53e42694e5
gnu: kaiju: Update to 1.6.2.
...
* gnu/packages/bioinformatics.scm (kaiju): Update to 1.6.2;
[inputs]: Add zlib.
2018-03-29 15:40:52 +02:00
e3cfef22c4
gnu: Use invoke and return #t from all builders.
...
* gnu/packages/admin.scm, gnu/packages/android.scm, gnu/packages/audio.scm,
gnu/packages/avr.scm, gnu/packages/base.scm, gnu/packages/bioinformatics.scm,
gnu/packages/certs.scm, gnu/packages/check.scm, gnu/packages/code.scm,
gnu/packages/commencement.scm, gnu/packages/dictionaries.scm,
gnu/packages/docbook.scm, gnu/packages/emacs.scm, gnu/packages/embedded.scm,
gnu/packages/fonts.scm, gnu/packages/games.scm, gnu/packages/gnome.scm,
gnu/packages/gnu-doc.scm, gnu/packages/guile.scm, gnu/packages/hurd.scm,
gnu/packages/javascript.scm, gnu/packages/libreoffice.scm,
gnu/packages/linux.scm, gnu/packages/lisp.scm, gnu/packages/lxde.scm,
gnu/packages/mail.scm, gnu/packages/markup.scm, gnu/packages/mate.scm,
gnu/packages/pkg-config.scm, gnu/packages/qt.scm, gnu/packages/rust.scm,
gnu/packages/scheme.scm, gnu/packages/sdl.scm, gnu/packages/statistics.scm,
gnu/packages/syncthing.scm, gnu/packages/tex.scm, gnu/packages/web.scm,
gnu/packages/wine.scm, gnu/packages/xfce.scm: In the builders of packages
using 'trivial-build-system', use invoke where appropriate, raise exceptions
on errors, and otherwise return #t.
2018-03-27 21:35:41 -04:00
904c3a4e99
gnu: r-annotate: Update to 1.56.2.
...
* gnu/packages/bioinformatics.scm (r-annotate): Update to 1.56.2.
2018-03-25 00:36:31 +01:00
618050a126
gnu: r-bookdown: Do not propagate ghc-pandoc.
...
This package propagates r-rmarkdown, which propagates its own variant of
Pandoc.
* gnu/packages/bioinformatics.scm (r-bookdown)[propagated-inputs]: Remove
ghc-pandoc.
2018-03-22 17:07:15 +01:00
363ee7a3f4
gnu: pigx-chipseq: Update to 0.0.10.
...
* gnu/packages/bioinformatics.scm (pigx-chipseq): Update to 0.0.10.
[inputs]: Remove r-rcas and duplicate of snakemake; add r-biocparallel,
r-biostrings, r-dplyr, r-genomicalignments, rsamtools, r-s4vectors, r-tibble,
r-tidyr, r-htmlwidgets, and r-rmarkdown.
2018-03-21 11:52:56 +01:00
d7a11f1a8d
gnu: pigx-chipseq: Update to 0.0.9.
...
* gnu/packages/bioinformatics.scm (pigx-chipseq): Update to 0.0.9.
[inputs]: Add coreutils and grep.
2018-03-20 19:47:37 +01:00
ac21be848a
Merge branch 'master' into core-updates
2018-03-20 14:22:06 -04:00
4f1e4f33a0
gnu: pigx-bsseq: Update to 0.0.8.
...
* gnu/packages/bioinformatics.scm (pigx-bsseq): Update to 0.0.8.
2018-03-20 14:56:44 +01:00
616446ffbf
gnu: pigx-rnaseq: Update to 0.0.3.
...
* gnu/packages/bioinformatics.scm (pigx-rnaseq): Update to 0.0.3.
[inputs]: Add gzip.
2018-03-20 12:20:51 +01:00
647888845c
Merge branch 'master' into core-updates
2018-03-20 00:49:05 -04:00
9dbdc830f6
gnu: pigx-bsseq: Update to 0.0.7.
...
* gnu/packages/bioinformatics.scm (pigx-bsseq): Update to 0.0.7.
[inputs]: Add coreutils, sed, and grep.
2018-03-19 21:06:51 +01:00
096589035e
gnu: bismark: Fix references to gunzip.
...
