioinformatics.scm (r-rsamtools): Update to 1.30.0.
 2017-11-07 08:15:35 +01:00
Ricardo Wurmus b719435ebb
gnu: r-biostrings: Update to 2.46.0. 
* gnu/packages/bioinformatics.scm (r-biostrings): Update to 2.46.0.
 2017-11-07 08:15:35 +01:00
Ricardo Wurmus 0f8d98f294
gnu: r-annotationdbi: Update to 1.40.0. 
* gnu/packages/bioinformatics.scm (r-annotationdbi): Update to 1.40.0.
 2017-11-07 08:15:34 +01:00
Ricardo Wurmus ca52123611
gnu: r-biobase: Update to 2.38.0. 
* gnu/packages/bioinformatics.scm (r-biobase): Update to 2.38.0.
 2017-11-07 08:15:34 +01:00
Ricardo Wurmus aa5c1f61f1
gnu: r-genomicranges: Update to 1.30.0. 
* gnu/packages/bioinformatics.scm (r-genomicranges): Update to 1.30.0.
 2017-11-07 08:15:34 +01:00
Ricardo Wurmus 2b6ae8bfd5
gnu: r-xvector: Update to 0.18.0. 
* gnu/packages/bioinformatics.scm (r-xvector): Update to 0.18.0.
 2017-11-07 08:15:34 +01:00
Ricardo Wurmus f642c0e4c7
gnu: r-limma: Update to 3.34.0. 
* gnu/packages/bioinformatics.scm (r-limma): Update to 3.34.0.
 2017-11-07 08:15:33 +01:00
Ricardo Wurmus 7f1bac3528
gnu: r-variantannotation: Update to 1.24.0. 
* gnu/packages/bioinformatics.scm (r-variantannotation): Update to 1.24.0.
 2017-11-07 08:15:33 +01:00
Ricardo Wurmus 8aab0235e0
gnu: r-genomeinfodb: Update to 1.14.0. 
* gnu/packages/bioinformatics.scm (r-genomeinfodb): Update to 1.14.0.
 2017-11-07 08:15:33 +01:00
Ricardo Wurmus 9e482c2069
gnu: r-iranges: Update to 2.12.0. 
* gnu/packages/bioinformatics.scm (r-iranges): Update to 2.12.0.
 2017-11-07 08:15:33 +01:00
Ricardo Wurmus 41f0f94976
gnu: r-s4vectors: Update to 0.16.0. 
* gnu/packages/bioinformatics.scm (r-s4vectors): Update to 0.16.0.
 2017-11-07 08:15:33 +01:00
Ricardo Wurmus 2167eafc1d
gnu: r-biocstyle: Update to 2.6.0. 
* gnu/packages/bioinformatics.scm (r-biocstyle): Update to 2.6.0.
 2017-11-07 08:15:32 +01:00
Ricardo Wurmus 3241461670
gnu: r-biocinstaller: Update to 1.28.0. 
* gnu/packages/bioinformatics.scm (r-biocinstaller): Update to 1.28.0.
 2017-11-07 08:15:32 +01:00
Ricardo Wurmus d61fc4e104
gnu: r-biocgenerics: Update to 0.24.0. 
* gnu/packages/bioinformatics.scm (r-biocgenerics): Update to 0.24.0.
 2017-11-07 08:15:32 +01:00
Ricardo Wurmus 704fe4d115
gnu: r-grohmm: Update to 1.12.0. 
* gnu/packages/bioinformatics.scm (r-grohmm): Update to 1.12.0.
 2017-11-07 08:15:32 +01:00
Ricardo Wurmus 843826e262
gnu: r-shortread: Update to 1.36.0. 
* gnu/packages/bioinformatics.scm (r-shortread): Update to 1.36.0.
 2017-11-07 08:15:31 +01:00
Ricardo Wurmus b53755258a
gnu: r-systempiper: Update to 1.12.0. 
* gnu/packages/bioinformatics.scm (r-systempiper): Update to 1.12.0.
 2017-11-07 08:15:31 +01:00
Ricardo Wurmus 9f52e53d5d
gnu: r-gseabase: Update to 1.40.0. 
* gnu/packages/bioinformatics.scm (r-gseabase): Update to 1.40.0.
 2017-11-07 08:15:31 +01:00
Ricardo Wurmus fad7c0c7bd
gnu: r-sva: Update to 3.26.0. 
* gnu/packages/bioinformatics.scm (r-sva): Update to 3.26.0.
 2017-11-07 08:15:31 +01:00
Ricardo Wurmus 91e1867972
gnu: r-methylkit: Update to 1.4.0. 
* gnu/packages/bioinformatics.scm (r-methylkit): Update to 1.4.0.
 2017-11-07 08:15:31 +01:00
Ricardo Wurmus c126ba69db
gnu: r-copywriter: Update to 2.10.0. 
* gnu/packages/bioinformatics.scm (r-copywriter): Update to 2.10.0.
 2017-11-07 08:15:30 +01:00
Ricardo Wurmus 598dacf657
gnu: r-annotationfilter: Update to 1.2.0. 
* gnu/packages/bioinformatics.scm (r-annotationfilter): Update to 1.2.0.
 2017-11-07 08:15:30 +01:00
Ricardo Wurmus e6b332d43b
gnu: r-rhdf5: Update to 2.22.0. 
* gnu/packages/bioinformatics.scm (r-rhdf5): Update to 2.22.0.
 2017-11-07 08:15:30 +01:00
Ricardo Wurmus 19e8929cbd
gnu: r-tximport: Update to 1.6.0. 
* gnu/packages/bioinformatics.scm (r-tximport): Update to 1.6.0.
 2017-11-07 08:15:30 +01:00
Ricardo Wurmus da153b7f94
gnu: r-bamsignals: Update to 1.10.0. 
* gnu/packages/bioinformatics.scm (r-bamsignals): Update to 1.10.0.
 2017-11-07 08:15:30 +01:00
Ricardo Wurmus 5c18470008
gnu: r-zlibbioc: Update to 1.24.0. 
* gnu/packages/bioinformatics.scm (r-zlibbioc): Update to 1.24.0.
 2017-11-07 08:15:29 +01:00
Ricardo Wurmus 1d0263b44e
gnu: r-rhtslib: Update to 1.10.0. 
* gnu/packages/bioinformatics.scm (r-rhtslib): Update to 1.10.0.
 2017-11-07 08:15:29 +01:00
Ricardo Wurmus c25154e5cb
gnu: r-rbgl: Update to 1.54.0. 
* gnu/packages/bioinformatics.scm (r-rbgl): Update to 1.54.0.
 2017-11-07 08:15:29 +01:00
Ricardo Wurmus 727706ad38
gnu: r-annotationforge: Update to 1.20.0. 
* gnu/packages/bioinformatics.scm (r-annotationforge): Update to 1.20.0.
 2017-11-07 08:15:29 +01:00
Ricardo Wurmus 3fd010ff30
gnu: r-dexseq: Update to 1.24.0. 
* gnu/packages/bioinformatics.scm (r-dexseq): Update to 1.24.0.
 2017-11-07 08:15:28 +01:00
Ricardo Wurmus 0166dc07ef
gnu: r-deseq2: Update to 1.18.0. 
* gnu/packages/bioinformatics.scm (r-deseq2): Update to 1.18.0.
 2017-11-07 08:15:28 +01:00
Ricardo Wurmus 554fac74aa
gnu: r-genefilter: Update to 1.60.0. 
* gnu/packages/bioinformatics.scm (r-genefilter): Update to 1.60.0.
 2017-11-07 08:15:28 +01:00
Ricardo Wurmus cb4d3ff2c4
gnu: r-geneplotter: Update to 1.56.0. 
* gnu/packages/bioinformatics.scm (r-geneplotter): Update to 1.56.0.
 2017-11-07 08:15:28 +01:00
Ricardo Wurmus 2d4e887dc0
gnu: r-annotate: Update to 1.56.0. 
* gnu/packages/bioinformatics.scm (r-annotate): Update to 1.56.0.
 2017-11-07 08:15:28 +01:00
Ricardo Wurmus 94fd86e5e1
gnu: r-dnacopy: Update to 1.52.0. 
* gnu/packages/bioinformatics.scm (r-dnacopy): Update to 1.52.0.
 2017-11-07 08:15:27 +01:00
Ricardo Wurmus c7782c3f1f
gnu: r-biocviews: Update to 1.46.0. 
* gnu/packages/bioinformatics.scm (r-biocviews): Update to 1.46.0.
[propagated-inputs]: Remove r-knitr.
 2017-11-07 08:15:27 +01:00
Ricardo Wurmus 7373b4167a
gnu: r-bioccheck: Update to 1.14.0. 
* gnu/packages/bioinformatics.scm (r-bioccheck): Update to 1.14.0.
[native-inputs]: Remove which.
[propagated-inputs]: Add r-stringdist.
 2017-11-07 08:15:27 +01:00
Ben Woodcroft 171ba2480f
gnu: diamond: Update to 0.9.12. 
* gnu/packages/bioinformatics.scm (diamond): Update to 0.9.12.
 2017-11-04 10:51:44 +10:00
Ricardo Wurmus 66865ab8ac
gnu: multiqc: Update to 1.3. 
* gnu/packages/bioinformatics.scm (multiqc): Update to 1.3.
[propagated-inputs]: Add python-enum34.
[license]: The license was changed to "GPLv3 or later" with this release.
 2017-11-03 17:18:52 +01:00
Ricardo Wurmus b12c6a664d
gnu: r-ape: Update to 5.0. 
* gnu/packages/bioinformatics.scm (r-ape): Update to 5.0.
[propagated-inputs]: Add r-rcpp.
 2017-11-03 14:14:38 +01:00
Ben Woodcroft 03d6e9dd08
gnu: vsearch: Update to 2.5.2. 
* gnu/packages/bioinformatics.scm (vsearch): Update to 2.5.2.
 2017-11-01 10:57:05 +10:00
Ben Woodcroft e126b79736
gnu: diamond: Update to 0.9.11. 
* gnu/packages/bioinformatics.scm (diamond): Update to 0.9.11.
 2017-11-01 10:57:03 +10:00
Ricardo Wurmus 7bf59f7021
gnu: Remove cufflinks. 
Cufflinks includes essential non-free code.
Fixes <https://bugs.gnu.org/28946>.

* gnu/packages/bioinformatics.scm (cufflinks): Remove variable.
 2017-10-31 08:17:06 +01:00
Ben Woodcroft ed5e9a33f8
gnu: vsearch: Update to 2.5.1. 
* gnu/packages/bioinformatics.scm (vsearch): Update to 2.5.1.
 2017-10-26 19:55:29 +10:00
Ben Woodcroft 6f141eff47
gnu: bwa: Update to 0.7.17. 
* gnu/packages/bioinformatics.scm (bwa): Update to 0.7.17.
 2017-10-25 09:29:22 +10:00
Ben Woodcroft ae6e00f6f9
gnu: bwa: Change source URL to GitHub. 
* gnu/packages/bioinformatics.scm (bwa)[source]: Change source URL to
GitHub.
 2017-10-25 09:29:22 +10:00
Tobias Geerinckx-Rice ce4dfde0d8
gnu: miso: Update to 0.5.4. 
* gnu/packages/bioinformatics.scm (miso): Update to 0.5.4.
 2017-10-23 14:49:29 +02:00
Tobias Geerinckx-Rice 5713bbf157
Use HTTPS for bioconductor.org. 
* doc/guix.texi (Invoking guix import, Invoking guix refresh): Use HTTPS for
bioconductor.org URLs.
* gnu/packages/bioinformatics.scm (r-annotate, r-geneplotter, r-genefilter)
(r-deseq2, r-dexseq, r-annotationforge, r-rbgl, r-gseabase, r-category)
(r-gostats, r-shortread, r-biocgenerics, r-biocinstaller, r-biocviews)
(r-biocstyle, r-bioccheck, r-s4vectors, r-iranges, r-genomeinfodbdata)
(r-genomeinfodb, r-xvector, r-genomicranges, r-biobase, r-annotationdbi)
(r-biomart, r-biocparallel, r-biostrings, r-rsamtools, r-delayedarray)
(r-summarizedexperiment, r-genomicalignments, r-rtracklayer)
(r-genomicfeatures, r-graph, r-topgo, r-bsgenome, r-impute, r-seqpattern)
(r-seqlogo, r-motifrg, r-bamsignals, r-mutationalpatterns, r-tximport)
(r-rhdf5, r-chipseq, r-sva, r-affy, r-vsn, r-mzid, r-msnid)
(r-interactivedisplaybase, r-annotationhub)[home-page]: Likewise.
* gnu/packages/bioinformatics.scm (r-txdb-hsapiens-ucsc-hg19-knowngene)
(r-go-db, r-bsgenome-hsapiens-1000genomes-hs37d5, r-org-hs-eg-db)
(r-org-ce-eg-db, r-org-dm-eg-db, r-org-mm-eg-db)
(r-bsgenome-hsapiens-ucsc-hg19, r-bsgenome-mmusculus-ucsc-mm9)
(r-bsgenome-mmusculus-ucsc-mm10, r-txdb-mmusculus-ucsc-mm10-knowngene)
(r-bsgenome-celegans-ucsc-ce6, r-bsgenome-celegans-ucsc-ce10)
(r-bsgenome-dmelanogaster-ucsc-dm3, r-copyhelper)[source, home-page]:
Likewise.
* gnu/packages/statistics.scm (r-rcurl)[source]: Likewise.
* guix/build-system/r.scm (bioconductor-uri): Likewise.
* guix/import/cran.scm (%cran-url, bioconductor-package?)
(bioconductor-data-package?, bioconductor-experiment-package?): Likewise.
 2017-10-21 17:43:40 +02:00
Ricardo Wurmus c0770feedd
gnu: f-seq: Fix location of commons-cli.jar. 
* gnu/packages/bioinformatics.scm (f-seq)[arguments]: Fix location of
commons-cli.jar in the wrapper script.
 2017-10-18 23:54:16 +02:00
Cyril Roelandt af6ce61088
gnu: python-biopython: Update to 1.70. 
* gnu/packages/python.scm (python-biopython, python2-biopython): Update to 1.70.
 2017-10-14 03:17:50 +02:00
Ricardo Wurmus dad66da493
gnu: Add plink-ng. 
* gnu/packages/bioinformatics.scm (plink-ng): New variable.
 2017-10-13 11:14:00 +02:00
Ricardo Wurmus dc8ddbfb07
gnu: Add paml. 
* gnu/packages/bioinformatics.scm (paml): New variable.
 2017-10-13 11:14:00 +02:00
Ricardo Wurmus b3936f35ae
gnu: clustal-omega: Update to 1.2.4. 
* gnu/packages/bioinformatics.scm (clustal-omega): Update to 1.2.4.
 2017-10-12 23:54:54 +02:00
Ricardo Wurmus c6643f2d52
gnu: f-seq: Truncate version string. 
* gnu/packages/bioinformatics.scm (f-seq)[version]: Truncate commit part of
the version string.
 2017-10-12 08:43:54 +02:00
Ricardo Wurmus 01d87d3c18
gnu: rcas-web: Update to 0.0.4. 
* gnu/packages/bioinformatics.scm (rcas-web): Update to 0.0.4.
 2017-10-11 21:37:37 +02:00
Marius Bakke ad3a937dae
Merge branch 'master' into staging 2017-10-07 12:54:40 +02:00
Ben Woodcroft 3ae76f7f57
gnu: vsearch: Update to 2.5.0. 
* gnu/packages/bioinformatics.scm (vsearch): Update to 2.5.0.
 2017-10-07 09:42:55 +10:00
Marius Bakke ffcff27272
Merge branch 'master' into staging 2017-09-24 19:18:35 +02:00
Ben Woodcroft 8c864901b6
gnu: proteinortho: Update to 5.16b. 
* gnu/packages/bioinformatics.scm (proteinortho): Update to 5.16b.
 2017-09-23 18:10:14 +10:00
Ricardo Wurmus 9fc513ad10
gnu: Use xxd instead of vim. 
* gnu/packages/audio.scm (faust-2)[native-inputs]: Replace vim with xxd.
* gnu/packages/avr.scm (microscheme)[native-inputs]: Likewise.
* gnu/packages/bioinformatics.scm (star)[native-inputs]: Likewise.
* gnu/packages/disk.scm (dosfstools)[native-inputs]: Likewise.
* gnu/packages/package-management.scm (diffoscope)[inputs]: Likewise.
 2017-09-22 12:21:09 +02:00
Kei Kebreau dc1d3cdef7
gnu: Use 'modify-phases' syntax. 
* gnu/packages/admin.scm (mingetty, clusterssh, wpa-supplicant-minimal,
wpa-supplicant, wakelan, acpica, tree, direvent, dstat)[arguments]: Use
'modify-phases' syntax.
* gnu/packages/algebra.scm (arb)[arguments]: Likewise.
* gnu/packages/apr.scm (apr-util)[arguments]: Likewise.
* gnu/packages/audio.scm (clalsadrv, fluidsynth, faad2, lv2-mda-piano,
lv2-mda-epiano, timidity++, vamp, soundtouch, portaudio, rsound,
zita-convolver, zita-alsa-pcmi)[arguments]: Likewise.
* gnu/packages/backup.scm (rdup, btar)[arguments]: Likewise.
* gnu/packages/bioinformatics.scm (bedops, bwa, crossmap, express,
flexbar, grit, hisat, ngs-sdk, subread)[arguments]: Likewise.
* gnu/packages/bittorrent.scm (transmission)[arguments]: Likewise.
* gnu/packages/cdrom.scm (cd-discid)[arguments]: Likewise.
* gnu/packages/compression.scm (sharutils)[arguments]: Likewise.
* gnu/packages/conky.scm (conky)[arguments]: Likewise.
* gnu/packages/databases.scm (bdb, bdb-5.3)[arguments]: Likewise.
* gnu/packages/debug.scm (delta, c-reduce)[arguments]: Likewise.
* gnu/packages/display-managers.scm (slim)[arguments]: Likewise.
* gnu/packages/dns.scm (dnsmasq)[arguments]: Likewise.
* gnu/packages/emacs.scm (geiser, emacs-wget, bbdb)[arguments]: Likewise.
* gnu/packages/engineering.scm (pcb)[arguments]: Likewise.
* gnu/packages/firmware.scm (ath9k-htc-firmware)[arguments]: Likewise.
* gnu/packages/flashing-tools.scm (flashrom)[arguments]: Likewise.
* gnu/packages/fltk.scm (fltk)[arguments]: Likewise.
* gnu/packages/freedesktop.scm (python-pyxdg)[arguments]: Likewise.
* gnu/packages/gd.scm (perl-gd)[arguments]: Likewise.
* gnu/packages/gkrellm.scm (gkrellm)[arguments]: Likewise.
* gnu/packages/glib.scm (glibmm)[arguments]: Likewise.
* gnu/packages/gl.scm (glew)[arguments]: Likewise.
* gnu/packages/gnome.scm (icon-naming-utils, orbit2, libbonobo, gnome-vfs,
libgnome, libbonoboui, goffice-0.8, dconf)[arguments]: Likewise.
* gnu/packages/gprolog.scm (gprolog)[arguments]: Likewise.
* gnu/packages/gps.scm (gpscorrelate)[arguments]: Likewise.
* gnu/packages/graphics.scm (agg)[arguments]: Likewise.
* gnu/packages/gtk.scm (ganv, girara, gtksourceview-2, guile-present,
python2-pycairo)[arguments]: Likewise.
* gnu/packages/guile.scm (guile-1.8)[arguments]: Likewise.
* gnu/packages/guile-wm.scm (guile-wm)[arguments]: Likewise.
* gnu/packages/hugs.scm (hugs)[arguments]: Likewise.
* gnu/packages/hurd.scm (gnumach-headers, hurd-headers, hurd-minimal)
[arguments]: Likewise.
* gnu/packages/image-viewers.scm (feh, sxiv)[arguments]: Likewise.
* gnu/packages/libcanberra.scm (libcanberra)[arguments]: Likewise.
* gnu/packages/linux.scm (bridge-utils, iw, fuse, unionfs-fuse/static,
lm-sensors, i2c-tools, xsensors, perf, mdadm, libaio, module-init-tools)
[arguments]: Likewise.
* gnu/packages/lisp.scm (ccl)[arguments]: Likewise.
* gnu/packages/lout.scm (lout)[arguments]: Likewise.
* gnu/packages/lua.scm (luajit)[arguments]: Likewise.
* gnu/packages/machine-learning.scm (shogun)[arguments]: Likewise.
* gnu/packages/mail.scm (exim)[arguments]: Likewise.
* gnu/packages/man.scm (man-pages, txt2man)[arguments]: Likewise.
* gnu/packages/maths.scm (lapack, superlu-dist, openlibm, openspecfun)
[arguments]: Likewise.
* gnu/packages/messaging.scm (bitlbee)[arguments]: Likewise.
* gnu/packages/mp3.scm (libmad, id3lib, mp3info)[arguments]: Likewise.
* gnu/packages/music.scm (solfege)[arguments]: Likewise.
* gnu/packages/noweb.scm (noweb)[arguments]: Likewise.
* gnu/packages/patchutils.scm (patchutils, quilt, colordiff)[arguments]:
Likewise.
* gnu/packages/pdf.scm (xpdf, zathura-cb, zathura-ps, zathura-djvu,
zathura-pdf-poppler, zathura, podofo, fbida)[arguments]: Likewise.
* gnu/packages/perl.scm (perl-file-list, perl-test-harness)[arguments]:
Likewise.
* gnu/packages/photo.scm (gphoto2)[arguments]: Likewise.
* gnu/packages/popt.scm (popt)[arguments]: Likewise.
* gnu/packages/pretty-print.scm (source-highlight, astyle)[arguments]:
Likewise.
* gnu/packages/pumpio.scm (pumpa)[arguments]: Likewise.
* gnu/packages/python.scm (python-passlib, python-pycrypto, python2-empy,
python-sqlalchemy, python-docopt)[arguments]: Likewise.
* gnu/packages/rdf.scm (lrdf)[arguments]: Likewise.
* gnu/packages/regex.scm (tre)[arguments]: Likewise.
* gnu/packages/rrdtool.scm (rrdtool)[arguments]: Likewise.
* gnu/packages/ruby.scm (ruby-2.1, ruby-1.8)[arguments]: Likewise.
* gnu/packages/sawfish.scm (sawfish)[arguments]: Likewise.
* gnu/packages/scheme.scm (racket)[arguments]: Likewise.
* gnu/packages/sdl.scm (guile-sdl)[arguments]: Likewise.
* gnu/packages/serveez.scm (serveez)[arguments]: Likewise.
* gnu/packages/skribilo.scm (skribilo)[arguments]: Likewise.
* gnu/packages/smalltalk.scm (smalltalk)[arguments]: Likewise.
* gnu/packages/suckless.scm (dmenu, slock)[arguments]: Likewise.
* gnu/packages/tcl.scm (expect)[arguments]: Likewise.
* gnu/packages/telephony.scm (commoncpp)[arguments]: Likewise.
* gnu/packages/textutils.scm (recode, libgtextutils)[arguments]:
Likewise.
* gnu/packages/time.scm (time)[arguments]: Likewise.
* gnu/packages/tor.scm (privoxy)[arguments]: Likewise.
* gnu/packages/uucp.scm (uucp)[arguments]: Likewise.
* gnu/packages/video.scm (libdvdnav-4)[arguments]: Likewise.
* gnu/packages/web-browsers.scm (lynx)[arguments]: Likewise.
* gnu/packages/web.scm (tinyproxy)[arguments]: Likewise.
* gnu/packages/wicd.scm (wicd)[arguments]: Likewise.
* gnu/packages/wm.scm (bspwm)[arguments]: Likewise.
* gnu/packages/xdisorg.scm (sxhkd, xcape)[arguments]: Likewise.
* gnu/packages/xfce.scm (xfconf)[arguments]: Likewise.
* gnu/packages/xfig.scm (transfig)[arguments]: Likewise.
* gnu/packages/xorg.scm (imake)[arguments]: Likewise.
 2017-09-20 20:58:04 -04:00
Ricardo Wurmus ebfd6a718a
gnu: r-rcas: Add missing inputs. 
* gnu/packages/bioinformatics.scm (r-rcas)[propagated-inputs]: Add r-pbapply.
 2017-09-18 14:23:03 +02:00
Ricardo Wurmus d82937fbe0
gnu: r-rcas: Update to 1.3.4. 
* gnu/packages/bioinformatics.scm (r-rcas): Update to 1.3.4.
 2017-09-18 11:33:26 +02:00
Kei Kebreau 4561498e1f
gnu: Fix build failures caused by commit 
d10092b849.

