e70f7a2306
gnu: prodigal: Update to 2.6.3.
...
* gnu/packages/bioinformatics.scm (prodigal): Update to 2.6.3.
2016-02-16 07:18:59 +10:00
258c0a365e
gnu: r-annotationdbi: Update to 1.32.3.
...
* gnu/packages/bioinformatics.scm (r-annotationdbi): Update to 1.32.3.
2016-02-15 16:11:22 +01:00
cf6edaba74
gnu: vsearch: Update to 1.10.0.
...
* gnu/packages/bioinformatics.scm (vsearch): Update to 1.10.0.
[origin]: Adapt to changes in bundling of cityhash.
2016-02-15 22:54:25 +10:00
0d0bcaa08e
gnu: macs: Update to 2.1.0.20151222.
...
* gnu/packages/bioinformatics.scm (macs): Update to 2.1.0.20151222.
2016-02-12 18:16:16 +01:00
43ec07f17c
gnu: macs: Use "pypi-uri".
...
* gnu/packages/bioinformatics.scm (macs)[source]: Use "pypi-uri" to
build source URI.
2016-02-12 18:16:16 +01:00
ce294c0445
gnu: Update sortmerna to 2.1.
...
* gnu/packages/bioinformatics.scm (sortmerna): Update to 2.1.
2016-02-02 22:42:38 +10:00
a78d62f432
gnu: sra-tools: Update to 2.5.7.
...
* gnu/packages/bioinformatics.scm (sra-tools): Update to 2.5.7.
2016-01-26 10:59:13 +10:00
fe91666b79
gnu: ncbi-vdb: Update to 2.5.7.
...
gnu/packages/bioinformatics.scm (ncbi-vdb): Update to 2.5.7.
2016-01-26 10:59:13 +10:00
d3b39bc231
gnu: ngs-sdk: Update to 1.2.3.
...
gnu/packages/bioinformatics.scm (ngs-sdk): Update to 1.2.3.
2016-01-26 10:59:13 +10:00
bcadaf0050
gnu: Add sortmerna.
...
* gnu/packages/bioinformatics.scm (sortmerna): New variable.
2016-01-25 08:35:11 +10:00
3a40a92c73
gnu: Add cufflinks.
...
* gnu/packages/bioinformatics.scm (cufflinks): New variable.
2016-01-23 09:15:11 +01:00
94ce537eac
gnu: Add TopHat.
...
* gnu/packages/bioinformatics.scm (tophat): New variable.
* gnu/packages/patches/tophat-build-with-later-seqan.patch: New file.
* gnu-system.am (dist_patch_DATA): Add it.
2016-01-23 08:53:10 +01:00
3062d750b4
gnu: star: Update to 2.5.1b.
...
* gnu/packages/bioinformatics.scm (star): Update to 2.5.1b.
[source]: Remove bundled htslib sources and pre-built binaries.
[arguments]: Add phase "do-not-use-bundled-htslib".
[inputs]: Add "htslib".
2016-01-23 08:40:14 +01:00
c0266e8d03
gnu: star: Use "modify-phases" syntax.
...
* gnu/packages/bioinformatics.scm (star)[arguments]: Use "modify-phases"
syntax.
2016-01-23 08:40:14 +01:00
897092875e
gnu: r-qtl: Update to 1.38-4.
...
* gnu/packages/bioinformatics.scm (r-qtl): Update to 1.38-4.
2016-01-21 11:16:12 +01:00
2309ed6862
gnu: samtools-0.1: Adapt to changes in "samtools" variable.
...
* gnu/packages/bioinformatics.scm (samtools-0.1)[arguments]: Add
"LIBCURSES" make flag; delete "configure" phase; disable tests outside
of "substitute-keyword-arguments".
2016-01-16 15:50:51 +01:00
3141b83d4d
gnu: r-go-db: Add missing input.
...
* gnu/packages/bioinformatics.scm (r-go-db)[propagated-inputs]: Add
"r-annotationdbi".
2016-01-14 14:43:59 +01:00
0047d26a22
gnu: bowtie: Update to 2.2.6.
...