* gnu/packages/bioinformatics.scm (bismark)[arguments]: Keep reference to
gunzip executable.
[inputs]: Add gzip.
2018-03-19 21:06:51 +01:00
51237011bf
gnu: pigx-scrnaseq: Update to 0.0.3.
...
* gnu/packages/bioinformatics.scm (pigx-scrnaseq): Update to 0.0.3.
[inputs]: Add coreutils and perl.
2018-03-19 21:06:50 +01:00
d8f08c85ad
gnu: pigx: Update to 0.0.2.
...
* gnu/packages/bioinformatics.scm (pigx): Update to 0.0.2.
2018-03-19 16:55:43 +01:00
d93a1c276b
gnu: r-rcas: Use ghc-pandoc-citeproc-with-pandoc-1.
...
* gnu/packages/bioinformatics.scm (r-rcas)[inputs]: Replace
ghc-pandoc-citeproc with ghc-pandoc-citeproc-with-pandoc-1.
2018-03-19 16:55:43 +01:00
32b7ccf9b4
gnu: pigx-chipseq: Update to 0.0.8.
...
* gnu/packages/bioinformatics.scm (pigx-chipseq): Update to 0.0.8.
[inputs]: Add python-magic, python-xlrd, and trim-galore.
[arguments]: Disable tests.
2018-03-19 11:07:55 +01:00
2915221bcb
gnu: pigx-scrnaseq: Use pandoc-1.
...
* gnu/packages/bioinformatics.scm (pigx-scrnaseq)[inputs]: Replace ghc-pandoc
with ghc-pandoc-1, and ghc-pandoc-citeproc with
ghc-pandoc-citeproc-with-pandoc-1.
2018-03-19 11:07:55 +01:00
9dcb4d22a4
gnu: pigx-bsseq: Use pandoc-1.
...
* gnu/packages/bioinformatics.scm (pigx-bsseq)[inputs]: Replace ghc-pandoc
with ghc-pandoc-1, and ghc-pandoc-citeproc with
ghc-pandoc-citeproc-with-pandoc-1.
2018-03-19 11:07:55 +01:00
fd757a8f21
gnu: pigx-chipseq: Use pandoc-1.
...
* gnu/packages/bioinformatics.scm (pigx-chipseq)[inputs]: Replace ghc-pandoc
with ghc-pandoc-1, and ghc-pandoc-citeproc with
ghc-pandoc-citeproc-with-pandoc-1.
2018-03-19 11:07:55 +01:00
1a29fc3ff9
gnu: pigx-rnaseq: Use pandoc-1.
...
* gnu/packages/bioinformatics.scm (pigx-rnaseq)[inputs]: Replace ghc-pandoc
with ghc-pandoc-1, and ghc-pandoc-citeproc with
ghc-pandoc-citeproc-with-pandoc-1.
2018-03-19 11:07:54 +01:00
9f388b1ee1
Merge branch 'master' into core-updates
2018-03-17 01:18:37 -04:00
c1c9cc664b
gnu: Add pigx.
...
* gnu/packages/bioinformatics.scm (pigx): New variable.
2018-03-16 15:40:31 +01:00
fe52a215e5
gnu: pigx-rnaseq: Disable memory hungry test.
...
* gnu/packages/bioinformatics.scm (pigx-rnaseq)[arguments]: Add phase to
disable a memory hungry test.
2018-03-16 15:40:31 +01:00
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
46264c73a6
gnu: Add pigx-scrnaseq.
...
* gnu/packages/bioinformatics.scm (pigx-scrnaseq): New variable.
2018-03-16 11:15:04 +01:00
b44437c549
gnu: kentutils: Build with mariadb.
...
* gnu/packages/bioinformatics.scm (kentutils)[inputs]: Replace mysql with
mariadb.
2018-03-16 10:01:07 +01:00
80420f114c
gnu: kentutils: Build with mariadb.
...
* gnu/packages/bioinformatics.scm (kentutils)[inputs]: Replace mysql with
mariadb.
2018-03-16 10:00:31 +01:00
32cbbac11a
gnu: Add Diversitree.
...
* gnu/packages/bioinformatics.scm (r-diversitree): New variable.
2018-03-15 10:57:51 -04:00
8c72ed923d
Merge branch 'master' into core-updates
2018-03-14 17:37:20 +01:00
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
fb94174fc3
gnu: Add pigx-bsseq.