* gnu/packages/bioinformatics.scm (seek)[arguments]: Restore previous phase
order.
* gnu/packages/ci.scm (cuirass)[arguments]: Add patch-/bin/sh phase.
 2017-09-10 18:21:35 -04:00
Roel Janssen 325c039c1d
gnu: Add r-sparql. 
* gnu/packages/bioinformatics.scm (r-sparql): New variable.
 2017-09-05 11:02:03 +02:00
Kei Kebreau d10092b849
gnu: Put autoconf-related phases immediately after the 'unpack phase. 
* gnu/packages/audio.scm (audacity, rtmidi)[arguments]: Correct phases
accordingly.
* gnu/packages/bioinformatics.scm (mash, seek, vsearch, emboss,
htslib-for-sambamba)[arguments]: Likewise.
* gnu/packages/ci.scm (cuirass)[arguments]: Likewise.
* gnu/packages/compression.scm (minizip, xdelta)[arguments]: Likewise.
* gnu/packages/cpp.scm (libzen)[arguments]: Likewise.
* gnu/packages/crypto.scm (opendht)[arguments]: Likewise.
* gnu/packages/databases.scm (4store, mdbtools)[arguments]: Likewise.
* gnu/packages/debug.scm (stress-make)[arguments]: Likewise.
* gnu/packages/dns.scm (dnscrypt-proxy, dnscrypt-wrapper)[arguments]:
Likewise.
* gnu/packages/emacs.scm (emacs-pdf-tools)[arguments]: Likewise.
* gnu/packages/embedded.scm (libjaylink, openocd)[arguments]: Likewise.
* gnu/packages/engineering.scm (gerbv)[arguments]: Likewise.
* gnu/packages/erlang.scm (erlang)[arguments]: Likewise.
* gnu/packages/ftp.scm (weex)[arguments]: Likewise.
* gnu/packages/gnome.scm (dia)[arguments]: Likewise.
* gnu/packages/gnunet.scm (gnurl, guile-gnunet)[arguments]: Likewise.
* gnu/packages/gtk.scm (guile-rsvg, graphene)[arguments]: Likewise.
* gnu/packages/guile.scm (guildhall, guile-ics, guile-sqlite3)[arguments]:
Likewise.
* gnu/packages/ibus.scm (ibus-libpinyin)[arguments]: Likewise.
* gnu/packages/irc.scm (weechat)[arguments]: Likewise.
* gnu/packages/java.scm (classpath-devel)[arguments]: Likewise.
* gnu/packages/libreoffice.scm (libetonyek)[arguments]: Likewise.
* gnu/packages/libusb.scm (hidapi)[arguments]: Likewise.
* gnu/packages/linux.scm (gpm)[arguments]: Likewise.
* gnu/packages/logging.scm (glog)[arguments]: Likewise.
* gnu/packages/machine-learning.scm (ghmm)[arguments]: Likewise.
* gnu/packages/mail.scm (dovecot-trees, dovecot-libsodium-plugin, esmtp)
[arguments]: Likewise.
* gnu/packages/messaging.scm (freetalk, libmesode, libstrophe)[arguments]:
Likewise.
* gnu/packages/microcom.scm (microcom)[arguments]: Likewise.
* gnu/packages/ocaml.scm (ocaml-ssl)[arguments]: Likewise.
* gnu/packages/parallel.scm (slurm)[arguments]: Likewise.
* gnu/packages/pdf.scm (libharu)[arguments]: Likewise.
* gnu/packages/samba.scm (cifs-utils)[arguments]: Likewise.
* gnu/packages/serialization.scm (msgpack)[arguments]: Likewise.
* gnu/packages/shells.scm (scsh)[arguments]: Likewise.
* gnu/packages/telephony.scm (libiax2)[arguments]: Likewise.
* gnu/packages/textutils.scm (dotconf)[arguments]: Likewise.
* gnu/packages/version-control.scm (findnewest)[arguments]: Likewise.
* gnu/packages/video.scm (libmediainfo, mediainfo)[arguments]: Likewise.
 2017-09-04 00:10:59 -04:00
Ricardo Wurmus 81195d139f
gnu: r-genomicalignments: Update to 1.12.2. 
* gnu/packages/bioinformatics.scm (r-genomicalignments): Update to 1.12.2.
 2017-09-01 15:11:58 +02:00
Ricardo Wurmus db2e43863c
gnu: r-vegan: Update to 2.4-4. 
* gnu/packages/bioinformatics.scm (r-vegan): Update to 2.4-4.
[native-inputs]: Remove r-knitr.
 2017-09-01 15:11:57 +02:00
Ricardo Wurmus 7b92acdf52
gnu: r-maldiquant: Update to 1.16.4. 
* gnu/packages/bioinformatics.scm (r-maldiquant): Update to 1.16.4.
 2017-09-01 15:11:57 +02:00
Ricardo Wurmus 6bd27981f6
gnu: r-bookdown: Update to 0.5. 
* gnu/packages/bioinformatics.scm (r-bookdown): Update to 0.5.
 2017-09-01 15:11:56 +02:00
Ricardo Wurmus 75690c9f6b
gnu: r-rcas: Correct license. 
* gnu/packages/bioinformatics.scm (r-rcas)[license]: Use correct license.
 2017-09-01 10:26:31 +02:00
Ricardo Wurmus eda8f36cd6
gnu: r-rcas: Update to 1.3.3. 
* gnu/packages/bioinformatics.scm (r-rcas): Update to 1.3.3.
 2017-09-01 10:26:30 +02:00
Ben Woodcroft f4bf420c84
gnu: vsearch: Update to 2.4.4. 
* gnu/packages/bioinformatics.scm (vsearch): Update to 2.4.4.
 2017-09-01 14:45:57 +08:00
Ben Woodcroft 25bd1fc1c1
gnu: metabat: Update to 2.12.1. 
* gnu/packages/patches/metabat-remove-compilation-date.patch: Delete file.
* gnu/local.mk (dist_patch_DATA): Remove it.
* gnu/packages/bioinformatics.scm (metabat): Update to 2.12.1.
[source]: Remove it.  Use url-fetch.
 2017-09-01 14:45:57 +08:00
Ben Woodcroft 0691851a64
gnu: bioinformatics: Work around more "dotless @INC" build failures. 
* gnu/packages/bioinformatics.scm (ncbi-vdb, sra-tools)[arguments]: Add
'set-perl-search-path' phase.
 2017-08-31 12:37:05 +08:00
Ben Woodcroft 690a904ad7
gnu: metabat: Update to 2.11.3. 
* gnu/packages/bioinformatics.scm (metabat): Update to 2.11.3.
[source]: Use git-fetch.  Remove boost-related patch.
* gnu/packages/patches/metabat-fix-boost-issue.patch: Delete file.
* gnu/local.mk (dist_patch_DATA): Remove it.
 2017-08-31 10:43:18 +08:00
Ricardo Wurmus 799247d2d9
gnu: multiqc: Update to 1.2. 
* gnu/packages/bioinformatics.scm (multiqc): Update to 1.2.
[source]: Remove patches.
[arguments]: Remove to enable tests.
[propagated-inputs]: Add python-spectra, python-requests, python-markdown,
python-lzstring.
* gnu/packages/patches/multiqc-fix-git-subprocess-error.patch: Delete file.
* gnu/local.mk (dist_patch_DATA): Remove it.
 2017-08-30 17:32:00 +02:00
Marius Bakke 2718a9cd09
Merge branch 'master' into core-updates 2017-08-21 02:40:37 +02:00
Ricardo Wurmus 17cddc1714
gnu: Add r-annotationfilter. 
* gnu/packages/bioinformatics.scm (r-annotationfilter): New variable.
 2017-08-20 14:00:04 +02:00
Ricardo Wurmus bf3fa99654
gnu: Add r-methylkit. 
* gnu/packages/bioinformatics.scm (r-methylkit): New variable.
 2017-08-17 18:00:17 +02:00
Ricardo Wurmus 212f612040
gnu: Add r-qvalue. 
* gnu/packages/bioinformatics.scm (r-qvalue): New variable.
 2017-08-17 17:26:12 +02:00
Ricardo Wurmus d4a1e918cb
gnu: Add r-fastseg. 
* gnu/packages/bioinformatics.scm (r-fastseg): New variable.
 2017-08-17 17:26:11 +02:00
Ricardo Wurmus 4a007ffafe
gnu: Add r-annotationhub. 
* gnu/packages/bioinformatics.scm (r-annotationhub): New variable.
 2017-08-17 17:25:47 +02:00
Ricardo Wurmus 5f96f30f5d
gnu: Add r-interactivedisplaybase. 
* gnu/packages/bioinformatics.scm (r-interactivedisplaybase): New variable.
 2017-08-17 17:25:46 +02:00
Efraim Flashner d534f3a4d3
gnu: r-mzr: Fix building on aarch64 and armhf. 
* gnu/packages/bioinformatics.scm (r-mzr)[inputs]: Add boost.
 2017-08-16 12:36:25 +03:00
Ben Woodcroft 06f31e50b1
gnu: diamond: Update to 0.9.10. 
* gnu/packages/bioinformatics.scm (diamond): Update to 0.9.10.
 2017-08-15 18:49:33 +10:00
Efraim Flashner 3837108e40
gnu: bcftools: Fix building on aarch64. 
* gnu/packages/patches/bcftools-regidx-unsigned-char.patch: New file.
* gnu/packages/bioinformatics.scm (bcftools)[source]: Use it.
* gnu/local.mk (dist_patch_DATA): Register it.
 2017-08-15 10:31:20 +03:00
Mark H Weaver 09ec5a0f0c
Merge branch 'master' into core-updates 2017-08-15 03:10:14 -04:00
Ricardo Wurmus 9634804890
gnu: Add bismark. 
* gnu/packages/bioinformatics.scm (bismark): New variable.
 2017-08-14 12:00:56 +02:00
Ricardo Wurmus 86763fdd70
gnu: Add r-dexseq. 
* gnu/packages/bioinformatics.scm (r-dexseq): New variable.
 2017-08-14 12:00:51 +02:00
Mark H Weaver cc294bcee6
Merge branch 'master' into core-updates 2017-08-09 17:25:31 -04:00
Ricardo Wurmus 1b22ecdac4
gnu: r-wgcna: Update to 1.61. 
* gnu/packages/bioinformatics.scm (r-wgcna): Update to 1.61.
[propagated-inputs]: Add r-rcpp, r-robust, r-survival.
 2017-08-09 20:08:13 +02:00
Ricardo Wurmus 18f5d2a70a
gnu: Add reference to (gnu packages graph). 
This is a follow-up to 1738138cb3.
 2017-08-09 15:43:35 +02:00
Mark H Weaver 2d9495da23
Merge branch 'master' into core-updates 2017-08-07 16:45:16 -04:00
Tobias Geerinckx-Rice 9d217d277e
gnu: r-bsgenome-hsapiens-ucsc-hg19: Restore original hash. 
* gnu/packages/bioinformatics.scm (r-bsgenome-hsapiens-ucsc-hg19)[source]:
Restore hash from before the tarball changed in place.  It changed back.

This reverts commit fd40857938.
 2017-08-07 01:58:39 +02:00
Mark H Weaver f167595ba1
Merge branch 'master' into core-updates 2017-08-06 00:23:20 -04:00
Ludovic Courtès a56bf101c6
gnu: perl: Work around more "dotless @INC" build issues. 
* gnu/packages/web.scm (perl-www-curl)[arguments]: Add 'set-search-path'
phase.
* gnu/packages/bioinformatics.scm (ngs-sdk)[arguments]: Augment
'configure' phase to set PERL5LIB.
* gnu/packages/image.scm (steghide)[arguments]: Add #:phases argument.
 2017-08-05 00:31:26 +02:00
Efraim Flashner 7cb6155088
gnu: bioinformatics.scm: Use (gnu packages cran) module. 
This is a follow up to a8cba9dd11.

