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1783 commits

Author SHA1 Message Date
Ricardo Wurmus
e7c6bc45ed
gnu: jamm: Remove broken "build" phase. 
* gnu/packages/bioinformatics.scm (jamm)[arguments]: Remove "build" phase.
 2019-01-11 06:08:43 +01:00
Efraim Flashner
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
Ricardo Wurmus
e942813aac
gnu: Add mantis. 
* gnu/packages/bioinformatics.scm (mantis): New variable.
 2019-01-07 11:56:18 +01:00
Pierre Neidhardt
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
Efraim Flashner
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
Christopher Baines
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
Ricardo Wurmus
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
Marius Bakke
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
Marius Bakke
f028823c0f
gnu: mosaik: Fix FTBFS from b90289dadc. 
* gnu/packages/bioinformatics.scm (mosaik)[inputs]: Add ZLIB:STATIC.
 2018-11-24 15:57:56 +01:00
Ricardo Wurmus
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
Ricardo Wurmus
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
Ricardo Wurmus
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
Ricardo Wurmus
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
Marius Bakke
4f70db97a0
Merge branch 'master' into core-updates 2018-11-20 01:14:12 +01:00
Roel Janssen
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
Roel Janssen
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
Roel Janssen
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
pimi
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
Roel Janssen
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
Mark H Weaver
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
Ricardo Wurmus
ee66a13563
gnu: Add jamm. 
* gnu/packages/bioinformatics.scm (jamm): New variable.
 2018-11-14 15:13:20 +01:00
Ricardo Wurmus
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
Ricardo Wurmus
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
Ricardo Wurmus
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
Ricardo Wurmus
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
Ricardo Wurmus
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
Ricardo Wurmus
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
Ricardo Wurmus
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
Ricardo Wurmus
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
Ricardo Wurmus
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
Ricardo Wurmus
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
Ricardo Wurmus
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
Ricardo Wurmus
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
Ricardo Wurmus
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
Ricardo Wurmus
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
Ricardo Wurmus
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
Ricardo Wurmus
9f527c9199
gnu: sailfish: Use INVOKE. 
* gnu/packages/bioinformatics.scm (sailfish)[arguments]: Use INVOKE instead of
SYSTEM*.
 2018-11-08 09:52:46 +01:00
Ricardo Wurmus
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
Ricardo Wurmus
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
Ricardo Wurmus
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
Ricardo Wurmus
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
Ricardo Wurmus
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
Ricardo Wurmus
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
Ricardo Wurmus
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
Ricardo Wurmus
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
Ricardo Wurmus
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
Ricardo Wurmus
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
Ricardo Wurmus
0881d62f25
gnu: newick-utils: Remove custom autoconf phase. 
* gnu/packages/bioinformatics.scm (newick-utils)[arguments]: Remove.
 2018-11-08 09:10:58 +01:00
Ricardo Wurmus
e35dce0170
gnu: mash: Remove custom autoconf phase. 
* gnu/packages/bioinformatics.scm (mash)[arguments]: Remove autoconf phase.
 2018-11-08 09:10:20 +01:00
Ricardo Wurmus
31c41a8cfe
gnu: vsearch: Remove custom autogen phase. 
* gnu/packages/bioinformatics.scm (vsearch)[arguments]: Remove.
 2018-11-08 09:04:34 +01:00
Ricardo Wurmus
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
Ricardo Wurmus
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
Ricardo Wurmus
c098c49b3e
gnu: sailfish: Fetch sources from git. 
* gnu/packages/bioinformatics.scm (sailfish)[source]: Fetch from git.
 2018-11-08 08:53:54 +01:00
Ricardo Wurmus
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
Ricardo Wurmus
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
Ricardo Wurmus
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
Ricardo Wurmus
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
Ricardo Wurmus
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
Ricardo Wurmus
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
Ricardo Wurmus
7145f4e519
gnu: ritornello: Fetch sources from git. 
