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1804 Commits

Author SHA1 Message Date
Ricardo Wurmus a4f038dc97
gnu: r-mzr: Update to 2.16.1. 
* gnu/packages/bioinformatics.scm (r-mzr): Update to 2.16.1.
 2019-01-12 23:35:17 +01:00
Ricardo Wurmus 46508c3a92
gnu: r-sva: Update to 3.30.1. 
* gnu/packages/bioinformatics.scm (r-sva): Update to 3.30.1.
 2019-01-12 23:35:17 +01:00
Ricardo Wurmus c20426ec5c
gnu: r-methylkit: Update to 1.8.1. 
* gnu/packages/bioinformatics.scm (r-methylkit): Update to 1.8.1.
 2019-01-12 23:35:17 +01:00
Ricardo Wurmus 5c72ebafeb
gnu: r-copywriter: Update to 2.14.1. 
* gnu/packages/bioinformatics.scm (r-copywriter): Update to 2.14.1.
 2019-01-12 23:35:17 +01:00
Ricardo Wurmus 86162c767e
gnu: r-rhdf5: Update to 2.26.2. 
* gnu/packages/bioinformatics.scm (r-rhdf5): Update to 2.26.2.
 2019-01-12 23:35:17 +01:00
Ricardo Wurmus 4c7b9222dd
gnu: r-tximport: Update to 1.10.1. 
* gnu/packages/bioinformatics.scm (r-tximport): Update to 1.10.1.
 2019-01-12 23:35:17 +01:00
Ricardo Wurmus 4bfde52178
gnu: r-genomicalignments: Update to 1.18.1. 
* gnu/packages/bioinformatics.scm (r-genomicalignments): Update to 1.18.1.
 2019-01-12 23:35:17 +01:00
Ricardo Wurmus 1fa12b2f06
gnu: r-biostrings: Update to 2.50.2. 
* gnu/packages/bioinformatics.scm (r-biostrings): Update to 2.50.2.
 2019-01-12 23:35:17 +01:00
Ricardo Wurmus d4fc834cf7
gnu: r-biocparallel: Update to 1.16.5. 
* gnu/packages/bioinformatics.scm (r-biocparallel): Update to 1.16.5.
 2019-01-12 23:35:17 +01:00
Ricardo Wurmus 52c977a05b
gnu: r-limma: Update to 3.38.3. 
* gnu/packages/bioinformatics.scm (r-limma): Update to 3.38.3.
 2019-01-12 23:35:17 +01:00
Ricardo Wurmus 3fd48846eb
gnu: r-variantannotation: Update to 1.28.8. 
* gnu/packages/bioinformatics.scm (r-variantannotation): Update to 1.28.8.
 2019-01-12 23:35:17 +01:00
Ricardo Wurmus a619850930
gnu: r-edger: Update to 3.24.3. 
* gnu/packages/bioinformatics.scm (r-edger): Update to 3.24.3.
 2019-01-12 23:35:17 +01:00
Ricardo Wurmus 00f105fe20
gnu: r-biocviews: Update to 1.50.10. 
* gnu/packages/bioinformatics.scm (r-biocviews): Update to 1.50.10.
 2019-01-12 23:35:16 +01:00
Ricardo Wurmus 9c1b2b2ae0
gnu: r-systempiper: Update to 1.16.1. 
* gnu/packages/bioinformatics.scm (r-systempiper): Update to 1.16.1.
 2019-01-12 23:35:16 +01:00
Ricardo Wurmus 3b8c884285
gnu: r-rbgl: Update to 1.58.1. 
* gnu/packages/bioinformatics.scm (r-rbgl): Update to 1.58.1.
 2019-01-12 23:35:16 +01:00
Ricardo Wurmus ffe16ef33c
gnu: r-dexseq: Update to 1.28.1. 
* gnu/packages/bioinformatics.scm (r-dexseq): Update to 1.28.1.
 2019-01-12 23:35:16 +01:00
Ricardo Wurmus f7e95c50b8
gnu: r-deseq2: Update to 1.22.2. 
* gnu/packages/bioinformatics.scm (r-deseq2): Update to 1.22.2.
 2019-01-12 23:35:16 +01:00
Ricardo Wurmus feb561f721
gnu: r-scran: Update to 1.10.2. 
* gnu/packages/bioinformatics.scm (r-scran): Update to 1.10.2.
 2019-01-12 23:35:16 +01:00
Ricardo Wurmus 80c4e75b87
gnu: r-seqminer: Update to 7.1. 
* gnu/packages/bioinformatics.scm (r-seqminer): Update to 7.1.
 2019-01-12 23:35:16 +01:00
Ricardo Wurmus 3bc0667f3c
gnu: r-bookdown: Update to 0.9. 
* gnu/packages/bioinformatics.scm (r-bookdown): Update to 0.9.
 2019-01-12 23:35:16 +01:00
Ricardo Wurmus 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
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