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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
338f860cc6
gnu: r-bamsignals: Update to 1.14.0.
...
* gnu/packages/bioinformatics.scm (r-bamsignals): Update to 1.14.0.
2018-11-07 12:27:14 +01:00
48196899cd
gnu: r-rhtslib: Update to 1.14.0.
...
* gnu/packages/bioinformatics.scm (r-rhtslib): Update to 1.14.0.
2018-11-07 12:27:14 +01:00
7d7c702c03
gnu: r-zlibbioc: Update to 1.28.0.
...
* gnu/packages/bioinformatics.scm (r-zlibbioc): Update to 1.28.0.
2018-11-07 12:27:14 +01:00
2919fefe12
gnu: r-motifrg: Update to 1.26.0.
...
* gnu/packages/bioinformatics.scm (r-motifrg): Update to 1.26.0.
2018-11-07 12:27:13 +01:00
34f1c60c78
gnu: r-seqlogo: Update to 1.48.0.
...
* gnu/packages/bioinformatics.scm (r-seqlogo): Update to 1.48.0.
2018-11-07 12:27:13 +01:00
c5b0815c44
gnu: r-genomation: Update to 1.14.0.
...
* gnu/packages/bioinformatics.scm (r-genomation): Update to 1.14.0.
2018-11-07 12:27:13 +01:00
45ba2caedb
gnu: r-seqpattern: Update to 1.14.0.
...
* gnu/packages/bioinformatics.scm (r-seqpattern): Update to 1.14.0.
2018-11-07 12:27:13 +01:00
d11bc259a8
gnu: r-impute: Update to 1.56.0.
...
* gnu/packages/bioinformatics.scm (r-impute): Update to 1.56.0.
2018-11-07 12:27:13 +01:00
78ecdbc00a
gnu: r-bsgenome: Update to 1.50.0.
...
* gnu/packages/bioinformatics.scm (r-bsgenome): Update to 1.50.0.
2018-11-07 12:27:13 +01:00
44fa14dfa3
gnu: r-topgo: Update to 2.34.0.
...
* gnu/packages/bioinformatics.scm (r-topgo): Update to 2.34.0.
2018-11-07 12:27:13 +01:00
8a0d57d26e
gnu: r-genomicfeatures: Update to 1.34.1.
...
* gnu/packages/bioinformatics.scm (r-genomicfeatures): Update to 1.34.1.
2018-11-07 12:27:13 +01:00
c5f1d1ce80
gnu: r-rtracklayer: Update to 1.42.0.
...
* gnu/packages/bioinformatics.scm (r-rtracklayer): Update to 1.42.0.
2018-11-07 12:27:13 +01:00
52b95337e8
gnu: r-genomicalignments: Update to 1.18.0.
...
* gnu/packages/bioinformatics.scm (r-genomicalignments): Update to 1.18.0.
2018-11-07 12:27:13 +01:00
9fd4350e5a
gnu: r-summarizedexperiment: Update to 1.12.0.
...
* gnu/packages/bioinformatics.scm (r-summarizedexperiment): Update to 1.12.0.
2018-11-07 12:27:13 +01:00
de4c38f80b
gnu: r-delayedarray: Update to 0.8.0.
...
* gnu/packages/bioinformatics.scm (r-delayedarray): Update to 0.8.0.
2018-11-07 12:27:13 +01:00
7f3778eb06
gnu: r-rsamtools: Update to 1.34.0.
...
* gnu/packages/bioinformatics.scm (r-rsamtools): Update to 1.34.0.
2018-11-07 12:27:13 +01:00
4804c59227
gnu: r-biostrings: Update to 2.50.0.
...
* gnu/packages/bioinformatics.scm (r-biostrings): Update to 2.50.0.
2018-11-07 12:27:13 +01:00
cd8828918f
gnu: r-biocparallel: Update to 1.16.0.
...
* gnu/packages/bioinformatics.scm (r-biocparallel): Update to 1.16.0.