* gnu/packages/bioinformatics.scm (ritornello)[source]: Fetch from git.
 2018-11-07 23:17:35 +01:00
Ricardo Wurmus
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
Ricardo Wurmus
6236524409
gnu: sortmerna: Fetch sources from git. 
* gnu/packages/bioinformatics.scm (sortmerna)[source]: Fetch from git.
 2018-11-07 23:17:35 +01:00
Ricardo Wurmus
273df99d7d
gnu: vsearch: Fetch source from git. 
* gnu/packages/bioinformatics.scm (vsearch)[source]: Fetch from git.
 2018-11-07 23:17:35 +01:00
Ricardo Wurmus
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
Ricardo Wurmus
37e285be43
gnu: preseq: Fetch sources from git. 
* gnu/packages/bioinformatics.scm (preseq)[source]: Fetch from git.
 2018-11-07 23:17:35 +01:00
Ricardo Wurmus
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
Ricardo Wurmus
019fcdf20a
gnu: seqtk: Fetch sources from git. 
* gnu/packages/bioinformatics.scm (seqtk)[source]: Fetch from git.
 2018-11-07 23:17:34 +01:00
Ricardo Wurmus
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
Ricardo Wurmus
d9ba126d17
gnu: python2-biom-format: Fix build. 
This is a follow-up to commit 239716fb0b.

* gnu/packages/bioinformatics.scm (python2-biom-format)[arguments]: Modify
phases of base package.
 2018-11-07 23:17:34 +01:00
Ricardo Wurmus
4715d4af17
gnu: raxml: Fetch sources from git. 
* gnu/packages/bioinformatics.scm (raxml)[source]: Fetch from git.
 2018-11-07 23:17:34 +01:00
Ricardo Wurmus
5e242b02c3
gnu: pyicoteo: Fetch sources from git. 
* gnu/packages/bioinformatics.scm (pyicoteo)[source]: Fetch from git.
 2018-11-07 23:17:34 +01:00
Ricardo Wurmus
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
Ricardo Wurmus
55698df260
gnu: libgff: Fetch sources from git. 
* gnu/packages/bioinformatics.scm (libgff)[source]: Fetch from git.
 2018-11-07 21:41:56 +01:00
Ricardo Wurmus
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
Ricardo Wurmus
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
Ricardo Wurmus
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
Ricardo Wurmus
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
Ricardo Wurmus
9d94ca0ebf
gnu: minced: Fetch sources from git. 
* gnu/packages/bioinformatics.scm (minced)[source]: Fetch from git.
 2018-11-07 21:41:55 +01:00
Ricardo Wurmus
b58d9e4aa2
gnu: metabat: Fetch sources from git. 
* gnu/packages/bioinformatics.scm (metabat)[source]: Fetch from git.
 2018-11-07 21:41:55 +01:00
Ricardo Wurmus
5c1f35e71b
gnu: mash: Update to 2.1. 
* gnu/packages/bioinformatics.scm (mash): Update to 2.1.
 2018-11-07 21:41:55 +01:00
Ricardo Wurmus
497fc04d8f
gnu: mash: Fetch sources from git. 
* gnu/packages/bioinformatics.scm (mash)[source]: Fetch from git.
 2018-11-07 21:41:55 +01:00
Ricardo Wurmus
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
Ricardo Wurmus
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
Ricardo Wurmus
f0731591a5
gnu: idr: Fetch sources from git. 
* gnu/packages/bioinformatics.scm (idr)[source]: Fetch from git.
 2018-11-07 20:41:58 +01:00
Ricardo Wurmus
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
Ricardo Wurmus
57be690d91
gnu: hisat2: Use versioned source URL. 
* gnu/packages/bioinformatics.scm (hisat2)[source]: Use versioned URL.
 2018-11-07 20:32:29 +01:00
Ricardo Wurmus
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
Ricardo Wurmus
8d75adbf03
gnu: grit: Fetch sources from git. 
