24155bf40d
gnu: Move Java compression packages to new module.
...
* gnu/packages/compression.scm (bitshuffle-for-snappy): Export variable.
(java-snappy, java-snappy-1, java-iq80-snappy, java-jbzip2, java-tukaani-xz):
Move these variables from here...
* gnu/packages/java-compression.scm: ...to this new file.
* gnu/local.mk (GNU_SYSTEM_MODULES): Add it.
* gnu/packages/java.scm, gnu/packages/bioinformatics.scm: Adjust module
references.
2019-01-12 12:14:28 +01:00
e7c6bc45ed
gnu: jamm: Remove broken "build" phase.
...
* gnu/packages/bioinformatics.scm (jamm)[arguments]: Remove "build" phase.
2019-01-11 06:08:43 +01:00
6fd2ed23ac
gnu: mantis: Limit to x86_64-linux.
...
* gnu/packages/bioinformatics.scm (mantis)[supported-systems]: New field.
2019-01-07 15:47:34 +02:00
e942813aac
gnu: Add mantis.
...
* gnu/packages/bioinformatics.scm (mantis): New variable.
2019-01-07 11:56:18 +01:00
8894668cd2
gnu: discrover: Comment on attempt of minimal texlive-union.
...
* gnu/packages/bioinformatics.scm (discrover): Comment on attempt of minimal
texlive-union.
2018-12-20 12:07:40 +01:00
2f3977b9a7
gnu: gess: Don't hardcode python version.
...
* gnu/packages/bioinformatics.scm (gess)[arguments]: Replace hardcoded
python version with parameterized one.
2018-12-17 12:08:05 +02:00
9718265eec
gnu: mash: Use C++ 14.
...
I'm looking to upgrade capnproto, and mash fails to build with 0.7. Therefore,
tweak the compilation to allow it to build with 0.7. The package also builds
with the current version of capnproto. I got the idea of changing the c++
version from here [1].
1: https://github.com/marbl/Mash/issues/98
* gnu/packages/bioinformatics.scm (mash)[arguments]: Add new use-c++14 phase.
2018-12-05 20:29:12 +00:00
42c3e00c20
gnu: pigx-rnaseq: Update to 0.0.5.
...
* gnu/packages/bioinformatics.scm (pigx-rnaseq): Update to 0.0.5.
[inputs]: Replace snakemake-4 with snakemake.
2018-12-04 16:21:50 +01:00
4b2d1dc4dc
gnu: bless: Adjust to zlib static output.
...
* gnu/packages/bioinformatics.scm (bless)[inputs]: Add ZLIB:STATIC.
[arguments]: Adjust #:make-flags accordingly.
2018-11-24 19:32:48 +01:00
f028823c0f
gnu: mosaik: Fix FTBFS from b90289dadc.
...
* gnu/packages/bioinformatics.scm (mosaik)[inputs]: Add ZLIB:STATIC.
2018-11-24 15:57:56 +01:00
d57ec906ba
gnu: pigx-scrnaseq: Use latest snakemake.
...
* gnu/packages/bioinformatics.scm (pigx-scrnaseq)[inputs]: Replace snakemake-4
with snakemake.
2018-11-23 16:30:48 +01:00
92d9a1e2c6
gnu: pigx-bsseq: Use latest snakemake.
...
* gnu/packages/bioinformatics.scm (pigx-bsseq)[inputs]: Replace snakemake-4
with snakemake.
2018-11-23 16:30:16 +01:00
c068d00746
gnu: pigx-chipseq: Use latest snakemake.
...
* gnu/packages/bioinformatics.scm (pigx-chipseq)[inputs]: Replace snakemake-4
with snakemake.
2018-11-23 16:29:35 +01:00
93d229cb86
gnu: python-loompy: Remove python-typing.
...
* gnu/packages/bioinformatics.scm (python-loompy)[propagated-inputs]: Remove
python-typing.