* gnu/packages/bioinformatics.scm: Add (gnu packages cran) to #:use-modules.
 2017-08-03 21:39:12 +03:00
Ricardo Wurmus 5e0de29892
gnu: r-seqminer: Update to 6.0. 
* gnu/packages/bioinformatics.scm (r-seqminer): Update to 6.0.
 2017-08-03 17:53:54 +02:00
Ricardo Wurmus 4e0c847d59
gnu: r-wgcna: Update to 1.60. 
* gnu/packages/bioinformatics.scm (r-wgcna): Update to 1.60.
 2017-08-03 17:53:54 +02:00
Ricardo Wurmus c8a9b2bcbf
gnu: r-qtl: Update to 1.41-6. 
* gnu/packages/bioinformatics.scm (r-qtl): Update to 1.41-6.
 2017-08-03 17:53:54 +02:00
Ricardo Wurmus 023aa8ff58
gnu: r-seqinr: Update to 3.4-5. 
* gnu/packages/bioinformatics.scm (r-seqinr): Update to 3.4-5.
 2017-08-03 17:53:54 +02:00
Ricardo Wurmus 7150f1c30c
gnu: r-optparse: Update to 1.4.4. 
* gnu/packages/bioinformatics.scm (r-optparse): Update to 1.4.4.
 2017-08-03 17:53:53 +02:00
Ricardo Wurmus 3f6ec083ec
gnu: r-bookdown: Update to 0.4. 
* gnu/packages/bioinformatics.scm (r-bookdown): Update to 0.4.
 2017-08-03 17:53:53 +02:00
Ben Woodcroft 75e6639f36
gnu: htseq: Use PyPI URI. 
This is a follow-up to 92971d68ac.

* gnu/packages/bioinformatics.scm (htseq)[source]: Use 'pypi-uri'.
 2017-08-03 21:08:13 +10:00
Ben Woodcroft 92971d68ac
gnu: htseq: Update to 0.9.1. 
* gnu/packages/bioinformatics.scm (htseq): Update to 0.9.1.
[arguments]: Use python-3 by removing field.
[native-inputs]: Add 'python-cython'.
[propagated-inputs]: Use python3 numpy package.
[inputs]: Use python3 pysam package.  Add 'python-matplotlib'.
(python2-htseq): New variable.
(clipper)[inputs]: Use it.
 2017-08-03 21:02:30 +10:00
Roel Janssen f1915a5dd0
gnu: r-deseq2: Update to 1.16.1. 
* gnu/packages/bioinformatics.scm (r-deseq2): Update to 1.16.1.
 2017-08-02 00:33:23 +02:00
Roel Janssen fd215c2978
gnu: r-annotationforge: Update to 1.18.1. 
* gnu/packages/bioinformatics.scm (r-annotationforge): Update to 1.18.1.
 2017-08-02 00:33:07 +02:00
Roel Janssen bd4a0bab5f
gnu: r-category: Update to 2.42.1. 
* gnu/packages/bioinformatics.scm (r-category): Update to 2.42.1.
 2017-08-02 00:32:46 +02:00
Roel Janssen 0ff478344b
gnu: r-biocstyle: Update to 2.4.1. 
* gnu/packages/bioinformatics.scm (r-biocstyle): Update to 2.4.1.
 2017-08-02 00:32:31 +02:00
Roel Janssen 9c4348d8c4
gnu: r-dnacopy: Update to 1.50.1. 
* gnu/packages/bioinformatics.scm (r-dnacopy): Update to 1.50.1.
 2017-08-02 00:32:11 +02:00
Roel Janssen 3ec25eb2a8
gnu: r-iranges: Update to 2.10.2. 
* gnu/packages/bioinformatics.scm (r-iranges): Update to 2.10.2.
 2017-08-02 00:31:46 +02:00
Roel Janssen 6252dd0f15
gnu: r-genomeinfodb: Update to 1.12.2. 
* gnu/packages/bioinformatics.scm (r-genomeinfodb): Update to 1.12.2.
 2017-08-02 00:31:28 +02:00
Roel Janssen 48f5d283b2
gnu: r-variantannotation: Update to 1.22.3. 
* gnu/packages/bioinformatics.scm (r-variantannotation): Update to 1.22.3.
 2017-08-02 00:31:08 +02:00
Roel Janssen 1b4738e23c
gnu: r-limma: Update to 3.32.5. 
* gnu/packages/bioinformatics.scm (r-limma): Update to 3.32.5.
 2017-08-02 00:30:49 +02:00
Roel Janssen 1898a7832f
gnu: r-biobase: Update to 2.36.2. 
* gnu/packages/bioinformatics.scm (r-biobase): Update to 2.36.2.
 2017-08-02 00:30:27 +02:00
Roel Janssen 62eb93a7d0
gnu: r-annotationdbi: Update to 1.38.2. 
* gnu/packages/bioinformatics.scm (r-annotationdbi): Update to 1.38.2.
 2017-08-02 00:28:32 +02:00
Roel Janssen 0c6494a1db
gnu: r-biomart: Update to 2.32.1. 
* gnu/packages/bioinformatics.scm (r-biomart): Update to 2.32.1.
 2017-08-02 00:28:16 +02:00
Roel Janssen 1ff74d074e
gnu: r-biocparallel: Update to 1.10.1. 
* gnu/packages/bioinformatics.scm (r-biocparallel): Update to 1.10.1.
 2017-08-02 00:27:57 +02:00
Roel Janssen 5077bc3e2e
gnu: r-biostrings: Update to 2.44.2. 
* gnu/packages/bioinformatics.scm (r-biostrings): Update to 2.44.2.
 2017-08-02 00:27:35 +02:00
Roel Janssen adf5d0a0bc
gnu: r-delayedarray: Update to 0.2.7. 
* gnu/packages/bioinformatics.scm (r-delayedarray): Update to 0.2.7.
 2017-08-02 00:27:16 +02:00
Roel Janssen f41150f13d
gnu: r-summarizedexperiment: Update to 1.6.3. 
* gnu/packages/bioinformatics.scm (r-summarizedexperiment): Update to 1.6.3.
 2017-08-02 00:26:55 +02:00
Roel Janssen 26760c80cd
gnu: r-genomicalignments: Update to 1.12.1. 
* gnu/packages/bioinformatics.scm (r-genomicalignments): Update to 1.12.1.
 2017-08-02 00:26:33 +02:00
Roel Janssen 15afa9bf8f
gnu: r-rtracklayer: Update to 1.36.4. 
* gnu/packages/bioinformatics.scm (r-rtracklayer): Update to 1.36.4.
 2017-08-02 00:26:00 +02:00
Roel Janssen 8cfaa9ab4e
gnu: r-genomicfeatures: Update to 1.28.4. 
* gnu/packages/bioinformatics.scm (r-genomicfeatures): Update to 1.28.4.
 2017-08-02 00:25:26 +02:00
Roel Janssen 9eb2714625
gnu: r-copywriter: Update to 2.8.1. 
* gnu/packages/bioinformatics.scm (r-copywriter): Update to 2.8.1.
 2017-08-02 00:25:00 +02:00
Roel Janssen bfa0d1e773
gnu: r-sva: Update to 3.24.4. 
* gnu/packages/bioinformatics.scm (r-sva): Update to 3.24.4.
 2017-08-02 00:24:27 +02:00
Marius Bakke aa9780daf9
Merge branch 'master' into core-updates 2017-08-01 23:42:28 +02:00
Efraim Flashner d931a4bbeb
gnu: metabat: Limit to x86_64 and i686 only. 
* gnu/packages/bioinformatics.scm (metabat)[supported-systems]: New field.
 2017-08-01 17:28:35 +03:00
Ben Woodcroft a9085f0c5c
gnu: metabat: Update to 2.11.2. 
* gnu/packages/bioinformatics.scm (metabat): Update to 2.11.2.
 2017-07-29 22:37:47 +10:00
Ben Woodcroft d3dce32216
gnu: metabat: Fix boost-related compilation issue. 
Reported by Leo Famulari.

