0661758e13
Merge branch 'master' into core-updates
2018-05-21 13:22:32 -04:00
c61d822621
gnu: f-seq: Factorise ‘install’ phase.
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* gnu/packages/bioinformatics.scm (f-seq)[arguments]: Let-bind more.
2018-05-19 05:30:11 +02:00
4ca9581119
gnu: multiqc: Fix build.
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* gnu/packages/bioinformatics.scm (multiqc)[arguments]: Add a
‘relax-requirements’ phase to fix building with python-matplotlib@2.2.
2018-05-17 23:08:30 +02:00
539bf8f2c0
Merge branch 'master' into core-updates
2018-05-17 01:00:50 -04:00
2c5289b263
gnu: diamond: Update to 0.9.22.
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* gnu/packages/bioinformatics.scm (diamond): Update to 0.9.22.
2018-05-12 11:01:21 +10:00
126c9e3ff7
gnu: bismark: Update to 0.19.1.
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* gnu/packages/bioinformatics.scm (bismark): Update to 0.19.1.
[source]: Fetch from git; remove non-free software in snippet.
[arguments]: Update install phase.
2018-05-09 18:37:33 +02:00
f895a7a4d4
gnu: trim-galore: Update to 0.4.5.
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* gnu/packages/bioinformatics.scm (trim-galore): Update to 0.4.5.
[source]: Fetch from git.
[arguments]: Remove custom unpack phase.
2018-05-09 18:37:33 +02:00
12bd588346
Merge branch 'master' into core-updates
2018-05-06 15:56:24 +02:00
a2cfe19041
gnu: Use HTTPS for www.boost.org.
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* gnu/packages/bioinformatics.scm (libgff)[license]: Use HTTPS.
* gnu/packages/boost.scm (boost-sync)[license]: Likewise.
(boost)[license]: Likewise.
[home-page]: Likewise, and use canonical ‘www’ subdomain.
2018-05-01 06:51:15 +02:00
3d5ad159b3
Merge branch 'master' into core-updates
2018-04-30 04:03:54 -04:00
dad9556c5d
gnu: roary: Update to 3.12.0.
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* gnu/packages/bioinformatics.scm (roary): Update to 3.12.0.
2018-04-28 01:52:52 +02:00
d36d5229ed
gnu: star: Update to 2.6.0a.
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* gnu/packages/bioinformatics.scm (star): Update to 2.6.0a.
2018-04-28 01:24:10 +02:00
457fd268ff
gnu: multiqc: Update to 1.5.
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* gnu/packages/bioinformatics.scm (multiqc): Update to 1.5.
2018-04-28 01:10:24 +02:00
4b93efec28
gnu: express: Link with shared protobuf library.
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* gnu/packages/bioinformatics.scm (express): Link with shared protobuf
library.
2018-04-28 01:07:15 +02:00
4ffa085875
gnu: bamtools: Update to 2.5.1.
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* gnu/packages/bioinformatics.scm (bamtools): Update to 2.5.1.
2018-04-28 00:56:59 +02:00
d0c75e73d4
gnu: taxtastic: Update to 0.8.5.
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* gnu/packages/bioinformatics.scm (taxtastic): Update to 0.8.5.
2018-04-28 00:43:16 +02:00
53ec1b7e8b
gnu: vsearch: Update to 2.8.0.
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* gnu/packages/bioinformatics.scm (vsearch): Update to 2.8.0.
2018-04-27 23:20:00 +10:00
171cf56c2f
gnu: diamond: Update to 0.9.21.
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* gnu/packages/bioinformatics.scm (diamond): Update to 0.9.21.
2018-04-27 23:20:00 +10:00
b43a9eb361
gnu: bedops: Update to 2.4.33.
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* gnu/packages/bioinformatics.scm (bedops): Update to 2.4.33.
2018-04-27 01:11:57 +02:00
c829c5ea85
gnu: samtools: Update to 1.8.
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* gnu/packages/bioinformatics.scm (samtools): Update to 1.8.
2018-04-27 01:11:47 +02:00
cbd9f91c32
gnu: bcftools: Update to 1.8.
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* gnu/packages/bioinformatics.scm (bcftools): Update to 1.8.
* gnu/local.mk: Remove patch.
* gnu/packages/patches/bcftools-regidx-unsigned-char.patch: Remove file.
2018-04-27 01:11:42 +02:00
8df0267ad4
gnu: htslib: Update to 1.8.
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* gnu/packages/bioinformatics.scm (htslib): Update to 1.8.
2018-04-27 01:11:24 +02:00
3d7f9cbe75
gnu: pigx-chipseq: Update to 0.0.15.
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* gnu/packages/bioinformatics.scm (pigx-chipseq): Update to 0.0.15.