* gnu/packages/bioinformatics.scm (bowtie): Update to 2.2.6.
[source]: Remove patch; do not set CC and CPP variables.
[inputs]: Add "tbb".
[arguments]: Pass "prefix" and "WITH_TBB" make flags; remove custom
"install" phase.
* gnu/packages/patches/bowtie-fix-makefile.patch: Remove file.
* gnu-system.am (dist_patch_DATA): Remove patch file.
2016-01-14 14:43:25 +01:00
6b6f7d6a0e
gnu: orfm: Update to 0.5.3.
...
* gnu/packages/bioinformatics.scm (orfm): Update to 0.5.3.
[native-inputs]: Add inputs required for tests.
[description]: Add commas.
2016-01-14 08:00:10 +10:00
c44734115a
gnu: samtools: Update to 1.3.
...
* gnu/packages/bioinformatics.scm (samtools): Update to 1.3.
[arguments]: Enable tests for all architectures; set ncurses in
configure-flags instead of make-flags; simplify "patch-tests" phase;
restore "configure" phase.
2016-01-13 15:12:22 +01:00
81f3e0c1f3
gnu: Add fxtract.
...
* gnu/packages/bioinformatics.scm (fxtract): New variable.
2016-01-12 07:49:19 +10:00
9b9b7ffd8e
gnu: bedtools: Update to 2.25.0.
...
* gnu/packages/bioinformatics.scm (bedtools): Update to 0.25.0.
[source]: Remove patch merged upstream.
[arguments]: Use 'modify-phases'. Remove
'patch-makefile-SHELL-definition' phase.
* gnu/packages/patches/bedtools-32bit-compilation.patch: Remove file.
* gnu-system.am (dist_patch_DATA): Remove it.
2016-01-11 00:36:13 +10:00
6573ac82ad
gnu: bedtools: Use modify-phases.
...
* gnu/packages/bioinformatics.scm (bedtools)[arguments]: Use modify-phases.
2016-01-11 00:36:13 +10:00
2409f37f28
gnu: Add missing (gnu packages gcc) import.
...
* gnu/packages/bioinformatics.scm: Use (gnu packages gcc). This is
required by 'r-impute' for 'gfortran'.
2016-01-08 14:18:46 +01:00
cb933df6da
gnu: Add genomation.
...
* gnu/packages/bioinformatics.scm (r-genomation): New variable.
2016-01-07 17:18:17 +01:00
03ea5a357e
gnu: Add seqPattern.
...
* gnu/packages/bioinformatics.scm (r-seqpattern): New variable.
2016-01-07 17:18:17 +01:00
c43a011de3
gnu: Add impute.
...
* gnu/packages/bioinformatics.scm (r-impute): New variable.
2016-01-07 17:18:17 +01:00
c63cef6699
gnu: Add BSgenome.
...
* gnu/packages/bioinformatics.scm (r-bsgenome): New variable.
2016-01-07 17:18:17 +01:00
d547ce5e70
gnu: Add topGO.
...
* gnu/packages/bioinformatics.scm (r-topgo): New variable.
2016-01-07 17:18:17 +01:00
fb25d8803f
gnu: Add GO.db.
...
* gnu/packages/bioinformatics.scm (r-go-db): New variable.
2016-01-07 17:18:16 +01:00
2fd7c04984
gnu: Add GenomicFeatures.
...
* gnu/packages/bioinformatics.scm (r-genomicfeatures): New variable.
2016-01-07 17:18:16 +01:00
317755ff0f
gnu: Add rtracklayer.
...
* gnu/packages/bioinformatics.scm (r-rtracklayer): New variable.
2016-01-07 17:18:16 +01:00
d8a828af78
gnu: Add GenomicAlignments.
...
* gnu/packages/bioinformatics.scm (r-genomicalignments): New variable.
2016-01-07 17:18:16 +01:00
6e76dda2d0
gnu: Add SummarizedExperiment.
...
* gnu/packages/bioinformatics.scm (r-summarizedexperiment): New variable.
2016-01-07 17:18:16 +01:00
f8d74f7018
gnu: Add Rsamtools.