2018-11-23 15:59:44 +01:00
4f70db97a0
Merge branch 'master' into core-updates
2018-11-20 01:14:12 +01:00
c2e26dc156
gnu: r-ensembldb: Update to 2.6.2.
...
* gnu/packages/bioinformatics.scm (r-ensembldb): Update to 2.6.2.
2018-11-19 16:46:32 +01:00
e038819138
gnu: r-msnbase: Update to 2.8.1.
...
* gnu/packages/bioinformatics.scm (r-msnbase): Update to 2.8.1.
2018-11-19 16:46:00 +01:00
4535a7b0f5
gnu: r-genomeinfodb: Update to 1.18.1.
...
* gnu/packages/bioinformatics.scm (r-genomeinfodb): Update to 1.18.1.
2018-11-19 16:33:35 +01:00
30f0d21b40
gnu: Add nanopolish.
...
* gnu/packages/bioinformatics.scm (nanopolish): New variable.
Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
2018-11-15 22:23:57 +01:00
2d86eaff5b
gnu: sambamba: Update to 0.6.8.
...
* gnu/packages/bioinformatics.scm (sambamba): Update to 0.6.8.
2018-11-15 13:09:01 +01:00
2e0f69057a
gnu: bioinformatics: Return #t from all phases and snippets.
...
* gnu/packages/bioinformatics.scm (bamtools, ribotaper, bioawk)
(codingquarry, fraggenescan, minced, pplacer, star, subread, sailfish)
(salmon): Return #t from all phases and snippets, use 'invoke' where
appropriate, and remove vestigal plumbing.
2018-11-14 23:44:18 -05:00
ee66a13563
gnu: Add jamm.
...
* gnu/packages/bioinformatics.scm (jamm): New variable.
2018-11-14 15:13:20 +01:00
51b262f310
gnu: r-txdb-mmusculus-ucsc-mm10-knowngene: Update to 3.4.4.
...
* gnu/packages/bioinformatics.scm (r-txdb-mmusculus-ucsc-mm10-knowngene):
Update to 3.4.4.
2018-11-13 23:34:40 +01:00
d34959b8d4
gnu: r-org-mm-eg-db: Update to 3.7.0.
...
* gnu/packages/bioinformatics.scm (r-org-mm-eg-db): Update to 3.7.0.
2018-11-13 23:34:40 +01:00
314511b862
gnu: r-org-dm-eg-db: Update to 3.7.0.
...
* gnu/packages/bioinformatics.scm (r-org-dm-eg-db): Update to 3.7.0.
2018-11-13 23:34:39 +01:00
76bd16bcf6
gnu: r-org-ce-eg-db: Update to 3.7.0.
...
* gnu/packages/bioinformatics.scm (r-org-ce-eg-db): Update to 3.7.0.
2018-11-13 23:34:39 +01:00
fc7683fa30
gnu: r-org-hs-eg-db: Update to 3.7.0.
...
* gnu/packages/bioinformatics.scm (r-org-hs-eg-db): Update to 3.7.0.
2018-11-13 23:34:39 +01:00
cb9e6ed702
gnu: r-genomationdata: Update to 1.14.0.
...
* gnu/packages/bioinformatics.scm (r-genomationdata): Update to 1.14.0.
2018-11-13 23:34:39 +01:00
13e70f6304
gnu: r-go-db: Update to 3.7.0.
...
* gnu/packages/bioinformatics.scm (r-go-db): Update to 3.7.0.
2018-11-13 23:34:39 +01:00
13a574652b
gnu: r-genomeinfodbdata: Update to 1.2.0.
...
* gnu/packages/bioinformatics.scm (r-genomeinfodbdata): Update to 1.2.0.
2018-11-13 23:34:39 +01:00
5f9b38ba34
gnu: r-s4vectors: Update to 0.20.1.
...
* gnu/packages/bioinformatics.scm (r-s4vectors): Update to 0.20.1.
2018-11-11 23:13:48 +01:00
03a415365a
gnu: r-ensembldb: Update to 2.6.1.
...
* gnu/packages/bioinformatics.scm (r-ensembldb): Update to 2.6.1.