2018-11-07 12:27:13 +01:00
3359d44210
gnu: r-biomart: Update to 2.38.0.
...
* gnu/packages/bioinformatics.scm (r-biomart): Update to 2.38.0.
2018-11-07 12:27:13 +01:00
3986e0dee5
gnu: r-annotationdbi: Update to 1.44.0.
...
* gnu/packages/bioinformatics.scm (r-annotationdbi): Update to 1.44.0.
2018-11-07 12:27:13 +01:00
5b82e12a99
gnu: r-biobase: Update to 2.42.0.
...
* gnu/packages/bioinformatics.scm (r-biobase): Update to 2.42.0.
2018-11-07 12:27:13 +01:00
8d3906a95f
gnu: r-genomicranges: Update to 1.34.0.
...
* gnu/packages/bioinformatics.scm (r-genomicranges): Update to 1.34.0.
2018-11-07 12:27:12 +01:00
fb10fb72ba
gnu: r-xvector: Update to 0.22.0.
...
* gnu/packages/bioinformatics.scm (r-xvector): Update to 0.22.0.
2018-11-07 12:27:12 +01:00
78d2ffdc73
gnu: r-limma: Update to 3.38.2.
...
* gnu/packages/bioinformatics.scm (r-limma): Update to 3.38.2.
2018-11-07 12:27:12 +01:00
ca2945c316
gnu: r-variantannotation: Update to 1.28.1.
...
* gnu/packages/bioinformatics.scm (r-variantannotation): Update to 1.28.1.
2018-11-07 12:27:12 +01:00
08cd2d5b59
gnu: r-edger: Update to 3.24.0.
...
* gnu/packages/bioinformatics.scm (r-edger): Update to 3.24.0.
2018-11-07 12:27:12 +01:00
12871693fe
gnu: r-genomeinfodb: Update to 1.18.0.
...
* gnu/packages/bioinformatics.scm (r-genomeinfodb): Update to 1.18.0.
2018-11-07 12:27:12 +01:00
9a8dd51979
gnu: r-iranges: Update to 2.16.0.
...
* gnu/packages/bioinformatics.scm (r-iranges): Update to 2.16.0.
2018-11-07 12:27:12 +01:00
a037453554
gnu: r-s4vectors: Update to 0.20.0.
...
* gnu/packages/bioinformatics.scm (r-s4vectors): Update to 0.20.0.
2018-11-07 12:27:12 +01:00
70f2758f71
gnu: r-dnacopy: Update to 1.56.0.
...
* gnu/packages/bioinformatics.scm (r-dnacopy): Update to 1.56.0.
2018-11-07 12:27:12 +01:00
a127d3522a
gnu: r-bioccheck: Update to 1.18.0.
...
* gnu/packages/bioinformatics.scm (r-bioccheck): Update to 1.18.0.
[propagated-inputs]: Add r-knitr and r-biocmanager; remove r-biocinstaller.
2018-11-07 12:27:12 +01:00
6087f5ce37
gnu: r-biocstyle: Update to 2.10.0.
...
* gnu/packages/bioinformatics.scm (r-biocstyle): Update to 2.10.0.
[propagated-inputs]: Add biocmanager.
2018-11-07 12:27:12 +01:00
c8dbb5fa7f
gnu: r-biocviews: Update to 1.50.1.
...
* gnu/packages/bioinformatics.scm (r-biocviews): Update to 1.50.1.
2018-11-07 12:27:12 +01:00
36d7d823a4
gnu: r-biocinstaller: Update to 1.32.1.
...
* gnu/packages/bioinformatics.scm (r-biocinstaller): Update to 1.32.1.
2018-11-07 12:27:12 +01:00
2f28ffd81d
gnu: r-biocgenerics: Update to 0.28.0.
...
* gnu/packages/bioinformatics.scm (r-biocgenerics): Update to 0.28.0.
2018-11-07 12:27:12 +01:00
5c996cab4c
gnu: r-grohmm: Update to 1.16.0.
...
* gnu/packages/bioinformatics.scm (r-grohmm): Update to 1.16.0.