...
* gnu/packages/bioinformatics.scm (r-rsamtools): New variable.
2016-01-07 17:18:16 +01:00
bf15935337
gnu: Add Biostrings.
...
* gnu/packages/bioinformatics.scm (r-biostrings): New variable.
2016-01-07 17:18:16 +01:00
e91d362e48
gnu: Add BiocParallel.
...
* gnu/packages/bioinformatics.scm (r-biocparallel): New variable.
2016-01-07 17:18:16 +01:00
c465fa72ed
gnu: Add biomaRt.
...
* gnu/packages/bioinformatics.scm (r-biomart): New variable.
2016-01-07 17:18:16 +01:00
8b7bce740d
gnu: Add AnnotationDbi.
...
* gnu/packages/bioinformatics.scm (r-annotationdbi): New variable.
2016-01-07 17:18:16 +01:00
555e3399dc
gnu: Add Biobase.
...
* gnu/packages/bioinformatics.scm (r-biobase): New variable.
2016-01-07 17:18:16 +01:00
5dfd276602
gnu: edirect: Update to 3.50.
...
* gnu/packages/bioinformatics.scm (edirect): Update to 3.50.
[native-inputs]: Remove "unzip".
2016-01-07 11:25:24 +01:00
d2540f80c2
gnu: Add and use default IcedTea.
...
* gnu/packages/java.scm (icedtea): New variable.
(swt)[native-inputs]: Replace "icedtea6" with "icedtea".
* gnu/packages/bioinformatics.scm (htsjdk)[native-inputs]: Likewise.
(ngs-java)[inputs]: Likewise.
* gnu/packages/kodi.scm (kodi)[native-inputs]: Replace "icedtea7" with
"icedtea".
* gnu/packages/ruby.scm (ruby-rjb)[native-inputs]: Replace "icedtea7"
with "icedtea".
2016-01-06 11:38:50 +01:00
43c565d2e7
gnu: Add Jellyfish.
...
* gnu/packages/bioinformatics.scm (jellyfish): New variable.
2016-01-06 11:10:46 +01:00
19f4554c94
gnu: Add fraggenescan.
...
* gnu/packages/bioinformatics.scm (fraggenescan): New variable.
2015-12-29 20:14:03 -05:00
e2cd1d0fb9
gnu: Add GenomicRanges.
...
* gnu/packages/bioinformatics.scm (r-genomicranges): New variable.
2015-12-21 17:22:16 +01:00
0e7d5560de
gnu: Add XVector.
...
* gnu/packages/bioinformatics.scm (r-xvector): New variable.
2015-12-21 17:22:16 +01:00
bf7764b74f
gnu: Add GenomeInfoDb.
...
* gnu/packages/bioinformatics.scm (r-genomeinfodb): New variable.
2015-12-21 17:22:16 +01:00
78addcb0eb
gnu: Add IRanges.
...
* gnu/packages/bioinformatics.scm (r-iranges): New variable.
2015-12-21 17:22:16 +01:00
7485129e4f
gnu: Add S4Vectors.
...
* gnu/packages/bioinformatics.scm (r-s4vectors): New variable.
2015-12-21 17:22:16 +01:00
d29b25c490
gnu: Add BiocGenerics.
...
* gnu/packages/bioinformatics.scm (r-biocgenerics): New variable.
2015-12-21 17:22:16 +01:00
9fba89e829
gnu: Add r-acsnminer.
...
* gnu/packages/bioinformatics.scm (r-acsnminer): New variable.
2015-12-21 17:21:26 +01:00
02f35bb5a7
gnu: mafft: Update to 7.267.
...
* gnu/packages/bioinformatics.scm (mafft): Update to 7.267.
[arguments]: Don't include mafft-homologs manpage.
[inputs]: Add gawk and grep.
[propagated-inputs]: Add coreutils.
2015-12-21 15:16:01 +01:00
5f7e17bef7
gnu: Add snap-aligner.
...
* gnu/packages/bioinformatics.scm (snap-aligner): New variable.
2015-12-11 14:34:51 +01:00
e815c094f7
gnu: python-biopython, python2-biopython: Update to 1.66.