...
* gnu/packages/bioinformatics.scm (pigx-bsseq): New variable.
2018-03-11 20:01:53 +01:00
531afc8a89
gnu: Add pigx-chipseq.
...
* gnu/packages/bioinformatics.scm (pigx-chipseq): New variable.
2018-03-11 20:01:53 +01:00
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
22a0c65969
gnu: Add r-phangorn.
...
* gnu/packages/bioinformatics.scm (r-phangorn): New variable.
2018-03-08 23:31:56 +01:00
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
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
0bdd5b8ab7
gnu: Add pigx-rnaseq.
...
* gnu/packages/bioinformatics.scm (pigx-rnaseq): New variable.
2018-03-07 23:25:36 +01:00
c072cf57b9
gnu: samtools: Update to 1.7.
...
* gnu/packages/bioinformatics.scm (samtools): Update to 1.7.
2018-03-06 16:03:04 +01:00
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
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
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
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
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
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
1adeef3194
gnu: Add dropseq-tools.
...
* gnu/packages/bioinformatics.scm (dropseq-tools): New variable.
2018-03-03 21:28:05 +01:00
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
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
9a599c17b7
gnu: Add java-htsjdk-latest.
...
* gnu/packages/bioinformatics.scm (java-htsjdk-latest): New variable.
2018-03-03 21:27:57 +01:00
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
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
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
22c09c335b
gnu: Add java-biojava-alignment.
...
* gnu/packages/bioinformatics.scm (java-biojava-alignment): New variable.
2018-03-03 21:27:48 +01:00
b28c803708
gnu: Add java-biojava-phylo.
...
* gnu/packages/bioinformatics.scm (java-biojava-phylo): New variable.
2018-03-03 21:27:46 +01:00
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
f09d16e594
gnu: Add java-forester.
...
* gnu/packages/bioinformatics.scm (java-forester): New variable.
2018-03-03 21:27:41 +01:00
5fef15e506
gnu: Add java-biojava-core.
...
* gnu/packages/bioinformatics.scm (java-biojava-core): New variable.
2018-03-03 21:27:36 +01:00
bd975831c6
gnu: Add fastqc.
...
* gnu/packages/bioinformatics.scm (fastqc): New variable.
2018-03-03 21:21:48 +01:00
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
ff9d1a2f0c
Merge branch 'master' into core-updates
2018-02-18 00:39:25 +01:00
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
150062f190
Merge branch 'master' into core-updates
2018-02-16 13:14:26 -05:00
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
152d30c346
gnu: Add python-loompy.
...
* gnu/packages/bioinformatics.scm (python-loompy): New variable.
2018-02-15 17:19:00 +01:00
3082de04c2
gnu: Add r-dropbead.
...
* gnu/packages/bioinformatics.scm (r-dropbead): New variable.
2018-02-15 17:18:54 +01:00
05f7296012
gnu: Add r-delayedmatrixstats.
...
* gnu/packages/bioinformatics.scm (r-delayedmatrixstats): New variable.
2018-02-15 17:18:52 +01:00
932c98326d
Merge branch 'master' into core-updates
2018-02-14 03:40:08 -05:00
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
288b8fd5e9
Merge branch 'master' into core-updates
2018-02-13 13:17:15 -05:00
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
7f1d9bef50
gnu: Add r-scran.
...
* gnu/packages/bioinformatics.scm (r-scran): New variable.
2018-02-12 15:29:44 +01:00
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
6fb1dc17a3
gnu: Add r-singlecellexperiment.
...
* gnu/packages/bioinformatics.scm (r-singlecellexperiment): New variable.
2018-02-12 15:29:43 +01:00
9ec0898824
gnu: Add r-beachmat.
...
* gnu/packages/bioinformatics.scm (r-beachmat): New variable.
2018-02-12 15:29:43 +01:00
748e9f163a
gnu: Add r-rhdf5lib.
...
* gnu/packages/bioinformatics.scm (r-rhdf5lib): New variable.
2018-02-12 15:29:43 +01:00
aba3e482b9
gnu: Add r-hdf5array.
...
* gnu/packages/bioinformatics.scm (r-hdf5array): New variable.