2018-11-07 12:27:12 +01:00
bf25930cf6
gnu: r-systempiper: Update to 1.16.0.
...
* gnu/packages/bioinformatics.scm (r-systempiper): Update to 1.16.0.
2018-11-07 12:27:12 +01:00
9adf78c21e
gnu: r-shortread: Update to 1.40.0.
...
* gnu/packages/bioinformatics.scm (r-shortread): Update to 1.40.0.
2018-11-07 12:27:12 +01:00
4a4b5b8537
gnu: r-gostats: Update to 2.48.0.
...
* gnu/packages/bioinformatics.scm (r-gostats): Update to 2.48.0.
2018-11-07 12:27:12 +01:00
95ae5acc89
gnu: r-category: Update to 2.48.0.
...
* gnu/packages/bioinformatics.scm (r-category): Update to 2.48.0.
2018-11-07 12:26:34 +01:00
6dfb0b25ae
gnu: r-gseabase: Update to 1.44.0.
...
* gnu/packages/bioinformatics.scm (r-gseabase): Update to 1.44.0.
2018-11-07 12:26:34 +01:00
19a6149190
gnu: r-rbgl: Update to 1.58.0.
...
* gnu/packages/bioinformatics.scm (r-rbgl): Update to 1.58.0.
2018-11-07 12:26:34 +01:00
2ff6604a53
gnu: r-annotationforge: Update to 1.24.0.
...
* gnu/packages/bioinformatics.scm (r-annotationforge): Update to 1.24.0.
2018-11-07 12:26:34 +01:00
856444a0a1
gnu: r-dexseq: Update to 1.28.0.
...
* gnu/packages/bioinformatics.scm (r-dexseq): Update to 1.28.0.
2018-11-07 12:26:34 +01:00
b5c552e654
gnu: r-deseq2: Update to 1.22.1.
...
* gnu/packages/bioinformatics.scm (r-deseq2): Update to 1.22.1.
2018-11-07 12:26:34 +01:00
85fb33a051
gnu: r-genefilter: Update to 1.64.0.
...
* gnu/packages/bioinformatics.scm (r-genefilter): Update to 1.64.0.
2018-11-07 12:26:34 +01:00
f4a95a0d15
gnu: r-geneplotter: Update to 1.60.0.
...
* gnu/packages/bioinformatics.scm (r-geneplotter): Update to 1.60.0.
2018-11-07 12:26:34 +01:00
dadd682c53
gnu: r-copynumber: Update to 1.22.0.
...
* gnu/packages/bioinformatics.scm (r-copynumber): Update to 1.22.0.
2018-11-07 12:26:34 +01:00
090d4c0159
gnu: r-annotate: Update to 1.60.0.
...
* gnu/packages/bioinformatics.scm (r-annotate): Update to 1.60.0.
2018-11-07 12:26:34 +01:00
6b451c0801
gnu: r-gprofiler: Update to 0.6.7.
...
* gnu/packages/bioinformatics.scm (r-gprofiler): Update to 0.6.7.
2018-10-30 21:42:48 +01:00
4fc6609a0c
gnu: r-keggrest: Update to 1.20.2.
...
* gnu/packages/bioinformatics.scm (r-keggrest): Update to 1.20.2.
2018-10-30 21:42:39 +01:00
67cfb83ff1
gnu: r-msnbase: Update to 2.6.4.
...
* gnu/packages/bioinformatics.scm (r-msnbase): Update to 2.6.4.
2018-10-30 21:42:31 +01:00
807d961cc9
gnu: r-methylkit: Update to 1.6.3.
...
* gnu/packages/bioinformatics.scm (r-methylkit): Update to 1.6.3.
2018-10-30 21:42:20 +01:00
ac0166450d
gnu: r-wgcna: Update to 1.66.
...
* gnu/packages/bioinformatics.scm (r-wgcna): Update to 1.66.
2018-10-30 21:42:09 +01:00
1182460750
gnu: r-go-db: Update to 3.6.0.