...
* gnu/packages/bioinformatics.scm (python-biopython, python2-biopython): Update to 1.66.
[source]: Use PyPi instead of biopython.org.
2015-12-10 14:35:56 +01:00
b49c5a58dc
gnu: preseq: Update to 2.0.
...
* gnu/packages/bioinformatics.scm (preseq): Update to 2.0.
[source]: Add file-name field, remove patches.
[arguments]: Remove unused build phases, add make flags.
[inputs]: Add smithlab-cpp.
* gnu/packages/patches/preseq-1.0.2-link-with-libbam.patch: Remove file.
* gnu/packages/patches/preseq-1.0.2-install-to-PREFIX.patch: Remove
file.
* gnu-system.am (dist_patch_DATA): Remove them.
2015-11-20 15:22:06 +01:00
c6a24d6e92
gnu: Add smithlab-cpp.
...
* gnu/packages/bioinformatics.scm (smithlab-cpp): New variable.
2015-11-20 15:22:06 +01:00
3d51ec919e
gnu: edirect: Update home page.
...
* gnu/packages/bioinformatics.scm (edirect)[home-page]: Append trailing
slash to home page.
2015-11-20 15:21:24 +01:00
c52a382c4a
gnu: sra-tools: Update to 2.5.4.
...
* gnu/packages/bioinformatics.scm (sra-tools): Update to 2.5.4.
2015-11-20 15:21:24 +01:00
9e5ef614aa
gnu: ncbi-vdb: Update to 2.5.4.
...
* gnu/packages/bioinformatics.scm (ncbi-vdb): Update to 2.5.4.
2015-11-20 15:21:24 +01:00
614a8977cb
gnu: ngs-java: Update to 1.2.2.
...
* gnu/packages/bioinformatics.scm (ngs-java): Update to 1.2.2.
[arguments]: Remove build phase "fix-java-symlink-installation".
2015-11-20 15:21:24 +01:00
d6a1cd7cae
gnu: ngs-sdk: Update to 1.2.2.
...
* gnu/packages/bioinformatics.scm (ngs-sdk): Update to 1.2.2.
2015-11-20 15:21:24 +01:00
9641a89957
gnu: bless: Build only for x86_64.
...
* gnu/packages/bioinformatics.scm (bless): Add supported-systems field.
2015-11-20 11:32:32 +01:00
0536727efe
gnu: htseq: Propagate numpy.
...
* gnu/packages/bioinformatics.scm (htseq)[inputs]: Move python2-numpy
from here ...
[propagated-inputs]: ... to here.
2015-11-20 11:32:32 +01:00
029d9f77ab
gnu: mosaik: Build only on x86_64.
...
* gnu/packages/bioinformatics.scm (mosaik)[supported-systems]: Add
field.
2015-11-12 12:36:40 +01:00
4d75e03ac9
gnu: bless: Correct indentation and home-page.
...
* gnu/packages/bioinformatics.scm (bless): Fix indentation.
[home-page]: Replace broken URL.
2015-11-06 22:31:29 +01:00
6c2b26e21e
gnu: Add BLESS.
...
* gnu/packages/bioinformatics.scm (bless): New variable.
Co-authored-by: Diane Trout <diane@ghic.org>
2015-11-06 18:20:50 +01:00
60af3d8241
gnu: hisat: Disable build on non-x86_64.
...
* gnu/packages/bioinformatics.scm (hisat)[supported-systems]: Add field.
2015-11-02 14:37:52 +01:00
f3674b1c80
gnu: Add express-beta-diversity.
...
* gnu/packages/bioinformatics.scm (express-beta-diversity): New variable.
Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2015-11-02 09:54:21 +01:00
9a067efdb2
gnu: pbtranscript-tofu: Update to 2.2.3.
...
* gnu/packages/bioinformatics.scm (pbtranscript-tofu): Update to 2.2.3.
[source]: Remove bundled Cython sources in a snippet. Replace
".tar.gz" extension in file-name field with "-checkout".
[arguments]: Replace "enter-directory-and-clean-up" phase with
"enter-directory" phase, and add "patch-setuppy" phase.