* gnu/packages/patches/metabat-fix-boost-issue.patch: New file.
* gnu/packages/bioinformatics.scm (metabat): Use it.
* gnu/local.mk (dist_patch_DATA): Add it.
 2017-07-23 22:35:52 +10:00
Ben Woodcroft f3f68a442c
gnu: metabat: Update to 2.11.1. 
* gnu/packages/bioinformatics.scm (metabat): Update to 2.11.1.
[source]: Add patch to fix compilation.
[arguments]: Adjust regular expressions modifying 'SConstruct'.
* gnu/packages/patches/metabat-fix-compilation.patch: New file.
* gnu/local.mk (dist_patch_DATA): Add it.
 2017-07-23 10:29:36 +10:00
Ben Woodcroft 897ab082b2
gnu: python-plastid: Update to 0.4.8. 
* gnu/packages/bioinformatics.scm (python-plastid): Update to 0.4.8.
 2017-07-23 10:29:36 +10:00
Ben Woodcroft 0620387a59
gnu: bcftools: Update to 1.5. 
* gnu/packages/bioinformatics.scm (bcftools): Update to 1.5.
[origin]: Remove fix-makefile patch.
[arguments]: Add configure flags, add LIBS make flag.  Do not delete
configure phase.
* gnu/packages/patches/bcftools-fix-makefile.patch: Remove file.
* gnu/local.mk (dist_patch_DATA): Remove it.
 2017-07-23 10:29:36 +10:00
Ben Woodcroft 63fa0ffcd4
gnu: samtools: Update to 1.5. 
* gnu/packages/bioinformatics.scm (samtools): Update to 1.5.
 2017-07-23 10:29:36 +10:00
Ben Woodcroft 4fb6d1280e
gnu: htslib: Update to 1.5. 
* gnu/packages/bioinformatics.scm (htslib): Update to 1.5.
 2017-07-23 10:29:35 +10:00
Ben Woodcroft 60739965da
gnu: python-pysam: Update to 0.11.2.2. 
* gnu/packages/bioinformatics.scm (python-pysam): Update to 0.11.2.2.
 2017-07-23 10:29:35 +10:00
Ben Woodcroft bca2c57658
gnu: bamm: Use htslib-1.3. 
* gnu/packages/bioinformatics (htslib-1.3): New variable.
(bamm)[inputs]: Replace htslib with htslib-1.3.
 2017-07-23 10:29:35 +10:00
Ben Woodcroft 98593f9f51
gnu: bcftools: Update to 1.4.1. 
* gnu/packages/bioinformatics.scm (bcftools): Update to 1.4.1.
[arguments]: Move Makefile modifications from here ...
[source]: ... to added patch.  Adjust patch for update to 1.4.
* gnu/packages/patches/bcftools-fix-makefile.patch: New file.
* gnu/local.mk (dist_patch_DATA): Register it.
 2017-07-23 10:29:35 +10:00
Ben Woodcroft 4ab1644049
gnu: samtools: Update to 1.4.1. 
* gnu/packages/bioinformatics.scm (samtools): Update to 1.4.1.
[arguments]: Add '--with-htslib=system' configure flag.
[inputs]: Add htslib.
 2017-07-23 10:29:34 +10:00
Ben Woodcroft a9e4a1e641
gnu: htslib: Update to 1.4.1. 
* gnu/packages/bioinformatics.scm (htslib): Update to 1.4.1.
[inputs]: Add curl, openssl.
 2017-07-23 10:29:34 +10:00
Ben Woodcroft c842d42593
gnu: samtools: Use "modify-phases" syntax. 
* gnu/packages/bioinformatics.scm (samtools)[arguments]: Use "modify-phases"
syntax.
 2017-07-23 10:29:34 +10:00
Ricardo Wurmus 3a4b0b126b
gnu: r-s4vectors: Update to 0.14.3. 
* gnu/packages/bioinformatics.scm (r-s4vectors): Update to 0.14.3.
 2017-07-22 17:31:19 +02:00
Ricardo Wurmus a35a1e9c13
gnu: r-genomicranges: Update to 1.28.4. 
* gnu/packages/bioinformatics.scm (r-genomicranges): Update to 1.28.4.
 2017-07-22 17:22:07 +02:00
Ricardo Wurmus fd40857938
gnu: r-bsgenome-hsapiens-ucsc-hg19: Update hash. 
* gnu/packages/bioinformatics.scm (r-bsgenome-hsapiens-ucsc-hg19)[source]:
Update hash because the tarball changed in place.
 2017-07-19 14:39:37 +02:00
Efraim Flashner 2324541bd0
gnu: sortmerna: Limit support to x86_64 and i686 only. 
* gnu/packages/bioinformatics.scm (sortmerna)[supported-systems]: New field.
 2017-07-19 14:37:47 +03:00
Efraim Flashner 2805f9b2a0
gnu: raxml: Limit to x86_64 and i686 only. 
* gnu/packages/bioinformatics.scm (raxml)[supported-systems]: New field.
 2017-07-18 09:00:10 +03:00
Ben Woodcroft 06e372360e
gnu: bowtie: Use 'modify-phases'. 
* gnu/packages/bioinformatics.scm (bowtie)[arguments]: Use 'modify-phases'
syntax.
 2017-07-14 19:23:37 +10:00
Ben Woodcroft d6e63cf31c
gnu: bowtie: Update to 2.3.2. 
* gnu/packages/bioinformatics.scm (bowtie): Update to 2.3.2.
[inputs]: Add zlib.
 2017-07-14 18:54:10 +10:00
Ricardo Wurmus fed7200862
gnu: deeptools: Update to 2.5.1. 
* gnu/packages/bioinformatics.scm (deeptools): Update to 2.5.1.
[arguments]: Remove.
[native-inputs]: Use "python-" instead of "python2-" variants.
[inputs]: Likewise; add python-py2bit.
 2017-07-09 17:07:27 +02:00
Ricardo Wurmus eb2200f3bd
gnu: Add python-py2bit. 
* gnu/packages/bioinformatics.scm (python-py2bit): New variable.
 2017-07-09 17:07:23 +02:00
Ben Woodcroft 4732e6ee84
gnu: blast+: Update to 2.6.0. 
* gnu/packages/bioinformatics.scm (blast+): Update to 2.6.0.
[origin]: Remove bundled pcre.  Add patch.
[arguments]: Replace paths in run_with_lock.c.  Configure with pcre.
[inputs]: Add pcre, perl, python.
* gnu/packages/patches/blast+-fix-makefile.patch: New file.
* gnu/local.mk (dist_patch_DATA): Add it.
 2017-07-08 12:05:59 +10:00
Leo Famulari 0a66c38764
Revert "gnu: blast+: Update to 2.6.0." 
This reverts commit 18dea67dc3.
 2017-07-06 19:38:55 -04:00
Efraim Flashner ce7e361fa3
gnu: gemma: Fix building on non-Intel architectures. 
* gnu/packages/patches/gemma-intel-compat.patch: New file.
* gnu/packages/bioinformatics.scm (gemma)[source]: Add patch.
[arguments]: Add NO_INTEL_COMPAT flag on non-Intel architectures.
* gnu/local.mk (dist_patch_DATA): Register patch.
 2017-07-04 22:55:44 +03:00
Ben J Woodcroft a522517cdb
gnu: diamond: Update to 0.9.9. 
* gnu/packages/bioinformatics.scm (diamond): Update to 0.9.9.
 2017-07-04 19:59:01 +10:00
Ben Woodcroft 18dea67dc3
gnu: blast+: Update to 2.6.0. 
* gnu/packages/bioinformatics.scm (blast+): Update to 2.6.0.
[origin]: Remove bundled pcre.
[arguments]: Replace paths in run_with_lock.c.  Configure with pcre.
[inputs]: Add pcre, perl, python.
 2017-07-04 19:58:42 +10:00
Ben Woodcroft ba773f65f0
gnu: cd-hit: Update to 4.6.8. 
* gnu/packages/bioinformatics.scm (cd-hit): Update to 4.6.8.
 2017-07-01 10:49:37 +10:00
Ben Woodcroft fd99d95b3f
gnu: bwa: Update to 0.7.15. 
* gnu/packages/bioinformatics.scm (bwa): Update to 0.7.15.
 2017-07-01 09:48:20 +10:00
Ricardo Wurmus 7ceb0a83e3
gnu: Add f-seq. 
* gnu/packages/bioinformatics.scm (f-seq): New variable.
 2017-06-25 22:26:07 +02:00
Ben Woodcroft dfc83eadaf
gnu: orfm: Update to 0.7.1. 
* gnu/packages/bioinformatics.scm (orfm): Update to 0.7.1.
 2017-06-24 14:46:46 +10:00
Ben Woodcroft ab8d728144
gnu: orfm: Update to 0.7.0. 
* gnu/packages/bioinformatics.scm (orfm): Update to 0.7.0.
 2017-06-23 22:22:50 +10:00
Ricardo Wurmus 94820951d6
gnu: Add kentutils. 
* gnu/packages/bioinformatics.scm (kentutils): New variable.
 2017-06-23 08:09:33 +02:00
Ricardo Wurmus c1dfe8c30b
gnu: python2-bx-python: Update to 0.7.3. 
* gnu/packages/bioinformatics.scm (python2-bx-python): Update to 0.7.3.
 2017-06-22 17:25:40 +02:00
Arun Isaac 148585c240
gnu: Move contents of zip module into compression module. 
* gnu/packages/zip.scm (zip, unzip, zziplib, perl-zip): Move to...
* gnu/packages/compression.scm: ...here.
* gnu/packages/zip.scm: Delete file.
* gnu/local.mk (GNU_SYSTEM_MODULES): Unregister deleted file.
* po/packages/POTFILES.in: Unregister deleted file.
* gnu/packages/{audio, avr, bioinformatics, busybox, cdrom, ci, compression,
docbook, documentation, fonts, fpga, game-development, games, gl, gnome,
gnuzilla, graphics, guile, haskell, image, java, kodi, ldc, libreoffice,
markup, maths, mc, monitoring, music, php, pretty-print, python, scheme,
smalltalk, statistics, synergy, tex, textutils, video, web-browsers, xml,
zip}.scm, guix/build-system/{ant, font}.scm, guix/{download, packages}.scm:
Adapt module import.
 2017-06-20 18:10:35 +05:30
Ben Woodcroft 0002be1d0b
gnu: diamond: Update to 0.9.8. 
* gnu/packages/bioinformatics.scm (diamond): Update to 0.9.8.
 2017-06-17 13:05:08 +10:00
Tobias Geerinckx-Rice a147fadd3b
gnu: tadbit: Fix typo in description. 
* gnu/packages/bioinformatics.scm (tadbit)[description]: Fix typo.
 2017-06-16 00:29:21 +02:00
Efraim Flashner 07bf6929b9
gnu: gemma: Fix indentation. 
* gnu/packages/bioinformatics.scm (gemma)[arguments]: Fix indentation.
 2017-06-15 10:32:03 +03:00
Efraim Flashner 2c9232ae69
gnu: gemma: Fix building on 32-bit architectures. 
* gnu/packages/bioinformatics.scm (gemma)[arguments]: On 32-bit
architectures add 'FORCE_32BIT' flag.
 2017-06-15 10:31:44 +03:00
Ricardo Wurmus 8befd0940b
gnu: Add tadbit. 
* gnu/packages/bioinformatics.scm (tadbit): New variable.
 2017-06-09 03:32:23 +02:00
Ricardo Wurmus aa163424b2
gnu: Add imp. 
* gnu/packages/bioinformatics.scm (imp): New variable.
 2017-06-09 03:31:51 +02:00
Ricardo Wurmus 282b01515b
gnu: Add phylip. 
* gnu/packages/bioinformatics.scm (phylip): New variable.
 2017-06-09 03:31:50 +02:00
Ricardo Wurmus 3420c905cd
gnu: Add gess. 
* gnu/packages/bioinformatics.scm (gess): New variable.
 2017-06-09 03:31:50 +02:00
Ricardo Wurmus 44f6c88909
gnu: Add trim-galore. 
* gnu/packages/bioinformatics.scm (trim-galore): New variable.
 2017-06-09 03:31:50 +02:00
Ricardo Wurmus b8fffd3a53
gnu: Add ritornello. 
* gnu/packages/bioinformatics.scm (ritornello): New variable.
 2017-06-09 03:31:50 +02:00
Ben Woodcroft f69ff11af7
gnu: diamond: Update to 0.9.6. 
* gnu/packages/bioinformatics.scm (diamond): Update to 0.9.6.
 2017-06-08 09:39:23 +10:00
Roel Janssen b9a601d9db
gnu: Add kaiju. 
* gnu/packages/bioinformatics.scm (kaiju): New variable.
 2017-06-02 12:38:23 +02:00
Ben Woodcroft 0d2b2fd4f4
gnu: diamond: Update to 0.9.3. 
* gnu/packages/bioinformatics.scm (diamond): Update to 0.9.3.
 2017-05-28 21:06:06 -04:00
Ben Woodcroft ca40d4e7c5
gnu: diamond: Update to 0.9.2. 
* gnu/packages/bioinformatics.scm (diamond): Update to 0.9.2.
 2017-05-27 22:03:00 -04:00
Ben Woodcroft b608765a2c
gnu: diamond: Update to 0.9.1. 
* gnu/packages/bioinformatics.scm (diamond): Update to 0.9.1.
 2017-05-22 21:17:41 +01:00
Ricardo Wurmus 296b3c631c
gnu: Add r-edaseq. 
* gnu/packages/bioinformatics.scm (r-edaseq): New variable.
 2017-05-22 18:54:59 +02:00
Ricardo Wurmus 7b46532779
gnu: Add r-deseq. 
* gnu/packages/bioinformatics.scm (r-deseq): New variable.
 2017-05-22 18:54:59 +02:00
Ricardo Wurmus d4b83651d1
gnu: Add r-aroma-light. 
* gnu/packages/bioinformatics.scm (r-aroma-light): New variable.
 2017-05-22 18:54:58 +02:00
Ben Woodcroft 74297231be
gnu: fraggenescan: Update to 1.30. 
* gnu/packages/bioinformatics.scm (fraggenescan): Update to 1.30.
[arguments]: Update patching of paths, install procedure.  Add new test
case.
 2017-05-22 11:44:20 +01:00
Ben Woodcroft 7569613076
gnu: roary: Update to 3.8.2. 
* gnu/packages/bioinformatics.scm (roary): Update to 3.8.2.
 2017-05-22 11:44:20 +01:00
Ben Woodcroft 3cbfc149c3
gnu: taxtastic: Update to 0.6.4. 
* gnu/packages/bioinformatics.scm (taxtastic): Update to 0.6.4.
[source]: Use PyPI URI.
 2017-05-22 11:44:19 +01:00
Roel Janssen b458413721
gnu: r-mutationalpatterns: Update to 1.2.1. 
* gnu/packages/bioinformatics.scm (r-mutationalpatterns): Update to 1.2.1.
 2017-05-22 09:44:08 +02:00
Ben Woodcroft ef81341f0e
gnu: diamond: Update to 0.9.0. 
* gnu/packages/bioinformatics.scm (diamond): Update to 0.9.0.
[license]: Change to AGPL3+.
 2017-05-21 16:08:03 +01:00
Ben Woodcroft 88682c9a72
gnu: fasttree: Update to 2.1.10. 
* gnu/packages/bioinformatics.scm (fasttree): Update to 2.1.10.
 2017-05-21 15:42:08 +01:00
Ben Woodcroft abc08cbae6
gnu: python-biom-format: Update to 2.1.6. 
* gnu/packages/bioinformatics.scm (python-biom-format): Update to 2.1.6.
[propagated-inputs]: Add python-pandas.
 2017-05-21 15:42:08 +01:00
Pjotr Prins 2b18ad054c
gnu: Add gemma. 
* gnu/packages/bioinformatics.scm (gemma): New variable.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2017-05-18 14:22:03 +02:00
Ludovic Courtès 2252f087d4
gnu: guile-json: Rename "guile2.2-json" to "guile-json". 
* gnu/packages/guile.scm (guile-json)[native-inputs]: Change GUILE-2.0
to GUILE-2.2.
(guile2.2-json): Define using 'deprecated-package'.
(guile2.0-json): New variable.
* gnu/packages/bioinformatics.scm (rcas-web)[inputs]: Update accordingly.
* gnu/packages/ci.scm (cuirass)[inputs]: Likewise.
* gnu/packages/package-management.scm (guix)[inputs]: Likewise.
 2017-05-13 22:25:22 +02:00
Ben Woodcroft c033f5d6b5
gnu: Add pplacer. 
* gnu/packages/bioinformatics.scm (pplacer, pplacer-scripts): New
variables.
 2017-05-10 22:13:55 +02:00
Ben Woodcroft ad0ae297d4
gnu: Add taxtastic. 
* gnu/packages/bioinformatics.scm (taxtastic): New variable.
 2017-05-10 22:13:55 +02:00
Petter 2f3108ad03
gnu: Avoid circular dependencies by Perl license. 
* guix/licenses.scm (perl-license): New variable.
* gnu/packages/bioinformatics.scm: Change (package-license perl) to perl-license.
* gnu/packages/compression.scm: Same.
* gnu/packages/databases.scm: Same.
* gnu/packages/gd.scm: Same.
* gnu/packages/language.scm: Same.
* gnu/packages/libevent.scm: Same.
* gnu/packages/mail.scm: Same.
* gnu/packages/messaging.scm: Same.
* gnu/packages/ncurses.scm: Same.
* gnu/packages/networking.scm: Same.
* gnu/packages/photo.scm: Same.
* gnu/packages/tcl.scm: Same.
* gnu/packages/tex.scm: Same.
* gnu/packages/tls.scm: Same.
* gnu/packages/web.scm: Same.
* gnu/packages/wm.scm: Same.
* gnu/packages/xml.scm: Same.
* gnu/packages/xorg.scm: Same.
* gnu/packages/zip.scm: Same.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2017-05-02 23:41:14 +02:00
Roel Janssen f432254237
gnu: vcftools: Update to 0.1.15. 
* gnu/packages/bioinformatics.scm (vcftools): Update to 0.1.15.
 2017-05-01 16:18:39 +02:00
Efraim Flashner 90f83099e8
gnu: r-genomeinfodbdata: Fix source url. 
* gnu/packages/bioinformatics.scm (r-genomeinfodbdata)[source]: Use
source uri and not bioconductor-uri shortener.
 2017-04-29 22:53:43 +03:00
Roel Janssen 524bfe2dbf
gnu: r-msnid: Update to 1.10.0. 
* gnu/packages/bioinformatics.scm (r-msnid): Update to 1.10.0.
 2017-04-28 11:05:42 +02:00
Roel Janssen 82359c72cb
gnu: r-msnbase: Update to 2.2.0. 
* gnu/packages/bioinformatics.scm (r-msnbase): Update to 2.2.0.
 2017-04-28 11:05:41 +02:00
Roel Janssen 5bfa6e090d
gnu: r-pcamethods: Update to 1.68.0. 
* gnu/packages/bioinformatics.scm (r-pcamethods): Update to 1.68.0.
 2017-04-28 11:05:40 +02:00
Roel Janssen 63bf2102cd
gnu: r-mzid: Update to 1.14.0. 
* gnu/packages/bioinformatics.scm (r-mzid): Update to 1.14.0.
 2017-04-28 11:05:38 +02:00
Roel Janssen 60c08b2ff4
gnu: r-vsn: Update to 3.44.0. 
* gnu/packages/bioinformatics.scm (r-vsn):
[source]: Update to 3.44.0,
[propagated-inputs]: Add r-hexbin.
 2017-04-28 11:05:37 +02:00
Roel Janssen bd3cc4cc52
gnu: r-affy: Update to 1.54.0. 
* gnu/packages/bioinformatics.scm (r-affy): Update to 1.54.0.
 2017-04-28 11:05:37 +02:00
Roel Janssen 71abcc4cbf
gnu: r-affyio: Update to 1.46.0. 
* gnu/packages/bioinformatics.scm (r-affyio): Update to 1.46.0.
 2017-04-28 11:05:36 +02:00
Roel Janssen e440ad6d4f
gnu: r-mzr: Update to 2.10.0. 
* gnu/packages/bioinformatics.scm (r-mzr): Update to 2.10.0.
 2017-04-28 11:05:35 +02:00
Roel Janssen 5b1337cc60
gnu: r-protgenerics: Update to 1.8.0. 
* gnu/packages/bioinformatics.scm (r-protgenerics): Update to 1.8.0.
 2017-04-28 11:05:33 +02:00
Roel Janssen 1d09d017db
gnu: r-sva: Update to 3.24.0. 
* gnu/packages/bioinformatics.scm (r-sva): Update to 3.24.0.
 2017-04-28 11:05:20 +02:00
Roel Janssen d52d2d623a
gnu: r-copywriter: Update to 2.8.0. 
* gnu/packages/bioinformatics.scm (r-copywriter): Update to 2.8.0.
 2017-04-28 11:05:19 +02:00
Roel Janssen 7d72f2a803
gnu: r-chipseq: Update to 1.26.0. 
* gnu/packages/bioinformatics.scm (r-chipseq): Update to 1.26.0.
 2017-04-28 11:05:18 +02:00
Roel Janssen 04049a5f2c
gnu: r-rhdf5: Update to 2.20.0. 
* gnu/packages/bioinformatics.scm (r-rhdf5): Update to 2.20.0.
 2017-04-28 11:05:18 +02:00
Roel Janssen ff58a1af98
gnu: r-tximport: Update to 1.4.0. 
* gnu/packages/bioinformatics.scm (r-tximport): Update to 1.4.0.
 2017-04-28 11:05:16 +02:00
Roel Janssen cf4ac4e465
gnu: r-mutationalpatterns: Update to 1.2.0. 
* gnu/packages/bioinformatics.scm (r-mutationalpatterns):
[source]: Update to 1.2.0,
[propagated-inputs]: Add r-bsgenome-hsapiens-1000genomes-hs37d5,
  r-bsgenome-hsapiens-ucsc-hg19.
 2017-04-28 11:05:13 +02:00
Roel Janssen ccd2aade98
gnu: r-bamsignals: Update to 1.8.0. 
* gnu/packages/bioinformatics.scm (r-bamsignals): Update to 1.8.0.
 2017-04-28 11:05:12 +02:00
Roel Janssen 37631ddc28
gnu: r-rhtslib: Update to 1.8.0. 
* gnu/packages/bioinformatics.scm (r-rhtslib): Update to 1.8.0.
 2017-04-28 11:05:11 +02:00
Roel Janssen 8444f6067a
gnu: r-zlibbioc: Update to 1.22.0. 
* gnu/packages/bioinformatics.scm (r-zlibbioc): Update to 1.22.0.
 2017-04-28 11:05:10 +02:00
Roel Janssen a7b90ea990
gnu: r-motifrg: Update to 1.20.0. 
* gnu/packages/bioinformatics.scm (r-motifrg): Update to 1.20.0.
 2017-04-28 11:05:09 +02:00
Roel Janssen 0fce7d9be5
gnu: r-seqlogo: Update to 1.42.0. 
* gnu/packages/bioinformatics.scm (r-seqlogo): Update to 1.42.0.
 2017-04-28 11:05:08 +02:00
Roel Janssen 3ae82c8dfe
gnu: r-genomation: Update to 1.8.0. 
* gnu/packages/bioinformatics.scm (r-genomation): Update to 1.8.0.
 2017-04-28 11:05:07 +02:00
Roel Janssen 08b9224d2d
gnu: r-seqpattern: Update to 1.8.0. 
* gnu/packages/bioinformatics.scm (r-seqpattern): Update to 1.8.0.
 2017-04-28 11:05:06 +02:00
Roel Janssen 5999359f56
gnu: r-impute: Update to 1.50.0. 
* gnu/packages/bioinformatics.scm (r-impute): Update to 1.50.0.
 2017-04-28 11:05:06 +02:00
Roel Janssen c54a702a28
gnu: r-bsgenome: Update to 1.44.0. 
* gnu/packages/bioinformatics.scm (r-bsgenome): Update to 1.44.0.
 2017-04-28 11:05:04 +02:00
Roel Janssen 6e70b6d63c
gnu: r-topgo: Update to 2.28.0. 
* gnu/packages/bioinformatics.scm (r-topgo): Update to 2.28.0.
 2017-04-28 11:05:03 +02:00
Roel Janssen 56373771b3
gnu: r-graph: Update to 1.54.0. 
* gnu/packages/bioinformatics.scm (r-graph): Update to 1.54.0.
 2017-04-28 11:05:02 +02:00
Roel Janssen 5d0301a339
gnu: r-genomicfeatures: Update to 1.28.0. 
* gnu/packages/bioinformatics.scm (r-genomicfeatures): Update to 1.28.0.
 2017-04-28 11:05:01 +02:00
Roel Janssen 2ea7155b04
gnu: r-rtracklayer: Update to 1.36.0. 
* gnu/packages/bioinformatics.scm (r-rtracklayer): Update to 1.36.0.
 2017-04-28 11:05:00 +02:00
Roel Janssen 5f16d1e47d
gnu: r-genomicalignments: Update to 1.12.0. 
* gnu/packages/bioinformatics.scm (r-genomicalignments): Update to 1.12.0.
 2017-04-28 11:04:59 +02:00
Roel Janssen d006ee31af
gnu: r-summarizedexperiment: Update to 1.6.0. 
* gnu/packages/bioinformatics.scm (r-summarizedexperiment):
[source]: Update to 1.6.0,
[propagated-inputs]: Add r-delayedarray.
 2017-04-28 11:04:58 +02:00
Roel Janssen 6bf5543be8
gnu: r-rsamtools: Update to 1.28.0. 
* gnu/packages/bioinformatics.scm (r-rsamtools): Update to 1.28.0.
 2017-04-28 11:04:57 +02:00
Roel Janssen 3ed41af6b5
gnu: r-biostrings: Update to 2.44.0. 
* gnu/packages/bioinformatics.scm (r-biostrings): Update to 2.44.0.
 2017-04-28 11:04:56 +02:00
Roel Janssen 502da6ffc7
gnu: r-biocparallel: Update to 1.10.0. 
* gnu/packages/bioinformatics.scm (r-biocparallel): Update to 1.10.0.
 2017-04-28 11:04:55 +02:00
Roel Janssen 78e7a589c9
gnu: r-biomart: Update to 2.32.0. 
* gnu/packages/bioinformatics.scm (r-biomart): Update to 2.32.0.
 2017-04-28 11:04:47 +02:00
Roel Janssen aafaab22d3
gnu: r-annotationdbi: Update to 1.38.0. 
* gnu/packages/bioinformatics.scm (r-annotationdbi): Update to 1.38.0.
 2017-04-28 11:04:46 +02:00
Roel Janssen b2fff403c8
gnu: r-biobase: Update to 2.36.0. 
* gnu/packages/bioinformatics.scm (r-biobase): Update to 2.36.0.
 2017-04-28 11:04:44 +02:00
Roel Janssen 1859712bef
gnu: r-genomicranges: Update to 1.28.0. 
* gnu/packages/bioinformatics.scm (r-genomicranges): Update to 1.28.0.
 2017-04-28 11:04:42 +02:00
Roel Janssen 17a02f5149
gnu: r-xvector: Update to 0.16.0. 
* gnu/packages/bioinformatics.scm (r-xvector): Update to 0.16.0.
 2017-04-28 11:04:42 +02:00
Roel Janssen abf5a14e11
gnu: r-limma: Update to 3.32.0. 
* gnu/packages/bioinformatics.scm (r-limma): Update to 3.32.0.
 2017-04-28 11:04:41 +02:00
Roel Janssen d2d7af9832
gnu: r-variantannotation: Update to 1.22.0. 
* gnu/packages/bioinformatics.scm (r-variantannotation): Update to 1.22.0.
 2017-04-28 11:04:40 +02:00
Roel Janssen 00ffd55fa1
gnu: r-edger: Update to 3.18.0. 
* gnu/packages/bioinformatics.scm (r-edger): Update to 3.18.0.
 2017-04-28 11:04:39 +02:00
Roel Janssen 38b99ccc57
gnu: r-genomeinfodb: Update to 1.12.0. 
* gnu/packages/bioinformatics.scm (r-genomeinfodb): [source] Update to 1.12.0,
[propagated-inputs]: Add r-genomeinfodbdata.
 2017-04-28 11:04:37 +02:00
Roel Janssen 7d9ab5d920
gnu: r-iranges: Update to 2.10.0. 
* gnu/packages/bioinformatics.scm (r-iranges): Update to 2.10.0.
 2017-04-28 11:04:36 +02:00
Roel Janssen f1f380185b
gnu: r-s4vectors: Update to 0.14.0. 
* gnu/packages/bioinformatics.scm (r-s4vectors): Update to 0.14.0.
 2017-04-28 11:04:34 +02:00
Roel Janssen 9b02d49cb0
gnu: r-dnacopy: Update to 1.50.0. 
* gnu/packages/bioinformatics.scm (r-dnacopy): Update to 1.50.0.
 2017-04-28 11:04:33 +02:00
Roel Janssen 2e11beec48
gnu: r-bioccheck: Update to 1.12.0. 
* gnu/packages/bioinformatics.scm (r-bioccheck): Update to 1.12.0.
 2017-04-28 11:04:32 +02:00
Roel Janssen 3bef24c968
gnu: r-biocstyle: Update to 2.4.0. 
* gnu/packages/bioinformatics.scm (r-biocstyle): [source] Update to 2.4.0.
[propagated-inputs]: Add r-bookdown, r-knitr, r-rmarkdown, r-yaml.
 2017-04-28 11:04:31 +02:00
Roel Janssen 68eac34974
gnu: r-biocviews: Update to 1.44.0. 
* gnu/packages/bioinformatics.scm (r-biocviews): Update to 1.44.0.
 2017-04-28 11:04:30 +02:00
Roel Janssen 3bef15286a
gnu: r-biocinstaller: Update to 1.26.0. 
* gnu/packages/bioinformatics.scm (r-biocinstaller): Update to 1.26.0.
 2017-04-28 11:04:28 +02:00
Roel Janssen 28a5b3f2c6
gnu: r-biocgenerics: Update to 0.22.0. 
* gnu/packages/bioinformatics.scm (r-biocgenerics): Update to 0.22.0.
 2017-04-28 11:04:26 +02:00
Roel Janssen 795a604526
gnu: r-grohmm: Update to 1.10.0. 
* gnu/packages/bioinformatics.scm (r-grohmm): Update to 1.10.0.
 2017-04-28 11:04:25 +02:00
Roel Janssen 026dc7e4fc
gnu: r-systempiper: Update to 1.10.0. 
* gnu/packages/bioinformatics.scm (r-systempiper): Update to 1.10.0.
 2017-04-28 11:04:24 +02:00
Roel Janssen 34c276f761
gnu: r-shortread: Update to 1.34.0. 
* gnu/packages/bioinformatics.scm (r-shortread): Update to 1.34.0.
 2017-04-28 11:04:22 +02:00
Roel Janssen 9511773423
gnu: r-gostats: Update to 2.42.0. 
* gnu/packages/bioinformatics.scm (r-gostats): Update to 2.42.0.
 2017-04-28 11:04:21 +02:00
Roel Janssen ca0289aee7
gnu: r-category: Update to 2.42.0. 
* gnu/packages/bioinformatics.scm (r-category): Update to 2.42.0.
 2017-04-28 11:04:20 +02:00
Roel Janssen c584a07ffd
gnu: r-gseabase: Update to 1.38.0. 
* gnu/packages/bioinformatics.scm (r-gseabase): Update to 1.38.0.
 2017-04-28 11:04:19 +02:00
Roel Janssen 8ab6f241ea
gnu: r-rbgl: Update to 1.52.0. 
* gnu/packages/bioinformatics.scm (r-rbgl): Update to 1.52.0.
 2017-04-28 11:04:16 +02:00
Roel Janssen 46972a4427
gnu: r-annotationforge: Update to 1.18.0. 
* gnu/packages/bioinformatics.scm (r-annotationforge): Update to 1.18.0.
 2017-04-28 11:04:12 +02:00
Roel Janssen 3ae74e451c
gnu: r-deseq2: Update to 1.16.0. 
* gnu/packages/bioinformatics.scm (r-deseq2): Update to 1.16.0.
 2017-04-28 11:04:09 +02:00
Roel Janssen b5bc3a3963
gnu: r-genefilter: Update to 1.58.0. 
* gnu/packages/bioinformatics.scm (r-genefilter): Update to 1.58.0.
 2017-04-28 11:04:06 +02:00
Roel Janssen 97a50e4f34
gnu: r-geneplotter: Update to 1.54.0. 
* gnu/packages/bioinformatics.scm (r-geneplotter): Update to 1.54.0.
 2017-04-28 11:03:59 +02:00
Roel Janssen dbab99b6d2
gnu: r-annotate: Update to 1.54.0. 
* gnu/packages/bioinformatics.scm (r-annotate): Update to 1.54.0.
 2017-04-28 11:03:47 +02:00
Roel Janssen ffef27f3d2
gnu: Add r-genomeinfodbdata. 
* gnu/packages/bioinformatics.scm (r-genomeinfodbdata): New variable.
 2017-04-28 10:17:06 +02:00
Roel Janssen 71e34e6b5b
gnu: Add r-delayedarray. 
* gnu/packages/bioinformatics.scm (r-delayedarray): New variable.
 2017-04-28 10:15:12 +02:00
Roel Janssen 2abfc5b827
gnu: Add r-bookdown. 
* gnu/packages/bioinformatics.scm (r-bookdown): New variable.
 2017-04-28 10:09:31 +02:00
Ricardo Wurmus 31c374e081
gnu: python-pysam: Disable tests. 
* gnu/packages/bioinformatics.scm (python-pysam): Disable tests.
 2017-04-25 14:05:59 +02:00
Ricardo Wurmus b2955e224e
gnu: python-pysam: Fix tests, again. 
* gnu/packages/bioinformatics.scm (python-pysam)[arguments]: Run nosetests
explicitly with a single process.
 2017-04-24 18:46:28 +02:00
Efraim Flashner c136240efc
gnu: diamond: Enable building on all architectures. 
* gnu/packages/bioinformatics.scm (diamond)[supported-systems]: Remove
field.
 2017-04-24 19:30:10 +03:00
Ricardo Wurmus 1a84edeb0b
gnu: r-seqminer: Update to 5.9. 
* gnu/packages/bioinformatics.scm (r-seqminer): Update to 5.9.
 2017-04-22 23:30:31 +02:00
Ben Woodcroft a7d12a9e71
gnu: proteinortho: Update to 5.16. 
* gnu/packages/bioinformatics.scm (proteinortho): Update to 5.16.
 2017-04-21 23:03:56 +10:00
Ben Woodcroft 37199768e8
gnu: diamond: Update to 0.8.38. 
* gnu/packages/bioinformatics.scm (diamond): Update to 0.8.38.
 2017-04-21 23:03:55 +10:00
Tobias Geerinckx-Rice d1e4ad1b02
gnu: Fix typos in descriptions. 
* gnu/packages/admin.scm (di)[description]: Likewise.
* gnu/packages/bioinformatics.scm (r-annotate)[description]: Likewise.
* gnu/packages/datastructures.scm (sparsehash)[description]: Likewise.
* gnu/packages/dns.scm (knot)[description]: Likewise.
* gnu/packages/emacs.scm (emacs-idle-highlight)[synopsis, description]:
Likewise.
* gnu/packages/gnome.scm (libpeas)[description]: Likewise.
* gnu/packages/gtk.scm (python2-pygtk)[description]: Likewise.
* gnu/packages/kde-frameworks.scm (kactivities)[description]: Fix typo.
* gnu/packages/libevent.scm (perl-anyevent)[description]: Likewise.
* gnu/packages/machine-learning.scm (ghmm)[description]: Likewise.
* gnu/packages/mail.scm (mlmmj)[description]: Likewise.
* gnu/packages/maths.scm (vc)[description]: Likewise.
* gnu/packages/music.scm (gx-super-fuzz-lv2)[description]: Likewise.
* gnu/packages/networking.scm (nload)[description]: Likewise.
* gnu/packages/python.scm (python-execnet)[description]: Likewise.
* gnu/packages/terminals.scm (tilda)[description]: Likewise.
* gnu/packages/python.scm (python-execnet, python-tables)
(python2-coverage-test-runner, python2-rope)[description]: Likewise.
 2017-04-17 02:04:08 +02:00
Ben Woodcroft 88eb119f95
gnu: mafft: Update to 7.310. 
* gnu/packages/bioinformatics.scm (mafft): Update to 7.310.
 2017-04-14 15:19:37 +10:00
Ben Woodcroft e9e0fab079
gnu: raxml: Update to 8.2.10. 
* gnu/packages/bioinformatics.scm (raxml): Update to 8.2.10.
 2017-04-09 21:44:14 +10:00
Ricardo Wurmus 6acdff5875
gnu: r-rsamtools: Update to 1.26.2. 
* gnu/packages/bioinformatics.scm (r-rsamtools): Update to 1.26.2.
 2017-04-09 13:34:53 +02:00
Ricardo Wurmus dc8ebe43af
gnu: r-biocparallel: Update to 1.8.2. 
* gnu/packages/bioinformatics.scm (r-biocparallel): Update to 1.8.2.
 2017-04-09 13:34:53 +02:00
Ricardo Wurmus 1d65b5379b
gnu: r-vegan: Update to 2.4-3. 
* gnu/packages/bioinformatics.scm (r-vegan): Update to 2.4-3.
[arguments]: Remove build phase "revert-test-deletion".
[native-inputs]: Remove "r-vegan-delete-tests-patch".
 2017-04-08 10:25:50 +02:00
Ben Woodcroft 37982693ca
gnu: vsearch: Update to 2.4.3. 
* gnu/packages/bioinformatics.scm (vsearch): Update to 2.4.3.
 2017-04-07 21:35:07 +10:00
Ricardo Wurmus e18c731ba0
gnu: r-seqinr: Update to 3.3-6. 
* gnu/packages/bioinformatics.scm (r-seqinr): Update to 3.3-6.
 2017-04-06 14:39:22 +02:00
Ricardo Wurmus 0685fe3c86
gnu: r-rcpparmadillo: Update to 0.7.700.0.0. 
* gnu/packages/statistics.scm (r-rcpparmadillo): Update to 0.7.700.0.0.
[source]: Do not delete bundled armadillo sources, because upstream no longer
hosts previous versions.
[propagated-inputs]: Remove "armadillo-for-rcpparmadillo".
[arguments]: Remove because we no longer need to link with the armadillo
library.
* gnu/packages/bioinformatics.scm (r-deseq2)[arguments]: Remove because we no
longer need to link with armadillo library.
 2017-04-06 14:39:22 +02:00
Ricardo Wurmus a3656b11d2
gnu: r-annotationforge: Update to 1.16.1. 
* gnu/packages/bioinformatics.scm (r-annotationforge): Update to 1.16.1.
 2017-04-06 14:39:22 +02:00
Ricardo Wurmus e0d7b31820
gnu: r-shortread: Update to 1.32.1. 
* gnu/packages/bioinformatics.scm (r-shortread): Update to 1.32.1.
 2017-04-06 14:39:21 +02:00
Ricardo Wurmus 2cea968e41
gnu: r-s4vectors: Update to 0.12.2. 
* gnu/packages/bioinformatics.scm (r-s4vectors): Update to 0.12.2.
 2017-04-06 14:39:21 +02:00
Ricardo Wurmus 7d05eb2dcc
gnu: r-iranges: Update to 2.8.2. 
* gnu/packages/bioinformatics.scm (r-iranges): Update to 2.8.2.
 2017-04-06 14:39:21 +02:00
Ricardo Wurmus e89cf15091
gnu: r-variantannotation: Update to 1.20.3. 
* gnu/packages/bioinformatics.scm (r-variantannotation): Update to 1.20.3.
 2017-04-06 14:39:21 +02:00
Ricardo Wurmus 3506a62762
gnu: r-limma: Update to 3.30.13. 
* gnu/packages/bioinformatics.scm (r-limma): Update to 3.30.13.
 2017-04-06 14:39:21 +02:00
Ricardo Wurmus 4cd4721dbb
gnu: r-genomicranges: Update to 1.26.4. 
* gnu/packages/bioinformatics.scm (r-genomicranges): Update to 1.26.4.
 2017-04-06 14:39:20 +02:00
Ricardo Wurmus 69b356efce
gnu: r-annotationdbi: Update to 1.36.2. 
* gnu/packages/bioinformatics.scm (r-annotationdbi): Update to 1.36.2.
 2017-04-06 14:39:20 +02:00
Ricardo Wurmus 5cc3b7a548
gnu: r-genomicalignments: Update to 1.10.1. 
* gnu/packages/bioinformatics.scm (r-genomicalignments): Update to 1.10.1.
 2017-04-06 14:39:20 +02:00
Ricardo Wurmus 25d8854723
gnu: r-rtracklayer: Update to 1.34.2. 
* gnu/packages/bioinformatics.scm (r-rtracklayer): Update to 1.34.2.
 2017-04-06 14:39:20 +02:00
Ricardo Wurmus 9ce6cb082e
gnu: r-genomicfeatures: Update to 1.26.4. 
* gnu/packages/bioinformatics.scm (r-genomicfeatures): Update to 1.26.4.
 2017-04-06 14:39:20 +02:00
Ricardo Wurmus 57ac1d2f03
gnu: r-seqminer: Update to 5.7. 
* gnu/packages/bioinformatics.scm (r-seqminer): Update to 5.7.
 2017-04-06 14:39:19 +02:00
Ricardo Wurmus e8bec95e69
gnu: r-maldiquant: Update to 1.16.2. 
* gnu/packages/bioinformatics.scm (r-maldiquant): Update to 1.16.2.
 2017-04-06 14:39:19 +02:00
Ricardo Wurmus 4cd07e487e
gnu: r-genomeinfodb: Update to 1.10.3. 
* gnu/packages/bioinformatics.scm (r-genomeinfodb): Update to 1.10.3.
[propagated-inputs]: Add "r-rcurl".
 2017-04-06 14:39:11 +02:00
Ricardo Wurmus acbeb2d56b
gnu: r-xvector: Update to 0.14.1. 
* gnu/packages/bioinformatics.scm (r-xvector): Update to 0.14.1.
 2017-04-06 14:39:11 +02:00
Ricardo Wurmus da250f733a
gnu: r-bioccheck: Update to 1.10.1. 
* gnu/packages/bioinformatics.scm (r-bioccheck): Update to 1.10.1.
[propagated-inputs]: Remove "r-knitr" and "r-devtools".
 2017-04-06 14:39:11 +02:00
Ricardo Wurmus 1108a920bd
gnu: sra-tools: Fix glibc naming conflict. 
* gnu/packages/bioinformatics.scm (sra-tools)[arguments]: Add build phase
"patch-away-glibc-conflict" to fix a definition conflict with glibc 2.25.
 2017-04-05 18:06:51 +02:00
Ricardo Wurmus beebe43176
gnu: sra-tools: Use "modify-phases" syntax. 
* gnu/packages/bioinformatics.scm (sra-tools)[arguments]: Use "modify-phases"
syntax.
 2017-04-05 18:06:51 +02:00
Ben Woodcroft fc5b12879f
gnu: diamond: Update to 0.8.37. 
* gnu/packages/bioinformatics.scm (diamond): Update to 0.8.37.
 2017-04-05 22:49:01 +10:00
Leo Famulari 7bf837fd43
gnu: Use HTTPS URLs for GitHub home-pages. 
* gnu/packages/bioinformatics.scm, gnu/packages/emacs.scm,
gnu/packages/haskell.scm, gnu/packages/libffi.scm, gnu/packages/lisp.scm,
gnu/packages/ocaml.scm, gnu/packages/openstack.scm, gnu/packages/python.scm,
gnu/packages/ruby.scm, gnu/packages/shells.scm, gnu/packages/statistics.scm,
gnu/packages/xdisorg.scm: Use HTTPS URLs for all packages with a home-page on
GitHub.
 2017-04-02 20:00:51 -04:00
Ben Woodcroft cf1d581464
gnu: khmer: Build with gcc-4. 
* gnu/packages/bioinformatics.scm (khmer)[inputs]: Add gcc-4.9.
 2017-04-02 10:14:17 +10:00
Marius Bakke 84157bb8bf
Merge branch 'master' into core-updates 
Most conflicts are from 6fd52309b8.
 2017-03-30 22:59:53 +02:00
Ricardo Wurmus fa702e1a29
gnu: discrover: Add missing includes. 
* gnu/packages/bioinformatics.scm (discrover)[arguments]: Add build phase
"add-missing-includes" to include "random" headers.
 2017-03-30 10:35:54 +02:00
Ricardo Wurmus 0d2c0562b8
gnu: stringtie: Remove typedef conflict. 
* gnu/packages/bioinformatics.scm (stringtie)[arguments]: Remove conflicting
typedef in a new build phase "remove-duplicate-typedef".
 2017-03-30 10:35:53 +02:00
Ludovic Courtès e1f02f92e9
Replace (compose not PROC) with simpler idioms. 
* gnu/packages/bioinformatics.scm (python-pysam)[arguments] <check>:
Use (negate proc) instead of (compose not proc).
* guix/import/cran.scm (recursive-import): Likewise.
* guix/import/elpa.scm (filter-dependencies): Use 'remove' instead of
'(filter (compose not proc) ...)'.
 2017-03-28 22:15:44 +02:00
Ricardo Wurmus 939b6b113b
gnu: star: Update to 2.5.3a. 
* gnu/packages/bioinformatics.scm (star): Update to 2.5.3a.
 2017-03-23 11:21:08 +01:00
Ricardo Wurmus 54262c5435
gnu: python-pysam: Run tests in parallel. 
* gnu/packages/bioinformatics.scm (python-pysam)[arguments]: Run nose tests in
parallel.
 2017-03-22 12:33:28 +01:00
Ricardo Wurmus 71dbf592c4
gnu: python-pysam: Run tests before installation. 
* gnu/packages/bioinformatics.scm (python-pysam)[arguments]: Adjust check
phase to be run before installation.
 2017-03-22 12:33:28 +01:00
Ricardo Wurmus 879b521cd0
gnu: python-pysam: Update to 0.10.0. 
* gnu/packages/bioinformatics.scm (python-pysam): Update to 0.10.0.
 2017-03-22 12:33:24 +01:00
Ludovic Courtès f6396d862f
gnu: Rename "guile-next" to "guile". 
* gnu/packages/guile.scm (guile-next): Rename to...
(guile-2.2): ... this.  Update users.
[name]: Change to "guile".
[synopsis]: Remove.
[properties]: Remove 'upstream-name', 'ftp-server', and
'ftp-directory'.
* gnu/packages/bioinformatics.scm (rcas-web): Update accordingly.
* gnu/packages/tls.scm (gnutls/guile-2.2): Likewise.
* tests/guix-build.sh: Use 'guile@2.2' instead of 'guile-next'.
* doc/guix.texi (Package Transformation Options): Update examples that
referred to "guile-next".
 2017-03-19 18:14:22 +01:00
Ricardo Wurmus 2d7c4ae3ee
gnu: r: Rename to r-minimal. 
* gnu/packages/statistics.scm (r): Rename to...
(r-minimal): ...this new variable.
(r-with-recommended-packages): Rename to...
(r): ...this.
* guix/build-system/r.scm (default-r): Reference r-minimal.
* gnu/packages/emacs.scm (emacs-ess)[inputs],
gnu/packages/machine-learning.scm (shogun)[inputs],
gnu/packages/python.scm (python-rpy2)[inputs],
gnu/packages/bioinformatics.scm (ribotaper)[inputs],
(couger)[propagated-inputs],
(roary)[inputs],
(rsem)[inputs],
(rcas-web)[inputs]: Change "r" to "r-minimal".
 2017-03-17 10:14:02 +01:00
Ricardo Wurmus aeb64f3cb2
gnu: r: Do not build recommended packages. 
* gnu/packages/statistics.scm (r)[arguments]: Rename phase
"build-recommended-packages-reproducibly" to "build-reproducibly"; add
configure flag "--without-recommended-packages".
* guix/import/cran.scm (default-r-packages): Remove recommended packages.
* gnu/packages/python.scm (python-rpy2)[inputs]: Add r-survival.
* gnu/packages/bioinformatics.scm (r-ape)[propagated-inputs]: Add r-lattice
and r-nlme.
(r-vegan)[propagated-inputs]: Add r-mass.
(r-genefilter)[propagated-inputs]: Add r-survival.
(r-grohmm)[propagated-inputs]: Add r-mass.
(r-bioccheck)[propagated-inputs]: Add r-codetools.
(r-summarizedexperiment)[propagated-inputs]: Add r-matrix.
(r-topgo)[propagated-inputs]: Add r-lattice.
(r-sva)[propagated-inputs]: Add r-mgcv.
(r-raremetals2)[propagated-inputs]: Add r-mass.
(r-vsn)[propagated-inputs]: Add r-lattice.
(r-pcamethods)[propagated-inputs]: Add r-mass.
* gnu/packages/bioinformatics.scm (r-ggplot2)[propagated-inputs]: Add r-mass.
(r-locfit)[propagated-inputs]: Add r-lattice.
(r-coda)[propagated-inputs]: Add r-lattice.
(r-irlba)[propagated-inputs]: Add r-matrix.
(r-glmnet)[propagated-inputs]: Add r-matrix.
(r-e1071)[propagated-inputs]: Add r-class.
(r-spams)[propagated-inputs]: Add r-lattice and r-matrix.
(r-hmisc)[propagated-inputs]: Add r-cluster, r-foreign, r-lattice, r-nnet, and
r-rpart.
(r-zoo)[propagated-inputs]: Add r-lattice.
(r-mixtools)[propagated-inputs]: Add r-boot and r-mass.
(r-flexmix)[propagated-inputs]: Add r-lattice and r-nnet.
(r-prabclus)[propagated-inputs]: Add r-mass.
(r-fpc)[propagated-inputs]: Add r-class, r-cluster, and r-mass.
(r-rcppeigen)[propagated-inputs]: Add r-matrix.
(r-matrixmodels)[propagated-inputs]: Add r-matrix.
(r-lme4)[propagated-inputs]: Add r-mass and r-nlme.
(r-pbkrtest)[propagated-inputs]: Add r-mass and r-matrix.
(r-car)[propagated-inputs]: Add r-mass, r-mgcv, and r-nnet.
(r-tclust)[propagated-inputs]: Add r-cluster.
 2017-03-17 10:14:02 +01:00
Raoul Jean Pierre Bonnal 2441c28414
gnu: Add r-seurat. 
* gnu/packages/bioinformatics.scm (r-seurat): New variable.