2018-11-09 19:41:54 +01:00
88514b9124
gnu: r-biostrings: Update to 2.50.1.
...
* gnu/packages/bioinformatics.scm (r-biostrings): Update to 2.50.1.
2018-11-09 19:41:53 +01:00
77bea84ba1
gnu: r-biocviews: Update to 1.50.5.
...
* gnu/packages/bioinformatics.scm (r-biocviews): Update to 1.50.5.
2018-11-09 19:41:53 +01:00
a1e83a9856
gnu: pplacer-scripts: Use INVOKE.
...
* gnu/packages/bioinformatics.scm (pplacer-scripts)[arguments]: Use INVOKE and
return #T unconditionally.
2018-11-08 10:06:35 +01:00
ce49fdcce9
gnu: roary: Use INVOKE.
...
* gnu/packages/bioinformatics.scm (roary)[arguments]: Use INVOKE and return #T
unconditionally.
2018-11-08 09:58:05 +01:00
a9542937c8
gnu: seek: Use INVOKE.
...
* gnu/packages/bioinformatics.scm (seek)[arguments]: Use INVOKE and return #T
unconditionally; patch "gen_tools_am" shebang in "bootstrap" phase.
2018-11-08 09:54:22 +01:00
9f527c9199
gnu: sailfish: Use INVOKE.
...
* gnu/packages/bioinformatics.scm (sailfish)[arguments]: Use INVOKE instead of
SYSTEM*.
2018-11-08 09:52:46 +01:00
86c6928ea3
gnu: vsearch: Update to 2.9.1.
...
* gnu/packages/bioinformatics.scm (vsearch): Update to 2.9.1.
* gnu/packages/patches/vsearch-unbundle-cityhash.patch: Update.
2018-11-08 09:46:42 +01:00
15c9609482
gnu: sra-tools: Update to 2.9.3.
...
* gnu/packages/bioinformatics.scm (sra-tools): Update to 2.9.3.
[arguments]: Remove build phase patch-away-glibc-conflict.
2018-11-08 09:46:05 +01:00
b17333414f
gnu: plink-ng: Fetch sources from git.
...
* gnu/packages/bioinformatics.scm (plink-ng)[source]: Fetch from git.
2018-11-08 09:30:59 +01:00
87408854ec
gnu: ncbi-vdb: Update to 2.9.3.
...
* gnu/packages/bioinformatics.scm (ncbi-vdb): Update to 2.9.3.
2018-11-08 09:30:16 +01:00
8d3eaa9262
gnu: ngs-sdk: Update to 2.9.3.
...
* gnu/packages/bioinformatics.scm (ngs-sdk): Update to 2.9.3.
2018-11-08 09:29:58 +01:00
3da3cedf76
gnu: ngs-sdk: Use INVOKE.
...
* gnu/packages/bioinformatics.scm (ngs-sdk)[arguments]: Use INVOKE and
return #T unconditionally.
2018-11-08 09:15:05 +01:00
e78e54d029
gnu: emboss: Use INVOKE.
...
* gnu/packages/bioinformatics.scm (emboss)[arguments]: Use INVOKE and
return #T unconditionally.
2018-11-08 09:14:09 +01:00
8b685c4720
gnu: taxtastic: Use INVOKE.
...
* gnu/packages/bioinformatics.scm (taxtastic)[arguments]: Use INVOKE and
return #T unconditionally.
2018-11-08 09:13:35 +01:00
2e2d88539c
gnu: sra-tools: Use INVOKE.
...
* gnu/packages/bioinformatics.scm (sra-tools)[arguments]: Use INVOKE and
return #T unconditionally.
2018-11-08 09:12:43 +01:00
179416467f
gnu: muscle: Use INVOKE.
...
* gnu/packages/bioinformatics.scm (muscle)[arguments]: Use INVOKE and
return #T unconditionally.
2018-11-08 09:11:38 +01:00
0881d62f25
gnu: newick-utils: Remove custom autoconf phase.