* gnu/packages/bioinformatics.scm (grit)[source]: Fetch from git.
 2018-11-07 20:27:10 +01:00
Ricardo Wurmus
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
Ricardo Wurmus
b113f39019
gnu: gemma: Fetch sources from git. 
* gnu/packages/bioinformatics.scm (gemma)[source]: Fetch from git.
 2018-11-07 20:26:45 +01:00
Ricardo Wurmus
91b71cfbba
gnu: fxtract: Fetch sources from git. 
* gnu/packages/bioinformatics.scm (fxtract)[source]: Fetch from git.
 2018-11-07 19:55:50 +01:00
Ricardo Wurmus
7ca49ab57a
gnu: ribodiff: Fetch sources from git. 
* gnu/packages/bioinformatics.scm (ribodiff)[source]: Fetch from git.
 2018-11-07 19:48:21 +01:00
Ricardo Wurmus
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
Ricardo Wurmus
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
Ricardo Wurmus
383cb7b8e6
gnu: bioawk: Fetch sources from git. 
* gnu/packages/bioinformatics.scm (bioawk)[source]: Fetch from git.
 2018-11-07 19:06:30 +01:00
Ricardo Wurmus
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
Ricardo Wurmus
8e58319c45
gnu: bamtools: Fetch sources from git. 
* gnu/packages/bioinformatics.scm (bamtools)[source]: Fetch from git.
 2018-11-07 18:44:30 +01:00
Ricardo Wurmus
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
Ricardo Wurmus
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
9255198423
gnu: r-mzr: Update to 2.16.0. 
* gnu/packages/bioinformatics.scm (r-mzr): Update to 2.16.0.
[inputs]: Remove netcdf.
[propagated-inputs]: Add r-ncdf4.
 2018-11-07 12:27:16 +01:00
Ricardo Wurmus
37200dbcc3
gnu: r-rhdf5lib: Update to 1.4.0. 
* gnu/packages/bioinformatics.scm (r-rhdf5lib): Update to 1.4.0.
[source]: Add snippet to remove bundled binaries.
[arguments]: Replace references to hdf5 with references to hdf5-1.10.
[native-inputs]: Likewise.
[propagated-inputs]: Replace hdf5 with hdf5-1.10.
 2018-11-07 12:27:16 +01:00
Ricardo Wurmus
8e48d36f26
gnu: r-hdf5array: Update to 1.10.0. 
* gnu/packages/bioinformatics.scm (r-hdf5array): Update to 1.10.0.
 2018-11-07 12:27:16 +01:00
Ricardo Wurmus
611a255d2b
gnu: r-rhdf5: Update to 2.26.0. 
* gnu/packages/bioinformatics.scm (r-rhdf5): Update to 2.26.0.
 2018-11-07 12:27:16 +01:00
Ricardo Wurmus
a1c2bf8e54
gnu: r-rcas: Update to 1.8.0. 
* gnu/packages/bioinformatics.scm (r-rcas): Update to 1.8.0.
[native-inputs]: Remove r-testthat and ghc-pandoc-citeproc.
[propagated-inputs]: Add r-annotationdbi, r-genomeinfodb, and r-genomicranges;
remove r-bsgenome-mmusculus-ucsc-mm9, r-bsgenome-celegans-ucsc-ce10,
r-bsgenome-dmelanogaster-ucsc-dm3, r-org-ce-eg-db, r-org-dm-eg-db, and
r-org-mm-eg-db.
 2018-11-07 12:27:16 +01:00
Ricardo Wurmus
900ce2bafd
gnu: r-delayedmatrixstats: Update to 1.4.0. 
* gnu/packages/bioinformatics.scm (r-delayedmatrixstats): Update to 1.4.0.
[propagated-inputs]: Add r-biocparallel and r-hdf5array.