Co-authored-by: Ricardo Wurmus <rekado@elephly.net>
 2017-03-16 14:54:58 +01:00
Ricardo Wurmus 79849358f8
gnu: sra-tools: Update to 2.8.2-1. 
* gnu/packages/bioinformatics.scm (sra-tools): Update to 2.8.2-1.
[arguments]: Add DEFAULT_CRT and DEFAULT_KFG to make flags.
 2017-03-16 13:40:36 +01:00
Ricardo Wurmus d5e1716239
gnu: ncbi-vdb: Install configuration files. 
* gnu/packages/bioinformatics.scm (ncbi-vdb)[arguments]: Add phase
"install-configuration-files".
 2017-03-16 13:39:53 +01:00
Ricardo Wurmus 558e23074e
gnu: ncbi-vdb: Override search path for java-ngs. 
* gnu/packages/bioinformatics.scm (ncbi-vdb)[arguments]: Patch "package.prl"
to ensure that java-ngs is found by the configure script; remove configure
flag "--with-ngs-java-prefix".
 2017-03-16 13:38:39 +01:00
Ricardo Wurmus 701111989e
gnu: ncbi-vdb: Use modify-phases syntax. 
* gnu/packages/bioinformatics.scm (ncbi-vdb)[arguments]: Use modify-phases
syntax.
 2017-03-16 10:20:56 +01:00
Ricardo Wurmus 5021f54787
gnu: ncbi-vdb: Update to 2.8.2. 
* gnu/packages/bioinformatics.scm (ncbi-vdb): Update to 2.8.2.
 2017-03-16 10:19:25 +01:00
Ricardo Wurmus 6c4ccf3228
gnu: ngs-sdk: Update to 1.3.0. 
* gnu/packages/bioinformatics.scm (ngs-sdk): Update to 1.3.0.
 2017-03-16 10:18:48 +01:00
Tobias Geerinckx-Rice f38607536e
gnu: Use INSTALL-FILE where appropriate. 
* gnu/packages/admin.scm (wpa-supplicant-minimal): Substitute the simpler
INSTALL-FILE for COPY-FILE when invoked with redundant arguments.
* gnu/packages/bioinformatics.scm (couger, aragorn, express-beta-diversity,
edirect, fasttree, rsem, samtools-0.1): Likewise.
* gnu/packages/code.scm (withershins): Likewise.
* gnu/packages/conky.scm (conky): Likewise.
* gnu/packages/debug.scm (delta, american-fuzzy-lop): Likewise.
* gnu/packages/emacs.scm (emacs-mit-scheme-doc): Likewise.
* gnu/packages/engineering.scm (librecad): Likewise.
 2017-03-15 22:19:39 +01:00
Tobias Geerinckx-Rice b2d748edff
gnu: samtools: End installation phases with truth. 
* gnu/packages/bioinformatics.scm (samtools, samtools-0.1)[arguments]:
Return #T instead of the undefined results of COPY-FILE or INSTALL-FILE.
 2017-03-15 01:10:30 +01:00
Ben Woodcroft fbf45d6ea7
gnu: vsearch: Update to 2.4.2. 
* gnu/packages/bioinformatics.scm (vsearch): Update to 2.4.2.
 2017-03-11 11:37:15 +10:00
Raoul Jean Pierre Bonnal 036cd0cb8b
gnu: Add r-ape. 
* gnu/packages/bioinformatics.scm (r-ape): New variable.