...
* gnu/packages/bioinformatics.scm (newick-utils)[arguments]: Remove.
2018-11-08 09:10:58 +01:00
e35dce0170
gnu: mash: Remove custom autoconf phase.
...
* gnu/packages/bioinformatics.scm (mash)[arguments]: Remove autoconf phase.
2018-11-08 09:10:20 +01:00
31c41a8cfe
gnu: vsearch: Remove custom autogen phase.
...
* gnu/packages/bioinformatics.scm (vsearch)[arguments]: Remove.
2018-11-08 09:04:34 +01:00
c527d36f02
gnu: java-picard-1.113: Use INVOKE.
...
* gnu/packages/bioinformatics.scm (java-picard-1.113)[arguments]: Use INVOKE
and return #T unconditionally.
2018-11-08 09:02:34 +01:00
e438c96558
gnu: fraggenescan: Use INVOKE.
...
* gnu/packages/bioinformatics.scm (fraggenescan)[arguments]: Use INVOKE in
build phases and return #T unconditionally.
2018-11-08 08:58:46 +01:00
c098c49b3e
gnu: sailfish: Fetch sources from git.
...
* gnu/packages/bioinformatics.scm (sailfish)[source]: Fetch from git.
2018-11-08 08:53:54 +01:00
4031e7f1ec
gnu: ngs-sdk: Fetch sources from git.
...
* gnu/packages/bioinformatics.scm (ngs-sdk)[source]: Fetch from git.
2018-11-08 08:53:53 +01:00
6a7d9ee39f
gnu: ncbi-vdb: Use INVOKE and end phases on #T.
...
* gnu/packages/bioinformatics.scm (ncbi-vdb)[arguments]: Use INVOKE and
unconditionally end phases with #T.
2018-11-08 08:53:53 +01:00
3398dfb764
gnu: ncbi-vdb: Fetch sources from git.
...
* gnu/packages/bioinformatics.scm (ncbi-vdb)[source]: Fetch from git.
[arguments]: Add phase to make checkout writable.
2018-11-08 08:53:53 +01:00
e0f1aa2d2b
gnu: tadbit: Fetch sources from git.
...
* gnu/packages/bioinformatics.scm (tadbit)[source]: Fetch from git.
[version]: Use "2.0.0" instead of "2.0".
2018-11-08 08:53:50 +01:00
f3f34b132c
gnu: filevercmp: Fetch sources from git.
...
* gnu/packages/bioinformatics.scm (filevercmp)[source]: Fetch from git.
[arguments]: Add #T to the end of the install phase.
2018-11-07 23:17:36 +01:00
3b888065da
gnu: ritornello: Update to 2.0.1.
...
* gnu/packages/bioinformatics.scm (ritornello): Update to 2.0.1.
[arguments]: Adjust file patching.
2018-11-07 23:17:36 +01:00
7145f4e519
gnu: ritornello: Fetch sources from git.
...
* gnu/packages/bioinformatics.scm (ritornello)[source]: Fetch from git.
2018-11-07 23:17:35 +01:00
e0a8fc85dd
gnu: snap-aligner: Fetch sources from git.
...
* gnu/packages/bioinformatics.scm (snap-aligner)[source]: Fetch from git.
[arguments]: Use INVOKE.
2018-11-07 23:17:35 +01:00
6236524409
gnu: sortmerna: Fetch sources from git.
...
* gnu/packages/bioinformatics.scm (sortmerna)[source]: Fetch from git.
2018-11-07 23:17:35 +01:00
273df99d7d
gnu: vsearch: Fetch source from git.
...
* gnu/packages/bioinformatics.scm (vsearch)[source]: Fetch from git.
2018-11-07 23:17:35 +01:00
67caa4b773
gnu: preseq: Update to 2.0.3.
...
* gnu/packages/bioinformatics.scm (preseq): Update to 2.0.3.
2018-11-07 23:17:35 +01:00
37e285be43
gnu: preseq: Fetch sources from git.
...