 2018-11-07 12:27:16 +01:00
Ricardo Wurmus
70a3a76ba7
gnu: r-scran: Update to 1.10.1. 
* gnu/packages/bioinformatics.scm (r-scran): Update to 1.10.1.
[propagated-inputs]: Add r-biocneighbors; remove r-dt, r-fnn, r-ggplot2,
r-shiny, and r-viridis.
 2018-11-07 12:27:16 +01:00
Ricardo Wurmus
48f2791496
gnu: r-scater: Update to 1.10.0. 
* gnu/packages/bioinformatics.scm (r-scater): Update to 1.10.0.
[propagated-inputs]: Add r-biocparallel; remove r-biobase, r-data-table,
r-edger, r-limma, r-rhdf5, r-rjson, r-shiny, r-shinydashboard, and r-tximport.
 2018-11-07 12:27:16 +01:00
Ricardo Wurmus
f93ec63ccf
gnu: r-singlecellexperiment: Update to 1.4.0. 
* gnu/packages/bioinformatics.scm (r-singlecellexperiment): Update to 1.4.0.
 2018-11-07 12:27:16 +01:00
Ricardo Wurmus
3c833608f3
gnu: r-beachmat: Update to 1.4.0. 
* gnu/packages/bioinformatics.scm (r-beachmat): Update to 1.4.0.
[propagated-inputs]: Add r-biocgenerics.
 2018-11-07 12:27:16 +01:00
Ricardo Wurmus
edb91244c3
gnu: r-qvalue: Update to 2.14.0. 
* gnu/packages/bioinformatics.scm (r-qvalue): Update to 2.14.0.
 2018-11-07 12:27:16 +01:00
Ricardo Wurmus
d055f199a9
gnu: r-hitc: Update to 1.26.0. 
* gnu/packages/bioinformatics.scm (r-hitc): Update to 1.26.0.
 2018-11-07 12:27:16 +01:00
Ricardo Wurmus
8023912934
gnu: r-fithic: Update to 1.8.0. 
* gnu/packages/bioinformatics.scm (r-fithic): Update to 1.8.0.
 2018-11-07 12:27:16 +01:00
Ricardo Wurmus
7468a76480
gnu: r-sushi: Update to 1.20.0. 
* gnu/packages/bioinformatics.scm (r-sushi): Update to 1.20.0.
 2018-11-07 12:27:16 +01:00
Ricardo Wurmus
85b16c05e8
gnu: r-gwascat: Update to 2.14.0. 
* gnu/packages/bioinformatics.scm (r-gwascat): Update to 2.14.0.
 2018-11-07 12:27:16 +01:00
Ricardo Wurmus
d57445c9b2
gnu: r-gviz: Update to 1.26.0. 
* gnu/packages/bioinformatics.scm (r-gviz): Update to 1.26.0.
 2018-11-07 12:27:16 +01:00
Ricardo Wurmus
ea55326dc7
gnu: r-gqtlstats: Update to 1.14.0. 
* gnu/packages/bioinformatics.scm (r-gqtlstats): Update to 1.14.0.
 2018-11-07 12:27:16 +01:00
Ricardo Wurmus
da679b5202
gnu: r-ldblock: Update to 1.12.0. 
* gnu/packages/bioinformatics.scm (r-ldblock): Update to 1.12.0.
 2018-11-07 12:27:16 +01:00
Ricardo Wurmus
4b91335566
gnu: r-erma: Update to 0.14.0. 
* gnu/packages/bioinformatics.scm (r-erma): Update to 0.14.0.
 2018-11-07 12:27:15 +01:00
Ricardo Wurmus
220ac15e3f
gnu: r-snpstats: Update to 1.32.0. 
* gnu/packages/bioinformatics.scm (r-snpstats): Update to 1.32.0.
 2018-11-07 12:27:15 +01:00
Ricardo Wurmus
181a843143
gnu: r-gqtlbase: Update to 1.14.0. 