Co-authored-by: Ben Woodcroft <donttrustben@gmail.com>
 2017-03-11 10:43:26 +10:00
Ben J. Woodcroft 79f09fa239
gnu: hmmer: Build reproducibly. 
* gnu/packages/patches/hmmer-remove-cpu-specificity.patch: New file.
* gnu/packages/bioinformatics.scm (hmmer): Use it.
 2017-03-10 20:31:30 +10:00
Ricardo Wurmus 5ded35d89d
gnu: Add sambamba. 
* gnu/packages/bioinformatics.scm (htslib-for-sambamba, sambamba): New
variables.
 2017-03-10 10:13:59 +01:00
Marius Bakke 3f98071ac5
Merge branch 'python-tests' 2017-03-03 16:55:43 +01:00
Ben Woodcroft a9f754d733
gnu: diamond: Update to 0.8.36. 
* gnu/packages/bioinformatics.scm (diamond): Update to 0.8.36.
 2017-03-02 21:19:26 +10:00
Ricardo Wurmus 48d66a9c99
gnu: bamtools: Update to 2.4.1. 
* gnu/packages/bioinformatics.scm (bamtools): Update to 2.4.1.
 2017-02-28 12:10:02 +01:00
Marius Bakke 2bb12f5a68
gnu: ribodiff: Fix test failure. 
* gnu/packages/bioinformatics.scm (ribodiff)[native-inputs]: Add PYTHON2-MOCK
  and PYTHON2-NOSE.
 2017-02-27 15:32:17 +01:00
Ricardo Wurmus 1885bb0c08
gnu: python-dendropy: Fix failing tests. 
* gnu/packages/patches/python-dendropy-fix-tests.patch: New file.
* gnu/local.mk (dist_patch_DATA): Add it.
* gnu/packages/bioinformatics.scm (python-dendropy)[source]: Add patch.
 2017-02-24 23:44:31 +01:00
Marius Bakke 424b1ae769
Merge branch 'master' into python-tests 2017-02-13 22:35:05 +01:00
Ben Woodcroft 206af46fe1
gnu: vsearch: Update to 2.4.0. 
* gnu/packages/bioinformatics.scm (vsearch): Update to 2.4.0.
[source]: Convert most operations in the snippet to patch form and adjust
for 2.4.0.
* gnu/packages/patches/vsearch-unbundle-cityhash.patch: New file.
* gnu/local.mk (dist_patch_DATA): Add it.
 2017-02-09 21:21:29 +10:00
Ricardo Wurmus 47055b273a
gnu: r-edger: Add r-statmod to inputs. 
* gnu/packages/bioinformatics.scm (r-edger)[propagated-inputs]: Add r-statmod.
 2017-02-01 22:12:01 +01:00
Tobias Geerinckx-Rice 58f91e4d03
download: url-fetch/tarball: Make ‘name’ truly optional. 
* guix/download.scm (url-fetch/tarbomb): Fall back to ‘file-name’ if
‘name’ is #f, like the regular ‘url-fetch’ does.
* gnu/packages/bioinformatics.scm (muscle)[source]: Remove ‘file-name’.
* gnu/packages/engineering.scm (fastcap)[source]: Likewise.
* gnu/packages/scheme.scm (scmutils)[source]: Likewise.
 2017-02-01 15:53:32 +01:00
Raoul Jean Pierre Bonnal 69f2b3bdf9
gnu: Add r-rhdf5. 2017-01-31 22:35:11 +01:00
Raoul Jean Pierre Bonnal d4af25b51b
gnu: Add r-tximport. 2017-01-31 22:35:08 +01:00
Roel Janssen aa3eeeb542
gnu: Add r-bsgenome-hsapiens-1000genomes-hs37d5. 
* gnu/packages/bioinformatics.scm (r-bsgenome-hsapiens-1000genomes-hs37d5):
  New variable.
 2017-01-30 12:11:04 +01:00
Ben Woodcroft c0dee46c85
gnu: r-vegan: Update to 2.4-2. 
* gnu/packages/bioinformatics.scm (r-vegan): Update to 2.4-2.
 2017-01-21 18:17:16 +10:00
Ben Woodcroft cda0f9a4a9
gnu: diamond: Update to 0.8.34. 
* gnu/packages/bioinformatics.scm (diamond): Update to 0.8.34.
 2017-01-21 17:28:11 +10:00
Ricardo Wurmus 2923f3e5b9
gnu: r-msnid: Expand abbreviation in description. 
* gnu/packages/bioinformatics.scm (r-msnid)[description]: Expand "MS/MS"
to "tandem mass spectrometry".
 2017-01-20 15:38:03 +01:00
Ricardo Wurmus e614d6398a
gnu: r-msnbase: Expand abbreviation in description. 
* gnu/packages/bioinformatics.scm (r-msnbase)[description]: Expand "MS"
to "mass spectrometry".
 2017-01-20 15:38:03 +01:00
Ricardo Wurmus 1778ea740e
gnu: multiqc: Add python-nose to inputs. 
* gnu/packages/bioinformatics.scm (multiqc)[propagated-inputs]: Add
python-nose.
 2017-01-18 16:09:49 +01:00
Ricardo Wurmus 66da3a9f31
gnu: Add r-msnid. 
* gnu/packages/bioinformatics.scm (r-msnid): New variable.
 2017-01-17 21:46:50 +01:00
Ricardo Wurmus 11879284cb
gnu: Add r-msnbase. 
* gnu/packages/bioinformatics.scm (r-msnbase): New variable.
 2017-01-17 21:46:50 +01:00
Ricardo Wurmus 6a67e181ac
gnu: Add r-pcamethods. 
* gnu/packages/bioinformatics.scm (r-pcamethods): New variable.
 2017-01-17 21:46:50 +01:00
Ricardo Wurmus 4aa7d592f1
gnu: Add r-mzid. 
* gnu/packages/bioinformatics.scm (r-mzid): New variable.
 2017-01-17 21:46:50 +01:00
Ricardo Wurmus 7c08afaf7b
gnu: Add r-vsn. 
* gnu/packages/bioinformatics.scm (r-vsn): New variable.
 2017-01-17 21:46:50 +01:00
Ricardo Wurmus 05c7e5fb76
gnu: Add r-affy. 
* gnu/packages/bioinformatics.scm (r-affy): New variable.
 2017-01-17 21:46:49 +01:00
Ricardo Wurmus 5c9d15055f
gnu: Add r-affyio. 
* gnu/packages/bioinformatics.scm (r-affyio): New variable.
 2017-01-17 21:46:49 +01:00
Ricardo Wurmus 71676a1f4c
gnu: Add r-mzr. 
* gnu/packages/bioinformatics.scm (r-mzr): New variable.
 2017-01-17 21:46:49 +01:00
Ricardo Wurmus ae26217430
gnu: Add r-protgenerics. 
* gnu/packages/bioinformatics.scm (r-protgenerics): New variable.
 2017-01-17 21:46:49 +01:00
Ricardo Wurmus 0e7d058e44
gnu: Add r-maldiquant. 
* gnu/packages/bioinformatics.scm (r-maldiquant): New variable.
 2017-01-17 21:46:49 +01:00
Ricardo Wurmus 1f40e73cb5
gnu: Add r-raremetals2. 
* gnu/packages/bioinformatics.scm (r-raremetals2): New variable.
 2017-01-17 21:46:48 +01:00
Ricardo Wurmus fb1e528ef1
gnu: Add r-seqminer. 
* gnu/packages/bioinformatics.scm (r-seqminer): New variable.
 2017-01-17 21:46:48 +01:00
Ricardo Wurmus 769fc6bb18
gnu: Add ribodiff. 
* gnu/packages/bioinformatics.scm (ribodiff): New variable.
 2017-01-17 21:46:48 +01:00
Ricardo Wurmus e84efc50d7
gnu: Add hisat2. 
* gnu/packages/bioinformatics.scm (hisat2): New variable.
 2017-01-17 21:46:48 +01:00
Ricardo Wurmus b91cfa22e1
gnu: Add r-centipede. 
* gnu/packages/bioinformatics.scm (r-centipede): New variable.
 2017-01-16 23:18:27 +01:00
Raoul Jean Pierre Bonnal dd42a330d1
gnu: Add r-sva. 
* gnu/packages/bioinformatics.scm (r-sva): New variable.
 2017-01-14 11:15:18 +01:00
Leo Famulari cc0725914e
Merge branch 'master' into python-tests 2017-01-13 10:21:17 -05:00
Roel Janssen c5173d74d6
gnu: Add r-txdb-mmusculus-ucsc-mm10-knowngene. 
* gnu/packages/bioinformatics.scm (r-txdb-mmusculus-ucsc-mm10-knowngene): New variable.
 2017-01-12 10:02:57 +01:00
Ricardo Wurmus 3a3bf2f819
gnu: Add r-copywriter. 
* gnu/packages/bioinformatics.scm (r-copywriter): New variable.
 2017-01-06 16:31:19 +01:00
Ricardo Wurmus d407bdb931
gnu: Add r-copyhelper. 
* gnu/packages/bioinformatics.scm (r-copyhelper): New variable.
 2017-01-06 16:31:14 +01:00
Ricardo Wurmus 6193563a36
gnu: Add r-chipseq. 
* gnu/packages/bioinformatics.scm (r-chipseq): New variable.
 2017-01-06 16:31:02 +01:00
Ben J Woodcroft dbf9d37114
gnu: bioruby: Update to 1.5.1. 
* gnu/packages/bioinformatics.scm (bioruby): Update to 1.5.1.
 2017-01-06 19:06:07 +10:00
Ben J Woodcroft 0c37e2a3d2
gnu: cd-hit: Update to 4.6.6. 
* gnu/packages/bioinformatics.scm (cd-hit): Update to 4.6.6.
 2017-01-06 19:06:03 +10:00
Tobias Geerinckx-Rice 3b3b60d037
gnu: Use HTTPS for all sourceforge.net home pages. 
* gnu/packages/admin.scm (mingetty, clusterssh)[home-page]: Use HTTPS.
* gnu/packages/audio.scm (libbs2b, soxr)[home-page]: Likewise.
* gnu/packages/bioinformatics.scm (bless)[home-page]: Likewise.
* gnu/packages/display-managers.scm (slim)[home-page]: Likewise.
* gnu/packages/games.scm (extremetuxracer)[home-page]: Likewise.
* gnu/packages/ghostscript.scm (gs-fonts)[home-page]: Likewise.
* gnu/packages/haskell.scm (ghc-regex-base, ghc-regex-posix,
ghc-regex-compat)[home-page]: Likewise.
* gnu/packages/image.scm (imlib2)[home-page]: Likewise.
* gnu/packages/libreoffice.scm (librevenge, libcmis, libodfgen, libmwaw)
[home-page]: Likewise.
* gnu/packages/linux.scm (hdparm, acpid, libavc1394, rng-tools)
[home-page]: Likewise.
* gnu/packages/mail.scm (esmtp)[home-page]: Likewise.
* gnu/packages/mp3.scm (ripperx)[home-page]: Likewise.
* gnu/packages/onc-rpc.scm (libtirpc)[home-page]: Likewise.
* gnu/packages/perl.scm (perl-czplib)[home-page]: Likewise.
* gnu/packages/python.scm (python-pyasn1-modules)[home-page]: Likewise.
* gnu/packages/xdisorg.scm (xosd)[home-page]: Likewise.
 2017-01-04 05:14:22 +01:00
Roel Janssen 407a280103
gnu: r-genomicranges: Update to 1.26.2. 
* gnu/packages/bioinformatics.scm (r-genomicranges): Update to 1.26.2.
 2017-01-03 13:28:35 +01:00
Roel Janssen ac370a3397
gnu: r-genomeinfodb: Update to 1.10.2. 
* gnu/packages/bioinformatics.scm (r-genomeinfodb): Update to 1.10.2.
 2017-01-03 12:47:36 +01:00
Ben Woodcroft 25d84d3122
gnu: python-dendropy: Update to 4.2.0. 
* gnu/packages/bioinformatics.scm (python-dendropy): Update to 4.2.0.
[source]: Remove patch.
(python2-dendropy)[source]: Use the same source as python-dendropy.
* gnu/packages/patches/python-dendropy-exclude-failing-tests.patch: Remove
file.
* gnu/local.mk (dist_patch_DATA): Remove it.
 2017-01-01 16:47:47 +10:00
Ben Woodcroft 322a583fcf
gnu: diamond: Update to 0.8.31. 
* gnu/packages/bioinformatics.scm (diamond): Update to 0.8.31.
 2017-01-01 16:47:47 +10:00
Ben Woodcroft a29929b32c
gnu: multiqc: Update to 0.9. 
Suggested by Raoul Bonnal <ilpuccio.febo@gmail.com>.