* gnu/packages/bioinformatics.scm (preseq)[source]: Fetch from git.
2018-11-07 23:17:35 +01:00
63f3255e13
gnu: seqtk: Update to 1.3.
...
* gnu/packages/bioinformatics.scm (seqtk): Update to 1.3.
[source]: Remove outdated snippet.
[arguments]: Use INVOKE and return #T unconditionally.
2018-11-07 23:17:35 +01:00
019fcdf20a
gnu: seqtk: Fetch sources from git.
...
* gnu/packages/bioinformatics.scm (seqtk)[source]: Fetch from git.
2018-11-07 23:17:34 +01:00
b9d0c3564b
gnu: raxml: Update to 8.2.12.
...
* gnu/packages/bioinformatics.scm (raxml): Update to 8.2.12.
2018-11-07 23:17:34 +01:00
d9ba126d17
gnu: python2-biom-format: Fix build.
...
This is a follow-up to commit 239716fb0b
2018-11-07 23:17:34 +01:00
4715d4af17
gnu: raxml: Fetch sources from git.
...
* gnu/packages/bioinformatics.scm (raxml)[source]: Fetch from git.
2018-11-07 23:17:34 +01:00
5e242b02c3
gnu: pyicoteo: Fetch sources from git.
...
* gnu/packages/bioinformatics.scm (pyicoteo)[source]: Fetch from git.
2018-11-07 23:17:34 +01:00
2b773a9273
gnu: sra-tools: Fetch sources from git.
...
* gnu/packages/bioinformatics.scm (sra-tools)[source]: Fetch from git.
2018-11-07 21:41:56 +01:00
55698df260
gnu: libgff: Fetch sources from git.
...
* gnu/packages/bioinformatics.scm (libgff)[source]: Fetch from git.
2018-11-07 21:41:56 +01:00
4257c10ad2
gnu: kentutils: Fetch sources from git.
...
* gnu/packages/bioinformatics.scm (kentutils)[source]: Fetch from git.
[arguments]: Add phase "fix-permissions".
2018-11-07 21:41:55 +01:00
1a20bcadf3
gnu: r-seqgl: Fetch sources from git.
...
* gnu/packages/bioinformatics.scm (r-seqgl)[source]: Fetch from git.
2018-11-07 21:41:55 +01:00
a2b9d6a8d0
gnu: pplacer: Fetch sources from git.
...
* gnu/packages/bioinformatics.scm (pplacer)[source]: Fetch from git.
[arguments]: Make files writable; use INVOKE.
2018-11-07 21:41:55 +01:00
6052264b56
gnu: minced: Update to 0.3.2.
...
* gnu/packages/bioinformatics.scm (minced): Update to 0.3.2.
2018-11-07 21:41:55 +01:00
9d94ca0ebf
gnu: minced: Fetch sources from git.
...
* gnu/packages/bioinformatics.scm (minced)[source]: Fetch from git.
2018-11-07 21:41:55 +01:00
b58d9e4aa2
gnu: metabat: Fetch sources from git.
...
* gnu/packages/bioinformatics.scm (metabat)[source]: Fetch from git.
2018-11-07 21:41:55 +01:00
5c1f35e71b
gnu: mash: Update to 2.1.
...
* gnu/packages/bioinformatics.scm (mash): Update to 2.1.
2018-11-07 21:41:55 +01:00
497fc04d8f
gnu: mash: Fetch sources from git.
...
* gnu/packages/bioinformatics.scm (mash)[source]: Fetch from git.
2018-11-07 21:41:55 +01:00
2dc28391f3
gnu: kaiju: Update to 1.6.3.
...
* gnu/packages/bioinformatics.scm (kaiju): Update to 1.6.3.
2018-11-07 20:47:22 +01:00
6fe323bf2e
gnu: kaiju: Fetch sources from git.
...
* gnu/packages/bioinformatics.scm (kaiju)[source]: Fetch from git.
[arguments]: Remove redundant installation step.