2018-02-11 11:42:09 +01:00
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
e7ca634912
Merge branch 'master' into core-updates
2018-02-03 22:46:07 -05:00
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
bee7bb315c
Merge branch 'master' into core-updates
2018-02-01 13:18:47 +01:00
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
b89d8a4271
Merge branch 'master' into core-updates
2018-01-26 00:15:26 -05:00
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
cd70f9bdb0
gnu: deeptools: Update URI.
...
* gnu/packages/bioinformatics.scm (deeptools)[source, home-page]: Update
URI.
2018-01-26 00:09:19 +01:00
a102d359a6
Merge branch 'master' into core-updates
2018-01-23 17:01:07 -05:00
625cdc3fde
gnu: star: Make reproducible.
...
* gnu/packages/bioinformatics.scm (star)[arguments]: Add build phase
"make-reproducible".
2018-01-22 22:49:10 +01:00
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
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
8d77a085a7
gnu: Add sailfish.
...
* gnu/packages/bioinformatics.scm (sailfish): New variable.
2018-01-21 14:18:09 +01:00
1fe0bde34d
gnu: Add libdivsufsort.
...
* gnu/packages/bioinformatics.scm (libdivsufsort): New variable.
2018-01-21 14:18:09 +01:00
c3b2ab9d3b
gnu: Add libgff.
...
* gnu/packages/bioinformatics.scm (libgff): New variable.
2018-01-21 14:18:09 +01:00
4adb40bffc
Merge branch 'master' into core-updates
2018-01-11 14:22:50 -08:00
f6e2d86f8e
gnu: seqmagick: Use 'pypi-uri'.
...
* gnu/packages/bioinformatics.scm (seqmagick)[source]: Use 'pypi-uri'.
2018-01-10 20:16:36 +10:00
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
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
4ed41f472b
Merge branch 'master' into core-updates
2018-01-03 14:18:01 -05:00
8057dee15b
gnu: htslib: Mark up description.
...
* gnu/packages/bioinformatics.scm (htslib)[description]: Use @command{}.
2018-01-02 16:13:23 +01:00
7edee34427
gnu: ribotaper: Wrap executables.
...
* gnu/packages/bioinformatics.scm (ribotaper)[arguments]: Add phase
"wrap-executables".
2018-01-02 12:07:06 +01:00
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
ddf38ece8a
gnu: htslib: Update to 1.6.
...
* gnu/packages/bioinformatics.scm (htslib): Update to 1.6.
2018-01-02 01:47:42 +01:00
23de2e1d5f
Merge remote-tracking branch 'origin/master' into core-updates
2017-12-31 14:10:25 +02:00
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
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
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
f76fc96866
Merge branch 'master' into core-updates
2017-12-21 13:58:35 -05:00
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
d112e5a8c2
gnu: Add kallisto.
...
* gnu/packages/bioinformatics.scm (kallisto): New variable.
2017-12-03 18:38:58 +01:00
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
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
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
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
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
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
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
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
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
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
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
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
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
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
efa6a1ddb5
gnu: Add r-copynumber.
...
* gnu/packages/bioinformatics.scm (r-copynumber): New variable.
2017-11-29 12:46:17 +01:00
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
d7fed31ad2
gnu: Add java-picard.
...
* gnu/packages/bioinformatics.scm (java-picard): New variable.
2017-11-27 12:12:40 +01:00
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
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
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
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
40590caf3b
gnu: idr: Correct license.
...
* gnu/packages/bioinformatics.scm (idr)[license]: Change to GPLv2+.
2017-11-21 23:17:43 +01:00
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
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
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
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
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
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
90dbd984f8
gnu: Remove duplicate from (gnu packages bioinformatics).
...
* gnu/packages/bioinformatics.scm (r-annotationfilter): Remove duplicate.
2017-11-18 11:18:39 +01:00
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
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
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
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
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
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
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
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
11ed4108fb
gnu: methylkit: Use new home page.
...
* gnu/packages/bioinformatics.scm (methylkit)[home-page]: Update.
2017-11-11 05:17:58 +01:00
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
0af4df7e61
gnu: cutadapt: Update to 1.14.
...
* gnu/packages/bioinformatics.scm (cutadapt): Update to 1.14.
2017-11-10 15:32:42 +01:00
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
34260a10d7
gnu: miso: Use pypi-uri.