* gnu/packages/bioinformatics.scm (multiqc): Update to 0.9.
[origin]: Add patch.
* gnu/packages/patches/multiqc-fix-git-subprocess-error.patch: New file.
* gnu/local.mk (dist_patch_DATA): Add it.
 2016-12-30 17:22:43 +10:00
Ricardo Wurmus 76b64381cb
gnu: r-genomicfeatures: Update to 1.26.2. 
* gnu/packages/bioinformatics.scm (r-genomicfeatures): Update to 1.26.2.
 2016-12-29 22:24:12 +01:00
Ricardo Wurmus 2f642e5229
gnu: r-biostrings: Update to 2.42.1. 
* gnu/packages/bioinformatics.scm (r-biostrings): Update to 2.42.1.
 2016-12-29 22:24:11 +01:00
Ricardo Wurmus 72c2693b9e
gnu: r-limma: Update to 3.30.7. 
* gnu/packages/bioinformatics.scm (r-limma): Update to 3.30.7.
 2016-12-29 22:24:11 +01:00
Ricardo Wurmus 5796af9981
gnu: r-variantannotation: Update to 1.20.2. 
* gnu/packages/bioinformatics.scm (r-variantannotation): Update to 1.20.2.
 2016-12-29 22:24:11 +01:00
Ricardo Wurmus 5d3acc0b36
gnu: r-edger: Update to 3.16.5. 
* gnu/packages/bioinformatics.scm (r-edger): Update to 3.16.5.
 2016-12-29 22:24:11 +01:00
Ricardo Wurmus 81a17b61e7
gnu: r-genomeinfodb: Update to 1.10.1. 
* gnu/packages/bioinformatics.scm (r-genomeinfodb): Update to 1.10.1.
 2016-12-29 22:24:11 +01:00
Ricardo Wurmus 54d9b568fc
gnu: r-iranges: Update to 2.8.1. 
* gnu/packages/bioinformatics.scm (r-iranges): Update to 2.8.1.
 2016-12-29 22:24:11 +01:00
Ricardo Wurmus 86fc9c4a2c
gnu: r-s4vectors: Update to 0.12.1. 
* gnu/packages/bioinformatics.scm (r-s4vectors): Update to 0.12.1.
 2016-12-29 22:24:11 +01:00
Ricardo Wurmus c8ad8b6976
gnu: r-biocstyle: Update to 2.2.1. 
* gnu/packages/bioinformatics.scm (r-biocstyle): Update to 2.2.1.
 2016-12-29 22:24:10 +01:00
Ricardo Wurmus 007ee80277
gnu: r-deseq2: Update to 1.14.1. 
* gnu/packages/bioinformatics.scm (r-deseq2): Update to 1.14.1.
 2016-12-29 22:24:10 +01:00
Ricardo Wurmus d0f0579e6f
gnu: r-annotate: Update to 1.52.1. 
* gnu/packages/bioinformatics.scm (r-annotate): Update to 1.52.1.
[propagated-inputs]: Add r-rcurl.
 2016-12-29 22:24:10 +01:00
Ricardo Wurmus 421f7772b4
gnu: r-qtl: Update to 1.40-8. 
* gnu/packages/bioinformatics.scm (r-qtl): Update to 1.40-8.
 2016-12-29 21:49:09 +01:00
Ricardo Wurmus 2c8d6c0be4
gnu: r-rcas: Update to 1.1.1. 
* gnu/packages/bioinformatics.scm (r-rcas): Update to 1.1.1.
[propagated-inputs]: Add plotrix.
 2016-12-27 14:50:55 +01:00
Ben Woodcroft 9916ef8bb6
gnu: diamond: Update to 0.8.30. 
* gnu/packages/bioinformatics.scm (diamond): Update to 0.8.30.
 2016-12-27 09:18:05 +10:00
Tobias Geerinckx-Rice 33d5b2464d
gnu: cutadapt: Use ‘modify-phases’ syntax. 
* gnu/packages/bioinformatics.scm (cutadapt)[arguments]: Use
‘modify-phases’.
 2016-12-20 05:36:55 +01:00
Tobias Geerinckx-Rice 1f94bff2d4
gnu: cutadapt: Update to 1.12. 
* gnu/packages/bioinformatics.scm (cutadapt): Update to 1.12.
[inputs]: Add python-xopen.
 2016-12-19 20:33:32 +01:00
Ben Woodcroft 3fffabce2a
gnu: Add attribution line for Raoul Bonnal. 
This is a follow-up commit to c9e9154e99.

* gnu/packages/bioinformatics.scm: Add attribution.
 2016-12-18 10:01:04 +10:00
Raoul Bonnal c9e9154e99
gnu: star: Update to 2.5.2b. 
* gnu/packages/bioinformatics (star): Update to 2.5.2b.
[source]: Delete precompiled binary.

Co-authored-by: Ben Woodcroft <donttrustben@gmail.com>
 2016-12-17 23:26:35 +10:00
Marius Bakke cdc2bb50b2
gnu: pbtranscript-tofu: Disable tests. 
* gnu/packages/bioinformatics.scm (pbtranscript-tofu)[arguments]: Set #:tests? #f.
 2016-12-16 18:15:47 +01:00
Marius Bakke 0d90875974
gnu: multiqc: Fix test dependencies. 
* gnu/packages/bioinformatics.scm (multiqc)[native-inputs]: Add python-nose.
 2016-12-16 13:28:49 +01:00
Marius Bakke 14386fc7d9
gnu: idr: Remove explicit wrapper. This is now done implicitly. 
* gnu/packages/bioinformatics.scm (idr)[arguments]: Remove #:phases.
 2016-12-16 13:16:39 +01:00
Marius Bakke b7a820fc97
gnu: idr: Correct inputs. 
* gnu/packages/bioinformatics.scm (idr)[inputs]: Move everything from here ...
[propagated-inputs]: ... to here. Add python-sympy.
 2016-12-16 13:11:20 +01:00
Marius Bakke 1c10a1d75c
gnu: idr: Disable tests. 
* gnu/packages/bioinformatics.scm (idr)[arguments]: Set #:tests? #f.
 2016-12-16 13:08:57 +01:00
Marius Bakke aaffb9c97b
gnu: deeptools: Fix test dependency. 
* gnu/packages/bioinformatics.scm (deeptools)[native-inputs]: Add python-nose.
 2016-12-16 04:27:35 +01:00
Marius Bakke d281be18bc
gnu: clipper: Fix test dependency. 
* gnu/packages/bioinformatics.scm (clipper)[native-inputs]: Add python2-nose.
 2016-12-16 04:26:32 +01:00
Tobias Geerinckx-Rice 0c6c9c00ab
gnu: Update more dead Google Code home pages. 
* gnu/packages/bioinformatics.scm (cutadapt, mosaik, pepr)[home-page]:
Update to their respective replacements.
 2016-12-14 22:08:51 +01:00
Marius Bakke da5ebd1007
gnu: python-biom-format: Fix tests. 
* gnu/packages/bioinformatics.scm (python-biom-format,
  python2-biom-format)[native-inputs]: Add python-nose.
 2016-12-14 19:18:26 +01:00
Ben Woodcroft 991e143d25
gnu: diamond: Update to 0.8.29. 
* gnu/packages/bioinformatics.scm (diamond): Update to 0.8.29.
 2016-12-13 20:01:56 +10:00
Ben Woodcroft ced1c496aa
gnu: orfm: Update to 0.6.1. 
* gnu/packages/bioinformatics.scm (orfm): Update to 0.6.1.
 2016-12-13 20:00:50 +10:00
Ben Woodcroft 2df3d147ef
gnu: orfm: Update to 0.6.0. 
* gnu/packages/bioinformatics.scm (orfm): Update to 0.6.0.
 2016-12-12 20:49:31 +10:00
Ben Woodcroft a225db5293
gnu: vsearch: Update to 2.3.4. 
* gnu/packages/bioinformatics.scm (vsearch): Update to 2.3.4.
 2016-12-10 10:45:13 +10:00
Ben Woodcroft 7922ab8fe8
gnu: pardre: Update to 1.1.5-1. 
* gnu/packages/bioinformatics.scm (pardre): update to 1.1.5-1.
[source]: Update source hash.
 2016-12-10 10:45:12 +10:00
Ben Woodcroft 1b7f17ef90
gnu: vsearch: Update to 2.3.3. 
* gnu/packages/bioinformatics.scm (vsearch): Update to 2.3.3.
 2016-12-08 22:39:10 +10:00
Ben Woodcroft e990c81d38
gnu: aragorn: Update to 1.2.38. 
* gnu/packages/bioinformatics.scm (aragorn): Update to 1.2.38.
 2016-12-04 10:51:54 +10:00
Hartmut Goebel 3bf4280659
Merge branch 'master' into python-build-system 2016-11-29 18:47:16 +01:00
Ricardo Wurmus bd3be46e7f
gnu: Add r-gkmsvm. 
* gnu/packages/bioinformatics.scm (r-gkmsvm): New variable.
 2016-11-28 22:43:18 +01:00
Ricardo Wurmus 2d9fb1702f
gnu: Add r-seqgl. 
* gnu/packages/bioinformatics.scm (r-seqgl): New variable.
 2016-11-28 22:43:17 +01:00
Ricardo Wurmus c827f20286
gnu: Add r-chipkernels. 
* gnu/packages/bioinformatics.scm (r-chipkernels): New variable.
 2016-11-28 22:43:17 +01:00
Ricardo Wurmus d71605294f
gnu: Add r-wgcna. 
* gnu/packages/bioinformatics.scm (r-wgcna): New variable.
 2016-11-28 22:43:17 +01:00
Ricardo Wurmus e619a5c245
gnu: Add r-r4rna. 
* gnu/packages/bioinformatics.scm (r-r4rna): New variable.
 2016-11-28 22:43:16 +01:00
Ben Woodcroft 9926875572
gnu: Add newick-utils. 
* gnu/packages/bioinformatics.scm (newick-utils): New variable.
 2016-11-28 09:00:41 +10:00
Ben Woodcroft 5e0a0f4226
gnu: roary: Update to 3.7.0. 
* gnu/packages/bioinformatics.scm (roary): Update to 3.7.0.
 2016-11-26 20:15:39 +10:00
Ben Woodcroft 31a9d653ad
gnu: Add proteinortho. 
* gnu/packages/bioinformatics.scm (proteinortho): New variable.
 2016-11-26 20:15:37 +10:00
Leo Famulari de32aa74b4
Merge branch 'master' into python-build-system 2016-11-25 11:20:21 -05:00
Ben Woodcroft 8e5f8c98e2
gnu: diamond: Update to 0.8.27. 
* gnu/packages/bioinformatics.scm (diamond): Update to 0.8.27.
 2016-11-22 21:01:21 +10:00
Petter daf72603eb
gnu: Remove redundancy where mkdir-p <dir> is followed by install-file <file> <dir>. 
* gnu/packages/bioinformatics.scm (bwa)[arguments]: Remove redundant mkdir-p.
(eigensoft)[arguments]: Likewise.
(snap-aligner)[arguments]: Likewise.
(pardre)[arguments]: Likewise.
(piranha)[arguments]: Likewise.
* gnu/packages/maths.scm (hypre)[arguments]: Likewise.
* gnu/packages/mp3.scm (mpc123)[arguments]: Likewise.
* gnu/packages/music.scm (tuxguitar)[arguments]: Likewise.
* gnu/packages/pdf.scm (impressive)[arguments]: Likewise.
* gnu/packages/qemu.scm (qemu)[arguments]: Likewise.

Signed-off-by: Leo Famulari <leo@famulari.name>
 2016-11-21 14:39:54 -05:00
Hartmut Goebel de5bc89093
gnu: python2-pbcore: Fix inputs: 
* gnu/packages/bioinformatics.scm (python2-pbcore) [inputs] change to
  [propagated-inputs]. [native-inputs]: Remove python-docutils, which
  comes with sphinx. [former propagated-inputs]: move all (which is only
  pyxb) to [inputs].
 2016-11-15 22:32:01 +01:00
Hartmut Goebel 54c85e12fd
gnu: python2-warpedlmm: Remove phase remove-bin-directory. 
This directory did contain contain wrappers for `nose`, which should not
be there anyway (since nose already was a native-input). The new
python build system no longer creates this directory, while the old one
did. (This difference is due to the bloody details of how packages are
installed.)

* gnu/packages/bioinformatics.scm (python2-warpedlmm)
  [modify-phases] Remove, since remove-bin-directory was the only
  modification here.
 2016-11-15 22:32:00 +01:00
Hartmut Goebel f2516de2fc
gnu: Fix python inputs, part 7: Ensure python-cython is a native-input. 
* gnu/packages/audio.scm (python-pyliblo): [inputs] Move python-cyton to
  [native-inputs].
* gnu/packages/bioinformatics.scm (python2-pybedtools): dito.
* gnu/packages/music.scm (beast, python-pyportmidi): dito.
* gnu/packages/python.scm (python2-fastlmm, python-kivy): dito.
 2016-11-15 22:31:07 +01:00
Hartmut Goebel f22efa0152
gnu: Fix python inputs, part 1: all inputs become propagated-inputs. 
This patch contains the changes where all [inputs] are changed to
[propagated-inputs]

* gnu/packages/python.scm (python-passlib, python-paramiko, python-ccm,
  python-babel, python-keyring python-pandas, python-tzlocal,
  python-parse-type, python-nose2, python-pytest, python-pytest-mock,
  python-pytest-xdist, python-scripttest, python-testtools, python-pytest-cov,
  python-testscenarios, python-pbr-0.11, python-oauthlib, python-jinja2,
  python-sphinx, python-tzlocal, python-bugz, python2-pytest-mock, behave,
  pelican, sqlalchemy-utils, python-pygridtools, python-urwidtrees,
  python-tornado, python2-tornado, python-debian, python-execnet,
  python-pytest-cache, pytest-localserver, python-clint, python-rply,
  python-hy, python-rauth, python-rsa, python-celery, python-vobject, s3cmd,
  python-prompt-toolkit, ptpython, python-requests-oauthlib, python-stem,
  python-binaryornot, python2-binaryornot, python-nltk, python-pymongo,
  python-schematics, python-url, python2-url, python-freezegun,
  python-glances, python-graphql-core, python-graphql-relay, python-graphene,
  python-nautilus, python-s3transfer): All [inputs] become
  [propagated-inputs].
* gnu/packages/bioinformatics.scm (python-biopython): Likewise.
* gnu/packages/django.scm (pytest-django): Likewise.
* gnu/packages/mail.scm (python-mailmanclient): Likewise.
* gnu/packages/password-utils.scm (python-bcrypt): Likewise.
* gnu/packages/propbuf.scm (python-protobuf): Likewise.
* gnu/packages/rdf.scm (python-rdflib): Likewise.

SQACH all become propagated
 2016-11-15 22:31:03 +01:00
Hartmut Goebel b41a05ce49
gnu: Remove work-arounds for bug 20765 (ensure uncompressed eggs). 
Bug 20765 is solved since we build all Python packages using
option "--single-version-externally-managed".

* gnu/packages/bioinformatics.scm (pbtranscript-tofu): Remove
  configure-flags. (pepr): remove phase "disable-egg-generation".
* gnu/packages/pdf.scm (reportlab): Remove configure-flags.
* gnu/packages/python.scm (python-sphinx-rtd-theme, python2-elib.intl,
  python-pkgconfig, python-pytest-pep8, python-pytest-flakes): Remove
  configure-flags. (python-pillow) remove phase
  "disable-egg-generation". (python-libarchive-c) Remove patching
  setup.cfg.
* gnu/packages/statistics.scm (python-patsy): remove phase
  "prevent-generation-of-egg-archive".
* gnu/packages/tls.scm (python-acme): remove phase
  "disable-egg-compression".
* gnu/packages/tor.scm (onionshare): Remove configure-flags.
 2016-11-15 22:31:02 +01:00
Hartmut Goebel 5c31f4aa7c
gnu: Remove python-setuptools and python2-setuptools from inputs (part 4a) 
This patch contains the changes for all modules beside python.scm where
setuptools are used in an inherited package and removing this input also
removes the need for inheriting the package. This is the case if adding
setuptools in the inherited package was the only change.

Change this to not inherit and remove the new needless call to
"strip-python2-variant (if applicable).