* gnu/packages/bioinformatics.scm (r-gqtlbase): Update to 1.14.0.
 2018-11-07 12:27:15 +01:00
Ricardo Wurmus
f20c766413
gnu: r-ggbio: Update to 1.30.0. 
* gnu/packages/bioinformatics.scm (r-ggbio): Update to 1.30.0.
 2018-11-07 12:27:15 +01:00
Ricardo Wurmus
e7a0bc1ccf
gnu: r-biovizbase: Update to 1.30.0. 
* gnu/packages/bioinformatics.scm (r-biovizbase): Update to 1.30.0.
 2018-11-07 12:27:15 +01:00
Ricardo Wurmus
cdab2dcfea
gnu: r-organismdbi: Update to 1.24.0. 
* gnu/packages/bioinformatics.scm (r-organismdbi): Update to 1.24.0.
[propagated-inputs]: Remove r-biocinstaller; add r-biocmanager.
 2018-11-07 12:27:15 +01:00
Ricardo Wurmus
e8e78c4966
gnu: r-ensembldb: Update to 2.6.0. 
* gnu/packages/bioinformatics.scm (r-ensembldb): Update to 2.6.0.
 2018-11-07 12:27:15 +01:00
Ricardo Wurmus
0c96e4b290
gnu: r-dirichletmultinomial: Update to 1.24.0. 
* gnu/packages/bioinformatics.scm (r-dirichletmultinomial): Update to 1.24.0.
 2018-11-07 12:27:15 +01:00
Ricardo Wurmus
5ae5a8ebfc
gnu: r-complexheatmap: Update to 1.20.0. 
* gnu/packages/bioinformatics.scm (r-complexheatmap): Update to 1.20.0.
 2018-11-07 12:27:15 +01:00
Ricardo Wurmus
d78c6aca55
gnu: r-genomicfiles: Update to 1.18.0. 
* gnu/packages/bioinformatics.scm (r-genomicfiles): Update to 1.18.0.
 2018-11-07 12:27:15 +01:00
Ricardo Wurmus
122e099e72
gnu: r-gage: Update to 2.32.0. 
* gnu/packages/bioinformatics.scm (r-gage): Update to 2.32.0.
 2018-11-07 12:27:15 +01:00
Ricardo Wurmus
4984212786
gnu: r-keggrest: Update to 1.22.0. 
* gnu/packages/bioinformatics.scm (r-keggrest): Update to 1.22.0.
 2018-11-07 12:27:15 +01:00
Ricardo Wurmus
95df764c01
gnu: r-fastseg: Update to 1.28.0. 
* gnu/packages/bioinformatics.scm (r-fastseg): Update to 1.28.0.
 2018-11-07 12:27:15 +01:00
Ricardo Wurmus
147633d4c1
gnu: r-annotationhub: Update to 2.14.1. 
* gnu/packages/bioinformatics.scm (r-annotationhub): Update to 2.14.1.
[propagated-inputs]: Remove r-biocinstaller; add r-biocmanager.
 2018-11-07 12:27:15 +01:00
Ricardo Wurmus
d7ea34bf99
gnu: r-interactivedisplaybase: Update to 1.20.0. 
* gnu/packages/bioinformatics.scm (r-interactivedisplaybase): Update to 1.20.0.
 2018-11-07 12:27:15 +01:00
Ricardo Wurmus
b03951f26b
gnu: r-edaseq: Update to 2.16.0. 
* gnu/packages/bioinformatics.scm (r-edaseq): Update to 2.16.0.
 2018-11-07 12:27:15 +01:00
Ricardo Wurmus
7812e6b82e
gnu: r-deseq: Update to 1.34.0. 
* gnu/packages/bioinformatics.scm (r-deseq): Update to 1.34.0.
 2018-11-07 12:27:15 +01:00
Ricardo Wurmus
800954eba4
gnu: r-aroma-light: Update to 3.12.0. 