...
* gnu/packages/bioinformatics.scm (miso)[source]: Use pypi-uri.
2017-11-08 17:41:08 +01:00
c49102ecca
gnu: Add r-hitc.
...
* gnu/packages/bioinformatics.scm (r-hitc): New variable.
2017-11-07 23:32:45 +01:00
30eb4e37c8
gnu: Add r-fithic.
...
* gnu/packages/bioinformatics.scm (r-fithic): New variable.
2017-11-07 23:32:45 +01:00
fbf5440637
gnu: Add r-sushi.
...
* gnu/packages/bioinformatics.scm (r-sushi): New variable.
2017-11-07 23:32:45 +01:00
2e4ce60e7c
gnu: Add r-gwascat.
...
* gnu/packages/bioinformatics.scm (r-gwascat): New variable.
2017-11-07 23:32:44 +01:00
4272000661
gnu: Add r-gviz.
...
* gnu/packages/bioinformatics.scm (r-gviz): New variable.
2017-11-07 23:32:44 +01:00
794ff347a9
gnu: Add r-gqtlstats.
...
* gnu/packages/bioinformatics.scm (r-gqtlstats): New variable.
2017-11-07 23:32:44 +01:00
66c39102e5
gnu: Add r-ldblock.
...
* gnu/packages/bioinformatics.scm (r-ldblock): New variable.
2017-11-07 23:32:44 +01:00
15f98b0d23
gnu: Add r-erma.
...
* gnu/packages/bioinformatics.scm (r-erma): New variable.
2017-11-07 23:32:43 +01:00
421c68e3f7
gnu: Add r-homo-sapiens.
...
* gnu/packages/bioinformatics.scm (r-homo-sapiens): New variable.
2017-11-07 23:32:43 +01:00
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
dd5fc8b78e
gnu: Add r-snpstats.
...
* gnu/packages/bioinformatics.scm (r-snpstats): New variable.
2017-11-07 23:32:43 +01:00
e2b927993e
gnu: Add r-gqtlbase.
...
* gnu/packages/bioinformatics.scm (r-gqtlbase): New variable.
2017-11-07 23:32:43 +01:00
96a392a0b2
gnu: Add r-gprofiler.
...
* gnu/packages/bioinformatics.scm (r-gprofiler): New variable.
2017-11-07 23:32:42 +01:00
60faf94597
gnu: Add r-ggbio.
...
* gnu/packages/bioinformatics.scm (r-ggbio): New variable.
2017-11-07 23:32:42 +01:00
7af1f40373
gnu: Add r-biovizbase.
...
* gnu/packages/bioinformatics.scm (r-biovizbase): New variable.
2017-11-07 23:32:42 +01:00
2f6f61fd8e
gnu: Add r-organismdbi.
...
* gnu/packages/bioinformatics.scm (r-organismdbi): New variable.
2017-11-07 23:32:42 +01:00
aa30ab5aee
gnu: Add r-ensembldb.
...
* gnu/packages/bioinformatics.scm (r-ensembldb): New variable.
2017-11-07 23:32:42 +01:00
763e98103a
gnu: Add r-annotationfilter.
...
* gnu/packages/bioinformatics.scm (r-annotationfilter): New variable.
2017-11-07 23:32:42 +01:00
04e2a2e969
gnu: Add r-dirichletmultinomial.
...
* gnu/packages/bioinformatics.scm (r-dirichletmultinomial): New variable.
2017-11-07 23:32:41 +01:00
3af149f524
gnu: Add r-complexheatmap.
...
* gnu/packages/bioinformatics.scm (r-complexheatmap): New variable.
2017-11-07 23:32:41 +01:00
902fb15d92
gnu: Add r-genomicfiles.
...
* gnu/packages/bioinformatics.scm (r-genomicfiles): New variable.
2017-11-07 23:32:41 +01:00
e160aa1f81
gnu: Add r-gage.
...
* gnu/packages/bioinformatics.scm (r-gage): New variable.
2017-11-07 12:39:51 +01:00
3121814ef1
gnu: Add r-keggrest.
...
* gnu/packages/bioinformatics.scm (r-keggrest): New variable.
2017-11-07 12:39:51 +01:00
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
Roel Janssen