d3dce32216
gnu: metabat: Fix boost-related compilation issue.
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Reported by Leo Famulari.
* gnu/packages/patches/metabat-fix-boost-issue.patch: New file.
* gnu/packages/bioinformatics.scm (metabat): Use it.
* gnu/local.mk (dist_patch_DATA): Add it.
2017-07-23 22:35:52 +10:00
f3f68a442c
gnu: metabat: Update to 2.11.1.
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* gnu/packages/bioinformatics.scm (metabat): Update to 2.11.1.
[source]: Add patch to fix compilation.
[arguments]: Adjust regular expressions modifying 'SConstruct'.
* gnu/packages/patches/metabat-fix-compilation.patch: New file.
* gnu/local.mk (dist_patch_DATA): Add it.
2017-07-23 10:29:36 +10:00
897ab082b2
gnu: python-plastid: Update to 0.4.8.
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* gnu/packages/bioinformatics.scm (python-plastid): Update to 0.4.8.
2017-07-23 10:29:36 +10:00
0620387a59
gnu: bcftools: Update to 1.5.
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* gnu/packages/bioinformatics.scm (bcftools): Update to 1.5.
[origin]: Remove fix-makefile patch.
[arguments]: Add configure flags, add LIBS make flag. Do not delete
configure phase.
* gnu/packages/patches/bcftools-fix-makefile.patch: Remove file.
* gnu/local.mk (dist_patch_DATA): Remove it.
2017-07-23 10:29:36 +10:00
63fa0ffcd4
gnu: samtools: Update to 1.5.
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* gnu/packages/bioinformatics.scm (samtools): Update to 1.5.
2017-07-23 10:29:36 +10:00
4fb6d1280e
gnu: htslib: Update to 1.5.
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* gnu/packages/bioinformatics.scm (htslib): Update to 1.5.
2017-07-23 10:29:35 +10:00
60739965da
gnu: python-pysam: Update to 0.11.2.2.
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* gnu/packages/bioinformatics.scm (python-pysam): Update to 0.11.2.2.
2017-07-23 10:29:35 +10:00
bca2c57658
gnu: bamm: Use htslib-1.3.
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* gnu/packages/bioinformatics (htslib-1.3): New variable.
(bamm)[inputs]: Replace htslib with htslib-1.3.
2017-07-23 10:29:35 +10:00
98593f9f51
gnu: bcftools: Update to 1.4.1.
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* gnu/packages/bioinformatics.scm (bcftools): Update to 1.4.1.
[arguments]: Move Makefile modifications from here ...
[source]: ... to added patch. Adjust patch for update to 1.4.
* gnu/packages/patches/bcftools-fix-makefile.patch: New file.
* gnu/local.mk (dist_patch_DATA): Register it.
2017-07-23 10:29:35 +10:00
4ab1644049
gnu: samtools: Update to 1.4.1.
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* gnu/packages/bioinformatics.scm (samtools): Update to 1.4.1.
[arguments]: Add '--with-htslib=system' configure flag.
[inputs]: Add htslib.
2017-07-23 10:29:34 +10:00
a9e4a1e641
gnu: htslib: Update to 1.4.1.
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* gnu/packages/bioinformatics.scm (htslib): Update to 1.4.1.
[inputs]: Add curl, openssl.
2017-07-23 10:29:34 +10:00
c842d42593
gnu: samtools: Use "modify-phases" syntax.
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* gnu/packages/bioinformatics.scm (samtools)[arguments]: Use "modify-phases"
syntax.
2017-07-23 10:29:34 +10:00
3a4b0b126b
gnu: r-s4vectors: Update to 0.14.3.
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* gnu/packages/bioinformatics.scm (r-s4vectors): Update to 0.14.3.
2017-07-22 17:31:19 +02:00
a35a1e9c13
gnu: r-genomicranges: Update to 1.28.4.
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* gnu/packages/bioinformatics.scm (r-genomicranges): Update to 1.28.4.
2017-07-22 17:22:07 +02:00
fd40857938
gnu: r-bsgenome-hsapiens-ucsc-hg19: Update hash.
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* gnu/packages/bioinformatics.scm (r-bsgenome-hsapiens-ucsc-hg19)[source]:
Update hash because the tarball changed in place.