...
* gnu/packages/bioinformatics.scm (r-go-db): Update to 3.6.0.
2018-10-30 21:42:00 +01:00
466bf3af89
gnu: r-genomicfeatures: Update to 1.32.3.
...
* gnu/packages/bioinformatics.scm (r-genomicfeatures): Update to 1.32.3.
2018-10-30 21:41:12 +01:00
dd0216e0e7
gnu: r-delayedarray: Update to 0.6.6.
...
* gnu/packages/bioinformatics.scm (r-delayedarray): Update to 0.6.6.
2018-10-30 21:40:57 +01:00
72408357fa
gnu: r-genomicranges: Update to 1.32.7.
...
* gnu/packages/bioinformatics.scm (r-genomicranges): Update to 1.32.7.
2018-10-30 21:40:48 +01:00
9dad1957ab
gnu: r-limma: Update to 3.36.5.
...
* gnu/packages/bioinformatics.scm (r-limma): Update to 3.36.5.
2018-10-30 21:40:40 +01:00
57cf6a14f0
gnu: r-edger: Update to 3.22.5.
...
* gnu/packages/bioinformatics.scm (r-edger): Update to 3.22.5.
2018-10-30 21:40:32 +01:00
eb890466fa
gnu: r-genomeinfodbdata: Update to 1.1.0.
...
* gnu/packages/bioinformatics.scm (r-genomeinfodbdata): Update to 1.1.0.
2018-10-30 21:40:22 +01:00
e563acb96b
gnu: r-iranges: Update to 2.14.12.
...
* gnu/packages/bioinformatics.scm (r-iranges): Update to 2.14.12.
2018-10-30 21:40:12 +01:00
192c19f484
gnu: r-vegan: Update to 2.5-3.
...
* gnu/packages/bioinformatics.scm (r-vegan): Update to 2.5-3.
2018-10-30 21:40:00 +01:00
f8ee22fc8b
gnu: flexbar: Update to 3.4.0.
...
* gnu/packages/bioinformatics.scm (flexbar): Update to 3.4.0.
[source]: Fetch from git.
[arguments]: Adjust check and install phases.
[home-page]: Update to new home at Github.
[license]: Change to bsd-3.
2018-10-21 23:06:47 +02:00
4d93a9a36c
gnu: seqan: Update to 2.4.0.
...
* gnu/packages/bioinformatics.scm (seqan): Update to 2.4.0.
[native-inputs]: Replace bzip2 with xz.
(seqan-1): New variable.
(tophat)[inputs]: Use seqan-1.
2018-10-21 23:06:47 +02:00
4b8f4536ce
gnu: khmer: Update to 2.1.2.
...
* gnu/packages/bioinformatics.scm (khmer): Update to 2.1.2.
[source]: Fetch from git; remove bundled libraries in snippet.
[arguments]: Remove "set-paths" phase; remove "post-install-check" phase;
remove "reset-gzip-timestamps" phase.
[native-inputs]: Remove seqan and python-nose; add python-cython,
python-pytest, and python-pytest-runner.
[inputs]: Remove gcc-4.9.
2018-10-21 23:06:47 +02:00
50e33c3a8c
gnu: python-screed: Update to 1.0.
...
* gnu/packages/bioinformatics.scm (python-screed): Update to 1.0.
[arguments]: Run tests after installation.
[native-inputs]: Add python-pytest, python-pytest-cov, and
python-pytest-runner; remove python-nose.
2018-10-21 23:06:47 +02:00
0db75f7a79
gnu: fasttree: Use INVOKE.
...
* gnu/packages/bioinformatics.scm (fasttree)[arguments]: Use INVOKE; simplify
install phase.
2018-10-21 23:06:46 +02:00
38622ccd14
gnu: express-beta-diversity: Update to 1.0.8.
...
* gnu/packages/bioinformatics.scm (express-beta-diversity): Update to 1.0.8.
[source]: Fetch from git.
