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 |
|
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 |