[inputs]: Add python2-h5py. Move python2-cython ...
[native-inputs]: ... to this field.
2015-10-28 16:26:58 +01:00
104c1986ac
gnu: subread: Use SSE optimizations on x86_64 only.
...
* gnu/packages/bioinformatics.scm (subread)[arguments]: Override CC and
CCFLAGS conditionally dependent on target system.
2015-10-27 12:06:55 +01:00
61d5fd03bf
gnu: crossmap: Update to 0.2.1.
...
* gnu/packages/bioinformatics.scm (crossmap): Update to 0.2.1.
2015-10-27 11:14:13 +01:00
fe4c37c244
gnu: Add MOSAIK.
...
* gnu/packages/bioinformatics.scm (mosaik): New variable.
2015-10-22 11:11:09 +02:00
ab29be81c5
gnu: ngs-sdk: Correct typo.
...
* gnu/packages/bioinformatics.scm (ngs-sdk): Correct typo.
2015-10-17 22:51:12 +02:00
a0dadf0cb1
gnu: ngs-sdk: Remove unsupported systems.
...
* gnu/packages/bioinformatics.scm (ngs-sdk)[supported-systems]: Keep only x86
based systems.
2015-10-17 22:43:14 +02:00
d9c44e9c6a
gnu: diamond: Restrict supported systems to x86_64-linux.
...
* gnu/packages/bioinformatics.scm (diamond) [supported-systems]: Restrict to
x86_64-linux.
2015-10-14 20:02:25 +03:00
db94f8c734
gnu: bwa: Disable on non-x86_64.
...
* gnu/packages/bioinformatics.scm (bwa)[supported-systems]: Add field.
2015-10-12 15:50:33 +02:00
6f04e51560
gnu: vsearch: Restrict supported systems to x86_64-linux.
...
* gnu/packages/bioinformatics.scm (vsearch)[supported-systems]: Restrict
to x86_64-linux.
Signed-off-by: Andreas Enge <andreas@enge.fr>
2015-10-03 13:59:11 +02:00
9ab5ea449e
gnu: clipper: Add 'file-name' field to source origin.
...
* gnu/packages/bioinformatics.scm (clipper)[source]: Add file-name.
2015-10-02 10:55:57 -04:00
a2950fa4dc
gnu: Add vsearch.
...
* gnu/packages/bioinformatics.scm (vsearch): New variable.
Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2015-10-01 10:51:28 +02:00
b2bddb07ef
gnu: Add bio-blastxmlparser.
...
* gnu/packages/bioinformatics.scm (bio-blastxmlparser): New variable.
2015-09-28 12:22:47 +02:00
e1556533d3
Merge branch 'core-updates'
2015-09-26 15:14:53 +02:00
d708b7a973
gnu: Add seqmagick.
...
* gnu/packages/bioinformatics.scm (seqmagick): New variable.
2015-09-25 16:16:28 +02:00
bd90127ad4
Merge branch 'master' into core-updates
2015-09-22 16:38:48 -04:00
a5002ae77c
gnu: Add R/qtl.
...
* gnu/packages/bioinformatics.scm (r-qtl): New variable.
Co-authored-by: Pjotr Prins <pjotr.guix@thebird.nl>
2015-09-20 00:32:45 +02:00
edb15985f1
gnu: Add bioruby.
...
* gnu/packages/bioinformatics.scm (bioruby): New variable.
2015-09-19 12:41:52 -04:00
41ddebdd2a
gnu: Add mafft.
...
* gnu/packages/bioinformatics.scm (mafft): New variable.
2015-09-16 23:06:14 +02:00
9c38b54027
gnu: Add bio-locus.
...
* gnu/packages/bioinformatics.scm (bio-locus): New variable.
2015-09-14 12:06:04 -04:00
801a0a2219
Revert "gnu: Add bio-locus."
...
This reverts commit b429c4fbb0
2015-09-14 12:05:15 -04:00
b429c4fbb0
gnu: Add bio-locus.
...
* gnu/packages/bioinformatics.scm (bio-locus): New variable.