2017-07-19 14:39:37 +02:00
2324541bd0
gnu: sortmerna: Limit support to x86_64 and i686 only.
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* gnu/packages/bioinformatics.scm (sortmerna)[supported-systems]: New field.
2017-07-19 14:37:47 +03:00
2805f9b2a0
gnu: raxml: Limit to x86_64 and i686 only.
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* gnu/packages/bioinformatics.scm (raxml)[supported-systems]: New field.
2017-07-18 09:00:10 +03:00
06e372360e
gnu: bowtie: Use 'modify-phases'.
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* gnu/packages/bioinformatics.scm (bowtie)[arguments]: Use 'modify-phases'
syntax.
2017-07-14 19:23:37 +10:00
d6e63cf31c
gnu: bowtie: Update to 2.3.2.
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* gnu/packages/bioinformatics.scm (bowtie): Update to 2.3.2.
[inputs]: Add zlib.
2017-07-14 18:54:10 +10:00
fed7200862
gnu: deeptools: Update to 2.5.1.
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* gnu/packages/bioinformatics.scm (deeptools): Update to 2.5.1.
[arguments]: Remove.
[native-inputs]: Use "python-" instead of "python2-" variants.
[inputs]: Likewise; add python-py2bit.
2017-07-09 17:07:27 +02:00
eb2200f3bd
gnu: Add python-py2bit.
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* gnu/packages/bioinformatics.scm (python-py2bit): New variable.
2017-07-09 17:07:23 +02:00
4732e6ee84
gnu: blast+: Update to 2.6.0.
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* gnu/packages/bioinformatics.scm (blast+): Update to 2.6.0.
[origin]: Remove bundled pcre. Add patch.
[arguments]: Replace paths in run_with_lock.c. Configure with pcre.
[inputs]: Add pcre, perl, python.
* gnu/packages/patches/blast+-fix-makefile.patch: New file.
* gnu/local.mk (dist_patch_DATA): Add it.
2017-07-08 12:05:59 +10:00
0a66c38764
Revert "gnu: blast+: Update to 2.6.0."
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This reverts commit 18dea67dc3
2017-07-06 19:38:55 -04:00
ce7e361fa3
gnu: gemma: Fix building on non-Intel architectures.
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* gnu/packages/patches/gemma-intel-compat.patch: New file.
* gnu/packages/bioinformatics.scm (gemma)[source]: Add patch.
[arguments]: Add NO_INTEL_COMPAT flag on non-Intel architectures.
* gnu/local.mk (dist_patch_DATA): Register patch.
2017-07-04 22:55:44 +03:00
a522517cdb
gnu: diamond: Update to 0.9.9.
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* gnu/packages/bioinformatics.scm (diamond): Update to 0.9.9.
2017-07-04 19:59:01 +10:00
18dea67dc3
gnu: blast+: Update to 2.6.0.
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* gnu/packages/bioinformatics.scm (blast+): Update to 2.6.0.
[origin]: Remove bundled pcre.
[arguments]: Replace paths in run_with_lock.c. Configure with pcre.
[inputs]: Add pcre, perl, python.
2017-07-04 19:58:42 +10:00
ba773f65f0
gnu: cd-hit: Update to 4.6.8.
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* gnu/packages/bioinformatics.scm (cd-hit): Update to 4.6.8.
2017-07-01 10:49:37 +10:00
fd99d95b3f
gnu: bwa: Update to 0.7.15.
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* gnu/packages/bioinformatics.scm (bwa): Update to 0.7.15.
2017-07-01 09:48:20 +10:00
7ceb0a83e3
gnu: Add f-seq.
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* gnu/packages/bioinformatics.scm (f-seq): New variable.
2017-06-25 22:26:07 +02:00
dfc83eadaf
gnu: orfm: Update to 0.7.1.
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* gnu/packages/bioinformatics.scm (orfm): Update to 0.7.1.
2017-06-24 14:46:46 +10:00
ab8d728144
gnu: orfm: Update to 0.7.0.
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* gnu/packages/bioinformatics.scm (orfm): Update to 0.7.0.
2017-06-23 22:22:50 +10:00
94820951d6
gnu: Add kentutils.
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* gnu/packages/bioinformatics.scm (kentutils): New variable.