2018-04-22 23:00:51 +02:00
c36ce47635
gnu: r-seurat: Update to 2.3.0.
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* gnu/packages/bioinformatics.scm (r-seurat): Update to 2.3.0.
[propagated-inputs]: Add r-cluster, r-dosnow, r-fitdistrplus, r-foreach,
r-lmtest, r-png, and r-rann.
2018-04-21 23:07:52 +02:00
aeca5f0c5b
gnu: r-scran: Update to 1.6.9.
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* gnu/packages/bioinformatics.scm (r-scran): Update to 1.6.9.
2018-04-21 23:07:52 +02:00
80323c3c13
gnu: r-hitc: Update to 1.22.1.
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* gnu/packages/bioinformatics.scm (r-hitc): Update to 1.22.1.
2018-04-21 23:07:52 +02:00
b6d7deca55
gnu: r-ldblock: Update to 1.8.1.
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* gnu/packages/bioinformatics.scm (r-ldblock): Update to 1.8.1.
2018-04-21 23:07:52 +02:00
fb1dcfac46
gnu: r-erma: Update to 0.10.1.
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* gnu/packages/bioinformatics.scm (r-erma): Update to 0.10.1.
2018-04-21 23:07:52 +02:00
8defca1d94
gnu: r-gprofiler: Update to 0.6.6.
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* gnu/packages/bioinformatics.scm (r-gprofiler): Update to 0.6.6.
2018-04-21 23:07:52 +02:00
fc6d3e2606
gnu: r-ggbio: Update to 1.26.1.
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* gnu/packages/bioinformatics.scm (r-ggbio): Update to 1.26.1.
2018-04-21 23:07:52 +02:00
0bd5c7b859
gnu: r-genomicalignments: Update to 1.14.2.
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* gnu/packages/bioinformatics.scm (r-genomicalignments): Update to 1.14.2.
2018-04-21 23:07:52 +02:00
4207770218
gnu: r-dexseq: Update to 1.24.4.
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* gnu/packages/bioinformatics.scm (r-dexseq): Update to 1.24.4.
2018-04-21 23:07:52 +02:00
3db5d04ccc
gnu: r-vegan: Update to 2.5-1.
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* gnu/packages/bioinformatics.scm (r-vegan): Update to 2.5-1.
[propagated-inputs]: Add r-knitr.
2018-04-21 23:07:52 +02:00
f89aa1521a
Merge branch 'master' into core-updates
2018-04-10 00:42:22 -04:00
482959ffa4
gnu: sambamba: Update to 0.6.7-10-g223fa20.
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* gnu/packages/bioinformatics.scm (sambamba)[source]: Fetch from git.
[arguments]: Disable parallel build; rename build phase "place-biod" to
"place-biod-and-undead"; add build phase "fix-ldc-version"; adjust phase
"unbundle-prerequisites".
[native-inputs]: Add python2-minimal; update biod sources; add undead sources.
2018-04-06 17:12:15 +02:00
262ee8eae2
gnu: htslib-for-sambamba: Fix build.
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* gnu/packages/bioinformatics.scm (htslib-for-sambamba)[arguments]: Do not
inherit htslib arguments.
2018-04-06 17:12:07 +02:00
fdc306879b
gnu: Add delly.
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* gnu/packages/bioinformatics.scm (delly): New variable.
* gnu/packages/patches/delly-use-system-libraries.patch: New file.
* gnu/local.mk: Include delly-use-system-libraries.patch.
Signed-off-by: Leo Famulari <leo@famulari.name>
2018-03-30 10:48:01 -04:00
f38ac742e6
gnu: mash: Update to 2.0.
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* gnu/packages/bioinformatics.scm (mash): Update to 2.0.
2018-03-30 12:18:35 +10:00
c7a8aa131d
gnu: mafft: Update to 7.394.
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* gnu/packages/bioinformatics.scm (mafft): Update to 7.394.
2018-03-30 12:18:35 +10:00
9a40b8d9b2
gnu: diamond: Update to 0.9.19.
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* gnu/packages/bioinformatics.scm (diamond): Update to 0.9.19.
2018-03-30 12:18:35 +10:00
5576cfabf3
Merge branch 'master' into core-updates
2018-03-29 17:34:41 +02:00
e086d2f68b
gnu: r-mutationalpatterns: Update to 1.4.3.
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* gnu/packages/bioinformatics.scm (r-mutationalpatterns): Update to 1.4.3;
[propagated-inputs]: Remove r-gridextra.
2018-03-29 15:50:44 +02:00
53e42694e5
gnu: kaiju: Update to 1.6.2.
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* 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.
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* 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.
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* 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.
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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.
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* 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.
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* 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.
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* gnu/packages/bioinformatics.scm (pigx-bsseq): Update to 0.0.8.
2018-03-20 14:56:44 +01:00
Mark H Weaver