2015-09-14 11:36:30 -04:00
75710da667
Merge branch 'master' into core-updates
2015-09-13 21:28:01 +02:00
1921b1de07
gnu: Add deeptools.
...
* gnu/packages/bioinformatics.scm (deeptools): New variable.
2015-09-02 10:38:43 +02:00
96c4621056
gnu: Use 'install-file' instead of 'mkdir-p' and 'copy-file' in obvious cases.
...
* gnu/packages/bioinformatics.scm (bedtools, bowtie, bwa, hisat, samtools,
plink, star): Use 'install-file' instead of 'mkdir-p' + 'copy-file'.
* gnu/packages/check.scm (catch-framework): Likewise.
* gnu/packages/code.scm (global): Likewise.
* gnu/packages/emacs.scm (magit-svn, haskell-mode, emacs-pdf-tools):
Likewise.
* gnu/packages/engineering.scm (fastcap, fasthenry): Likewise.
* gnu/packages/gnuzilla.scm (nss): Likewise.
* gnu/packages/guile.scm (guile-minikanren): Likewise.
* gnu/packages/java.scm (swt): Likewise.
* gnu/packages/make-bootstrap.scm (%static-binaries): Likewise.
* gnu/packages/maths.scm (lpsolve): Likewise.
* gnu/packages/mp3.scm (mpc123): Likewise.
* gnu/packages/ninja.scm (ninja): Likewise.
* gnu/packages/python.scm (python-numpy, python-pyparsing): Likewise.
* gnu/packages/screen.scm (dtach): Likewise.
* gnu/packages/synergy.scm (synergy): Likewise.
* gnu/packages/textutils.scm (utf8proc): Likewise.
* gnu/packages/version-control.scm (git-test-sequence): Likewise.
* gnu/packages/wicd.scm (wicd): Likewise.
2015-08-29 01:25:08 +02:00
f7283db37d
gnu: Add BioPerl.
...
* gnu/packages/bioinformatics.scm (bioperl-minimal): New variable.
2015-08-26 17:54:52 +02:00
c1670a8196
gnu: shogun: Move package to machine-learning.scm.
...
* gnu/packages/bioinformatics.scm (shogun): Move from here...
* gnu/packages/machine-learning.scm (shogun): ...to here.
2015-08-14 17:17:05 +02:00
b81cb1f2f3
gnu: bedtools: Add patch to fix compilation on 32 bit systems.
...
* gnu/packages/patches/bedtools-32bit-compilation.patch: New file.
* gnu/packages/bioinformatics.scm (bedtools)[source]: Add patch.
* gnu-system.am (dist_patch_DATA): Register patch.
Signed-off-by: Andreas Enge <andreas@enge.fr>
2015-07-25 19:16:49 +02:00
bd4af2f940
gnu: bedtools: Update to 2.24.0.
...
* gnu/packages/bioinformatics.scm (bedtools): Update to 2.24.0.
2015-07-25 00:02:54 -04:00
8dc797fa28
gnu: Add aragorn.
...
* gnu/packages/bioinformatics.scm (aragorn): New variable.
2015-07-21 16:39:38 +02:00
5ede5f2f1c
gnu: metabat: Minor tweaks.
...
* gnu/packages/bioinformatics.scm (metabat)[arguments]: Fix indentation in
'fix-includes' phase.
[license]: Fix misspelling.
2015-07-19 15:27:15 -04:00
8fd790eb87
gnu: Add metabat.
...
* gnu/packages/bioinformatics.scm (metabat): New variable.
2015-07-19 15:17:08 -04:00
9f04196d88
gnu: preseq: Move "use-samtools-headers" phase.
...
* gnu/packages/bioinformatics.scm (preseq)[arguments]: Move phase
"use-samtools-headers" after "enter-dir" phase.
2015-07-09 12:12:07 +02:00
Ben Woodcroft
Ricardo Wurmus
Ben J. Woodcroft
Pjotr Prins
Ricardo Wurmus
Mathieu Lirzin
Ben Woodcroft
Andreas Enge
Mark H Weaver
Ludovic Courtès
David Thompson