2018-11-07 20:46:36 +01:00
f0731591a5
gnu: idr: Fetch sources from git.
...
* gnu/packages/bioinformatics.scm (idr)[source]: Fetch from git.
2018-11-07 20:41:58 +01:00
b8a6230df3
gnu: java-htsjdk: Fetch sources from git.
...
* gnu/packages/bioinformatics.scm (java-htsjdk)[source]: Fetch from git.
2018-11-07 20:36:07 +01:00
57be690d91
gnu: hisat2: Use versioned source URL.
...
* gnu/packages/bioinformatics.scm (hisat2)[source]: Use versioned URL.
2018-11-07 20:32:29 +01:00
c8f02c1dcb
gnu: grit: Update to 2.0.5.
...
* gnu/packages/bioinformatics.scm (grit): Update to 2.0.5.
[arguments]: Simplify.
2018-11-07 20:30:44 +01:00
8d75adbf03
gnu: grit: Fetch sources from git.
...
* gnu/packages/bioinformatics.scm (grit)[source]: Fetch from git.
2018-11-07 20:27:10 +01:00
152bebd9e0
gnu: gemma: Update to 0.98.
...
* gnu/local.mk (dist_patch_DATA): Remove patch.
* gnu/packages/patches/gemma-intel-compat.patch: Remove file.
* gnu/packages/bioinformatics.scm (gemma): Update to 0.98.
[source]: Remove patch.
[inputs]: Add eigen, gfortran:lib, and openblas.
[arguments]: Add phase "find-eigen".
2018-11-07 20:26:46 +01:00
b113f39019
gnu: gemma: Fetch sources from git.
...
* gnu/packages/bioinformatics.scm (gemma)[source]: Fetch from git.
2018-11-07 20:26:45 +01:00
91b71cfbba
gnu: fxtract: Fetch sources from git.
...
* gnu/packages/bioinformatics.scm (fxtract)[source]: Fetch from git.
2018-11-07 19:55:50 +01:00
7ca49ab57a
gnu: ribodiff: Fetch sources from git.
...
* gnu/packages/bioinformatics.scm (ribodiff)[source]: Fetch from git.
2018-11-07 19:48:21 +01:00
239716fb0b
gnu: python-biom-format: Update to 2.1.7.
...
* gnu/packages/bioinformatics.scm (python-biom-format): Update to 2.1.7.
[arguments]: Add phases "use-cython", "disable-broken-test", and
"make-files-writable".
[propagated-inputs]: Add python-flake8.
[native-inputs]: Add python-cython, python-pytest, and python-pytest-cov.
2018-11-07 19:47:07 +01:00
007a81d5cf
gnu: python-biom-format: Fetch source from git.
...
* gnu/packages/bioinformatics.scm (python-biom-format)[source]: Fetch from
git.
2018-11-07 19:10:36 +01:00
383cb7b8e6
gnu: bioawk: Fetch sources from git.
...
* gnu/packages/bioinformatics.scm (bioawk)[source]: Fetch from git.
2018-11-07 19:06:30 +01:00
20ee3e8b76
gnu: bedtools-2.18: Fetch sources from stable URL.
...
* gnu/packages/bioinformatics.scm (bedtools-2.18)[source]: Use stable release
tarball instead of generated tag tarball.
2018-11-07 18:52:46 +01:00
8e58319c45
gnu: bamtools: Fetch sources from git.
...
* gnu/packages/bioinformatics.scm (bamtools)[source]: Fetch from git.
2018-11-07 18:44:30 +01:00
21335fdbec
gnu: ngless: Install links to required tools.
...
* gnu/packages/bioinformatics.scm (ngless)[arguments]: Install links to tools.
[inputs]: Add prodigal, bwa, samtools, and minimap2.
2018-11-07 17:19:53 +01:00
fff67cc8a7
gnu: prodigal: Fetch sources from git.
...
* gnu/packages/bioinformatics.scm (prodigal)[source]: Fetch from git.
2018-11-07 17:19:53 +01:00
Ricardo Wurmus