* gnu/packages/bioinformatics.scm (python-biopython, python2-biopython,
  python-twobitreader, python2-twobitreader,
  python-plastid, python2-plastid,
  python2-pybigwig,
  python2-screed,
  sra-tools): No longer "inherit" Python 2 packages
  inheriting from a Python 3 package if the sole reason for inheriting was
  adding python-setuptools respective python2-setuptools to [inputs],
  [native-inputs] or [propagated-inputs]. Remove now needless [properties]
  "python2-variant" where applicable.
* gnu/packages/django.scm (python-pytest-django, python2-pytest-django,
  python-django-filter, python2-django-filter): Likewise.
* gnu/packages/gnupg.scm (python2-pygpgme): Likewise.
* gnu/packages/mail.scm (python-mailmanclient, python2-mailmanclient):
  Likewise.
* gnu/packages/mpd.scm (python-msp, python2-mpd2): Likewise.
* gnu/packages/music.scm (python-pylast, python2-pylast): Likewise.
* gnu/packages/openstack.scm (python-requests-mock, python2-requests-mock,
  python2-git-review): Likewise.
* gnu/packages/password-utils.scm (python2-bcrypt): Likewise.
* gnu/packages/protobuf.scm (python-protobuf, python2-protobuf): Likewise.
* gnu/packages/statistics.scm (python-patsy, python2-patsy): Likewise.
* gnu/packages/web.scm (python2-feedparser): Likewise.
 2016-11-15 22:28:59 +01:00
Hartmut Goebel 00e10c6e67
gnu: Remove python-setuptools and python2-setuptools from inputs (part 3) 
This patch contains the changes where setuptools are used in an inherited
package and removing this input keeps the need for inheriting the package.

* gnu/packages/bioinformatics.scm (python2-biom-format): Remove
  python-setuptools respective python2-setuptools from [inputs],
  [native-inputs] and [propagated-inputs] in Python 2 packages inheriting from
  a Python 3 package.
* gnu/packages/python.scm (python2-pytest-mock,
  python2-oauthlib,
  python2-seaborn,
  python2-tornado,
  python2-terminado,
  python2-rauth,
  python2-anyjson,
  python2-amqp,
  python2-kombu,
  python2-billiard,
  python2-celery,
  python2-jellyfish,
  python2-binaryornot,
  python2-natsort,
  python2-graphene): Likewise.
* gnu/packages/statistics.scm (python2-statsmodels): Likewise.
 2016-11-15 22:28:38 +01:00
Hartmut Goebel f3b98f4fec
gnu: Remove python-setuptools and python2-setuptools from inputs (part 2) 
This patch contains the changes where removing setuptools from the inputs
affected some code-lines beside.

* gnu/packages/admin.scm (ansible): Remove all [inputs], [native-inputs] and
  [propagated-inputs] where python-setuptools or python2-setuptools are the
  sole entries. Remove python-setuptools and python2-setuptools listed on a
  line by its own from [inputs], [native-inputs] and [propagated-inputs].

* gnu/packages/backup.scm (duplicity): Likewise.
* gnu/packages/bioinformatics.scm (bamm, python2-pybedtools,
  python2-bx-python, python2-dendropy, python-pysam, python2-pysam, clipper,
  crossmap, cutadapt, deeptools, grit, idr, python2-warpedlmm,
  pbtranscript-tofu, seqmagick): Likewise.
* gnu/packages/docbook.scm (dblatex): Likewise.
* gnu/packages/freedesktop.scm (python-pyxdg, python2-pyxdg): Likewise.
* gnu/packages/lirc.scm (python2-lirc): Likewise.
* gnu/packages/mp3.scm (eyed3): Likewise.
* gnu/packages/nutrition.scm (gourmet): Likewise.
* gnu/packages/openstack.scm (python-hacking, python2-hacking,
  python-os-testr, python2-os-testr,
  python-stevedore, python2-stevedore,
  python-tempest-lib, python2-tempest-lib,
  python-oslo.log, python2-oslo.log,
  python-keystoneclient, python2-keystoneclient): Likewise.
* gnu/packages/password-utils.scm (assword): Likewise.
* gnu/packages/python.scm (python-passlib, python2-passlib,
  python-babel, python2-babel,
  python-parse-type,
  python-pytest, python2-pytest,
  python-scripttest, python2-scripttest,
  python-testtools, python2-testtools,
  python-testscenarios, python2-testscenarios,
  python-subunit, python2-subunit,
  python-pbr-0.11,
  python-pbr, python2-pbr,
  python-testrepository, python2-testrepository,
  behave,
  python-wheel, python2-wheel,
  python-requests, python2-requests,
  python-jsonschema, python2-jsonschema,
  python-pyjwt, python2-pyjwt,
  python-virtualenv, python2-virtualenv,
  python-jinja2, python2-jinja2,
  python-joblib, python2-joblib,
  python-sphinx, python2-sphinx,
  python-feedgenerator, python2-feedgenerator,
  python-scikit-image, python2-scikit-image,
  python-redis, python2-redis,
  python2-fastlmm,
  python-numpydoc, python2-numpydoc,
  python-matplotlib, python2-matplotlib,
  python2-pysnptools,
  python-rpy2, python2-rpy2,
  python-pillow, python2-pillow,
  python-pycparser, python2-pycparser,
  python-cffi, python2-cffi,
  python-cairocffi, python2-cairocffi,
  python-drmaa, python2-drmaa,
  python-pathpy, python2-pathpy,
  python-simplegeneric, python2-simplegeneric,
  python-ipython, python2-ipython,
  python-apsw, python2-apsw,
  python-lxml, python2-lxml,
  python-networkx, python2-networkx,
  python-pyzmq, python2-pyzmq,
  python-mccabe, python2-mccabe,
  python-mccabe-0.2.1,
  python-flake8, python2-flake8,
  python-flake8-2.2.4,
  python-mistune, python2-mistune,
  python-ptyprocess, python2-ptyprocess,
  python-llfuse, python2-llfuse,
  python-webob, python2-webob,
  python-xlrd, python2-xlrd,
  python-tables, python2-tables,
  python-pip, python2-pip,
  python-libarchive-c, python2-libarchive-c,
  python-docopt, python2-docopt,
  python-pyrfc3339, python2-pyrfc3339,
  python-configobj, python2-configobj,
  python-clint, python2-clint,
  python-rply, python2-rply,
  python2-rpython,
  python-widgetsnbextension, python2-widgetsnbextension
  jupyter,
  python-jupyter-console, python2-jupyter-console,
  python-hy, python2-hy,
  python-urllib3, python2-urllib3,
  python-rsa, python2-rsa,
  python-tox, python2-tox,
  python2-hypothesis,
  python-paste, python2-paste,
  python-pastescript, python2-pastescript,
  python2-unicodecsv,
  python-pkgconfig, python2-pkgconfig,
  python2-rope,
  python-sqlparse, python2-sqlparse,
  python-gevent, python2-gevent,
  python-tabulate, python2-tabulate,
  python-arrow, python2-arrow,
  python-cleo, python2-cleo,
  python-fake-factory, python2-fake-factory,
  ptpython): Likewise.
* gnu/packages/rdf.scm (python-rdflib, python2-rdflib): Likewise.
* gnu/packages/terminals.scm (asciinema): Likewise.
* gnu/packages/version-control.scm (git-annex-remote-hubic): Likewise.
* gnu/packages/xdisorg.scm (arandr): Likewise.
 2016-11-15 22:27:31 +01:00
Hartmut Goebel 5d85493284
gnu: Remove python-setuptools and python2-setuptools from inputs (part 1b) 
This patch contains the changes in all modules beside python.scm where
removing setuptools from the inputs could be achieved by removing complete
lines.

* gnu/packages/admin.scm (graphios, thefuck): Remove all [inputs],
  [native-inputs] and [propagated-inputs] where python-setuptools or
  python2-setuptools are the sole entries. Remove python-setuptools and
  python2-setuptools listed on a line by its own from [inputs],
  [native-inputs] and [propagated-inputs].
* gnu/packages/backup.scm (rdiff-backup): Likewise.
* gnu/packages/bioinformatics.scm (htseq, macs, python2-pbcore, rseqc,
  multiqc): Likewise.
* gnu/packages/django.scm (python-django, python2-django,
  python-django-simple-math-captcha, python2-django-simple-math-captcha):
  Likewise.
* gnu/packages/docker.scm (python-docker-py, docker-compose): Likewise.
* gnu/packages/game-development.scm (python-pygame): Likewise.
* gnu/packages/key-mon.scm (key-mon): Likewise.
* gnu/packages/mail.scm (khard): Likewise.
* gnu/packages/music.scm (beets, python2-pyechonest): Likewise.
* gnu/packages/openstack.scm (python-bandit, python2-bandit,
  python-debtcollector, python2-debtcollector,
  python-mox3, python2-mox3,
  python-os-client-config, python2-os-client-config,
  python-oslo.config, python2-oslo.config,
  python-oslo.context, python2-oslo.context,
  python-oslo.i18n, python2-oslo.i18n,
  python-oslo.serialization, python2-oslo.serialization,
  python-oslosphinx, python2-oslosphinx,
  python-oslotest, python2-oslotest,
  python-oslo.utils, python2-oslo.utils,
  python-swiftclient, python2-swiftclient): Likewise.
* gnu/packages/pdf.scm (pdfposter): Likewise.
* gnu/packages/tls.scm (python-acme, python2-acme): Likewise.
 2016-11-15 21:58:44 +01:00
Ricardo Wurmus 84590149e6
gnu: hisat: Fix typo. 
* gnu/packages/bioinformatics.scm (hisat)[arguments]: Fix directory
name in install phase.
 2016-11-15 20:21:08 +01:00
Ricardo Wurmus 7c45670b32
gnu: r-org-mm-eg-db: Update to 3.4.0. 
* gnu/packages/bioinformatics.scm (r-org-mm-eg-db): Update to 3.4.0.
 2016-11-11 09:08:08 +01:00
Ricardo Wurmus 0cfac6f270
gnu: r-org-dm-eg-db: Update to 3.4.0. 
* gnu/packages/bioinformatics.scm (r-org-dm-eg-db): Update to 3.4.0.
 2016-11-11 09:08:08 +01:00
Ricardo Wurmus f04a3eff98
gnu: r-org-ce-eg-db: Update to 3.4.0. 
* gnu/packages/bioinformatics.scm (r-org-ce-eg-db): Update to 3.4.0.
 2016-11-11 09:08:08 +01:00
Ricardo Wurmus 83f9a6fb60
gnu: r-org-hs-eg-db: Update to 3.4.0. 
* gnu/packages/bioinformatics.scm (r-org-hs-eg-db): Update to 3.4.0.
 2016-11-11 09:08:07 +01:00
Ben Woodcroft 3cf7c31720
gnu: diamond: Update to 0.8.26. 
* gnu/packages/bioinformatics.scm (diamond): Update to 0.8.26.
 2016-11-07 21:31:09 +10:00
Ricardo Wurmus ed8fbe5e62
gnu: r-rcas: Update to 1.0.0. 
* gnu/packages/bioinformatics.scm (r-rcas): Update to 1.0.0.
 2016-11-03 19:01:46 +01:00
Ricardo Wurmus 16a8bd3194
gnu: r-rtracklayer: Update to 1.34.1. 
* gnu/packages/bioinformatics.scm (r-rtracklayer): Update to 1.34.1.
 2016-11-03 19:01:46 +01:00
Ricardo Wurmus c15ae9b008
gnu: r-biocparallel: Update to 1.8.1. 
* gnu/packages/bioinformatics.scm (r-biocparallel): Update to 1.8.1.
 2016-11-03 19:01:46 +01:00
Ricardo Wurmus 5b3b2d2f02
gnu: r-limma: Update to 3.30.2. 
* gnu/packages/bioinformatics.scm (r-limma): Update to 3.30.2.
 2016-11-03 19:01:46 +01:00
Ricardo Wurmus ed3054231d
gnu: r-edger: Update to 3.16.1. 
* gnu/packages/bioinformatics.scm (r-edger): Update to 3.16.1.
 2016-11-03 19:01:45 +01:00
Leo Famulari 044ac8d294
gnu: python-twobitreader: Update to 3.1.4. 
* gnu/packages/bioinformatics.scm (python-twobitreader, python2-twobitreader):
Update to 3.1.4.
 2016-10-28 13:59:11 -04:00
Leo Famulari 900fb8d005
gnu: python-twobitreader: Disable the test suite. 
The tests were silently skipped with Python 3.4. With Python 3.5, this caused
the build of python-twobitreader to fail.

* gnu/packages/bioinformatics.scm (python-twobitreader,
python2-twobitreader)[arguments]: Disable the tests.
 2016-10-28 13:59:11 -04:00
Roel Janssen 7500e42b3e
gnu: Add r-mutationalpatterns. 
* gnu/packages/bioinformatics.scm (r-mutationalpatterns): New variable.
 2016-10-27 20:07:05 +02:00
Ricardo Wurmus a46cc723ff
gnu: r-seqinr: Update to 3.3-3. 
* gnu/packages/bioinformatics.scm (r-seqinr): Update to 3.3-3.
 2016-10-26 16:23:26 +02:00
Ricardo Wurmus c70271ec48
gnu: bioperl-minimal: Update to 1.7.0. 
* gnu/packages/bioinformatics.scm (bioperl-minimal): Update to 1.7.0.
 2016-10-26 16:23:24 +02:00
Ricardo Wurmus 59198f8fff
gnu: r-genomationdata: Update to 1.6.0. 
* gnu/packages/bioinformatics.scm (r-genomationdata): Update to 1.6.0.
 2016-10-26 09:28:23 +02:00
Ricardo Wurmus e357bec836
gnu: r-bamsignals: Update to 1.6.0. 
* gnu/packages/bioinformatics.scm (r-bamsignals): Update to 1.6.0.
 2016-10-26 09:28:23 +02:00
Ricardo Wurmus 53ca52f013
gnu: r-rhtslib: Update to 1.6.0. 
* gnu/packages/bioinformatics.scm (r-rhtslib): Update to 1.6.0.
[native-inputs]: Add autoconf.
 2016-10-26 09:28:23 +02:00
Ricardo Wurmus da22da862b
gnu: r-zlibbioc: Update to 1.20.0. 
* gnu/packages/bioinformatics.scm (r-zlibbioc): Update to 1.20.0.
 2016-10-26 09:28:22 +02:00
Ricardo Wurmus 809251e164
gnu: r-motifrg: Update to 1.18.0. 
* gnu/packages/bioinformatics.scm (r-motifrg): Update to 1.18.0.
 2016-10-26 09:28:22 +02:00
Ricardo Wurmus 21d6c7a3e1
gnu: r-seqlogo: Update to 1.40.0. 
* gnu/packages/bioinformatics.scm (r-seqlogo): Update to 1.40.0.
 2016-10-26 09:28:22 +02:00
Ricardo Wurmus 51c3c4900f
gnu: r-genomation: Update to 1.6.0. 
* gnu/packages/bioinformatics.scm (r-genomation): Update to 1.6.0.
[propagated-inputs]: Add r-rcpp, r-htslib, r-runit, r-s4vectors.
[inputs]: Add zlib.
 2016-10-26 09:28:21 +02:00
Ricardo Wurmus e92dd6f5e0
gnu: r-seqpattern: Update to 1.6.0. 
* gnu/packages/bioinformatics.scm (r-seqpattern): Update to 1.6.0.
[propagated-inputs]: Add r-kernsmooth.
 2016-10-26 09:28:21 +02:00
Ricardo Wurmus acf6f7e0c3
gnu: r-impute: Update to 1.48.0. 
* gnu/packages/bioinformatics.scm (r-impute): Update to 1.48.0.
 2016-10-26 09:28:21 +02:00
Ricardo Wurmus 3d74c04451
gnu: r-bsgenome: Update to 1.42.0. 
* gnu/packages/bioinformatics.scm (r-bsgenome): Update to 1.42.0.
 2016-10-26 09:28:20 +02:00
Ricardo Wurmus 30ec4de738
gnu: r-topgo: Update to 2.26.0. 
* gnu/packages/bioinformatics.scm (r-topgo): Update to 2.26.0.
[propagated-inputs]: Add r-dbi.
 2016-10-26 09:28:20 +02:00
Ricardo Wurmus 3587b464fc
gnu: r-graph: Update to 1.52.0. 
* gnu/packages/bioinformatics.scm (r-graph): Update to 1.52.0.
 2016-10-26 09:28:19 +02:00
Ricardo Wurmus d1b1587cad
gnu: r-go-db: Update to 3.4.0. 
* gnu/packages/bioinformatics.scm (r-go-db): Update to 3.4.0.
 2016-10-26 09:28:19 +02:00
Ricardo Wurmus b17aac083e
gnu: r-genomicfeatures: Update to 1.26.0. 
* gnu/packages/bioinformatics.scm (r-genomicfeatures): Update to 1.26.0.
 2016-10-26 09:28:18 +02:00
Ricardo Wurmus 6a45fd9aea
gnu: r-rtracklayer: Update to 1.34.0. 
* gnu/packages/bioinformatics.scm (r-rtracklayer): Update to 1.34.0.
 2016-10-26 09:28:18 +02:00
Ricardo Wurmus 4ab32f0cd6
gnu: r-genomicalignments: Update to 1.10.0. 
* gnu/packages/bioinformatics.scm (r-genomicalignments): Update to
1.10.0.
 2016-10-26 09:28:18 +02:00
Ricardo Wurmus 08da08d296
gnu: r-summarizedexperiment: Update to 1.4.0. 
* gnu/packages/bioinformatics.scm (r-summarizedexperiment): Update to
1.4.0.
 2016-10-26 09:28:17 +02:00
Ricardo Wurmus c0ccef41ae
gnu: r-rsamtools: Update to 1.26.1. 
* gnu/packages/bioinformatics.scm (r-rsamtools): Update to 1.26.1.
 2016-10-26 09:28:17 +02:00
Ricardo Wurmus 47d39b6e7a
gnu: r-biostrings: Update to 2.42.0. 
* gnu/packages/bioinformatics.scm (r-biostrings): Update to 2.42.0.
 2016-10-26 09:28:17 +02:00
Ricardo Wurmus 89559a124e
gnu: r-biocparallel: Update to 1.8.0. 
* gnu/packages/bioinformatics.scm (r-biocparallel): Update to 1.8.0.
 2016-10-26 09:28:16 +02:00
Ricardo Wurmus 9405333186
gnu: r-biomart: Update to 2.30.0. 
* gnu/packages/bioinformatics.scm (r-biomart): Update to 2.30.0.
 2016-10-26 09:28:16 +02:00
Ricardo Wurmus e45dc05781
gnu: r-annotationdbi: Update to 1.36.0. 
* gnu/packages/bioinformatics.scm (r-annotationdbi): Update to 1.36.0.
 2016-10-26 09:28:16 +02:00