2017-06-23 08:09:33 +02:00
c1dfe8c30b
gnu: python2-bx-python: Update to 0.7.3.
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* gnu/packages/bioinformatics.scm (python2-bx-python): Update to 0.7.3.
2017-06-22 17:25:40 +02:00
148585c240
gnu: Move contents of zip module into compression module.
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* gnu/packages/zip.scm (zip, unzip, zziplib, perl-zip): Move to...
* gnu/packages/compression.scm: ...here.
* gnu/packages/zip.scm: Delete file.
* gnu/local.mk (GNU_SYSTEM_MODULES): Unregister deleted file.
* po/packages/POTFILES.in: Unregister deleted file.
* gnu/packages/{audio, avr, bioinformatics, busybox, cdrom, ci, compression,
docbook, documentation, fonts, fpga, game-development, games, gl, gnome,
gnuzilla, graphics, guile, haskell, image, java, kodi, ldc, libreoffice,
markup, maths, mc, monitoring, music, php, pretty-print, python, scheme,
smalltalk, statistics, synergy, tex, textutils, video, web-browsers, xml,
zip}.scm, guix/build-system/{ant, font}.scm, guix/{download, packages}.scm:
Adapt module import.
2017-06-20 18:10:35 +05:30
0002be1d0b
gnu: diamond: Update to 0.9.8.
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* gnu/packages/bioinformatics.scm (diamond): Update to 0.9.8.
2017-06-17 13:05:08 +10:00
a147fadd3b
gnu: tadbit: Fix typo in description.
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* gnu/packages/bioinformatics.scm (tadbit)[description]: Fix typo.
2017-06-16 00:29:21 +02:00
07bf6929b9
gnu: gemma: Fix indentation.
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* gnu/packages/bioinformatics.scm (gemma)[arguments]: Fix indentation.
2017-06-15 10:32:03 +03:00
2c9232ae69
gnu: gemma: Fix building on 32-bit architectures.
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* gnu/packages/bioinformatics.scm (gemma)[arguments]: On 32-bit
architectures add 'FORCE_32BIT' flag.
2017-06-15 10:31:44 +03:00
8befd0940b
gnu: Add tadbit.
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* gnu/packages/bioinformatics.scm (tadbit): New variable.
2017-06-09 03:32:23 +02:00
aa163424b2
gnu: Add imp.
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* gnu/packages/bioinformatics.scm (imp): New variable.
2017-06-09 03:31:51 +02:00
282b01515b
gnu: Add phylip.
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* gnu/packages/bioinformatics.scm (phylip): New variable.
2017-06-09 03:31:50 +02:00
3420c905cd
gnu: Add gess.
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* gnu/packages/bioinformatics.scm (gess): New variable.
2017-06-09 03:31:50 +02:00
44f6c88909
gnu: Add trim-galore.
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* gnu/packages/bioinformatics.scm (trim-galore): New variable.
2017-06-09 03:31:50 +02:00
b8fffd3a53
gnu: Add ritornello.
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* gnu/packages/bioinformatics.scm (ritornello): New variable.
2017-06-09 03:31:50 +02:00
f69ff11af7
gnu: diamond: Update to 0.9.6.
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* gnu/packages/bioinformatics.scm (diamond): Update to 0.9.6.
2017-06-08 09:39:23 +10:00
b9a601d9db
gnu: Add kaiju.
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* gnu/packages/bioinformatics.scm (kaiju): New variable.
2017-06-02 12:38:23 +02:00
0d2b2fd4f4
gnu: diamond: Update to 0.9.3.
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* gnu/packages/bioinformatics.scm (diamond): Update to 0.9.3.
2017-05-28 21:06:06 -04:00
ca40d4e7c5
gnu: diamond: Update to 0.9.2.
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* gnu/packages/bioinformatics.scm (diamond): Update to 0.9.2.
2017-05-27 22:03:00 -04:00
b608765a2c
gnu: diamond: Update to 0.9.1.
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* gnu/packages/bioinformatics.scm (diamond): Update to 0.9.1.
2017-05-22 21:17:41 +01:00
296b3c631c
gnu: Add r-edaseq.
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* gnu/packages/bioinformatics.scm (r-edaseq): New variable.
2017-05-22 18:54:59 +02:00
Ben Woodcroft