* gnu/packages/bioinformatics.scm (r-aroma-light): Update to 3.12.0.
 2018-11-07 12:27:15 +01:00
Ricardo Wurmus
675d91a035
gnu: r-msnid: Update to 1.16.0. 
* gnu/packages/bioinformatics.scm (r-msnid): Update to 1.16.0.
 2018-11-07 12:27:14 +01:00
Ricardo Wurmus
762aca7270
gnu: r-msnbase: Update to 2.8.0. 
* gnu/packages/bioinformatics.scm (r-msnbase): Update to 2.8.0.
 2018-11-07 12:27:14 +01:00
Ricardo Wurmus
73d7475246
gnu: r-pcamethods: Update to 1.74.0. 
* gnu/packages/bioinformatics.scm (r-pcamethods): Update to 1.74.0.
 2018-11-07 12:27:14 +01:00
Ricardo Wurmus
2c4311dc7c
gnu: r-mzid: Update to 1.20.0. 
* gnu/packages/bioinformatics.scm (r-mzid): Update to 1.20.0.
 2018-11-07 12:27:14 +01:00
Ricardo Wurmus
0e16fc4699
gnu: r-vsn: Update to 3.50.0. 
* gnu/packages/bioinformatics.scm (r-vsn): Update to 3.50.0.
 2018-11-07 12:27:14 +01:00
Ricardo Wurmus
2b085484c0
gnu: r-affy: Update to 1.60.0. 
* gnu/packages/bioinformatics.scm (r-affy): Update to 1.60.0.
[propagated-inputs]: Remove r-biocinstaller; add r-biocmanager.
 2018-11-07 12:27:14 +01:00
Ricardo Wurmus
511abd7add
gnu: r-affyio: Update to 1.52.0. 
* gnu/packages/bioinformatics.scm (r-affyio): Update to 1.52.0.
 2018-11-07 12:27:14 +01:00
Ricardo Wurmus
691ce09fd3
gnu: r-protgenerics: Update to 1.14.0. 
* gnu/packages/bioinformatics.scm (r-protgenerics): Update to 1.14.0.
 2018-11-07 12:27:14 +01:00
Ricardo Wurmus
8af8688339
gnu: r-sva: Update to 3.30.0. 
* gnu/packages/bioinformatics.scm (r-sva): Update to 3.30.0.
 2018-11-07 12:27:14 +01:00
Ricardo Wurmus
18604a76e4
gnu: r-methylkit: Update to 1.8.0. 
* gnu/packages/bioinformatics.scm (r-methylkit): Update to 1.8.0.
 2018-11-07 12:27:14 +01:00
Ricardo Wurmus
739a856db8
gnu: r-copywriter: Update to 2.14.0. 
* gnu/packages/bioinformatics.scm (r-copywriter): Update to 2.14.0.
 2018-11-07 12:27:14 +01:00
Ricardo Wurmus
2e9d8116fb
gnu: r-chipseq: Update to 1.32.0. 
* gnu/packages/bioinformatics.scm (r-chipseq): Update to 1.32.0.
 2018-11-07 12:27:14 +01:00
Ricardo Wurmus
cec8f0920b
gnu: r-annotationfilter: Update to 1.6.0. 
* gnu/packages/bioinformatics.scm (r-annotationfilter): Update to 1.6.0.
 2018-11-07 12:27:14 +01:00
Ricardo Wurmus
d2b60be596
gnu: r-tximport: Update to 1.10.0. 
* gnu/packages/bioinformatics.scm (r-tximport): Update to 1.10.0.
 2018-11-07 12:27:14 +01:00
Ricardo Wurmus
ad90921ddc
gnu: r-mutationalpatterns: Update to 1.8.0. 
* gnu/packages/bioinformatics.scm (r-mutationalpatterns): Update to 1.8.0.
 2018-11-07 12:27:14 +01:00