[arguments]: Use INVOKE; remove "exit-source" build phase; simplify.
2018-10-21 23:06:46 +02:00
c96ca68f31
gnu: edirect: Update to 10.2.20181018.
...
* gnu/packages/bioinformatics.scm (edirect): Update to 10.2.20181018.
[arguments]: Add simple check phase; simplify other phases.
[inputs]: Add perl-xml-simple.
2018-10-21 23:06:46 +02:00
949fa34b84
gnu: eigensoft: Update to 7.2.1.
...
* gnu/packages/bioinformatics.scm (eigensoft): Update to 7.2.1.
[arguments]: Remove Makefile modification.
2018-10-21 23:06:46 +02:00
5748fe5fcc
gnu: discrover: Fetch from git.
...
* gnu/packages/bioinformatics.scm (discrover)[source]: Fetch from git.
2018-10-21 23:06:46 +02:00
1c06399358
gnu: diamond: Fetch from git.
...
* gnu/packages/bioinformatics.scm (diamond)[source]: Fetch from git.
2018-10-21 23:06:46 +02:00
7a1e62ca67
gnu: delly: Update to 0.7.9.
...
* gnu/packages/bioinformatics.scm (delly): Update to 0.7.9.
[source]: Fetch from git.
[arguments]: Add phase install-templates; use default install phase.
[native-inputs]: Remove python-2.
[home-page]: Use new home page.
* gnu/packages/patches/delly-use-system-libraries.patch: Delete file.
* gnu/local.mk (dist_patch_DATA): Remove patch.
2018-10-21 23:06:46 +02:00
4d494a4fa3
gnu: deeptools: Update to 3.1.3.
...
* gnu/packages/bioinformatics.scm (deeptools): Update to 3.1.3.
2018-10-21 23:06:46 +02:00
42643fc24d
gnu: python-dendropy: Fetch from git.
...
* gnu/packages/bioinformatics.scm (python-dendropy)[source]: Fetch from git.
2018-10-21 23:06:46 +02:00
6b31040ae6
gnu: python-py2bit: Update to 0.3.0.
...
* gnu/packages/bioinformatics.scm (python-py2bit): Update to 0.3.0.
2018-10-21 23:06:45 +02:00
6b7260bad1
gnu: cutadapt: Update to 1.18.
...
* gnu/packages/bioinformatics.scm (cutadapt): Update to 1.18.
[inputs]: Add python-dnaio.
2018-10-21 23:06:45 +02:00
a5b0038cbd
gnu: Add python-dnaio.
...
* gnu/packages/bioinformatics.scm (python-dnaio): New variable.
2018-10-21 23:06:45 +02:00
7321920cd3
gnu: crossmap: Update to 0.2.9.
...
* gnu/packages/bioinformatics.scm (crossmap): Update to 0.2.9.
* gnu/packages/patches/crossmap-allow-system-pysam.patch: Delete file.
* gnu/local.mk (dist_patch_DATA): Remove patch.
2018-10-21 23:06:45 +02:00
8640f9ec91
gnu: python-twobitreader: Update to 3.1.6.
...
* gnu/packages/bioinformatics.scm (python-twobitreader): Update to 3.1.6.
[source]: Fetch from git.
2018-10-21 23:06:45 +02:00
f5cec0068a
gnu: Add python-bx-python.
...
* gnu/packages/bioinformatics.scm (python-bx-python): New variable.
(python2-bx-python): Define in terms of python-bx-python.
2018-10-21 23:06:45 +02:00
2ba2d62c69
gnu: python2-bx-python: Update to 0.8.2.
...
* gnu/packages/bioinformatics.scm (python2-bx-python): Update to 0.8.2.
[source]: Remove obsolete snippet.
[inputs]: Move python2-numpy from here...
[propagated-inputs]: ...to here; add python2-six.
[native-inputs]: Add python2-lzo and python2-cython.
[home-page]: Update to new home at Github.
2018-10-21 23:06:45 +02:00
1d18ee6dfd
gnu: bwa-pssm: Fetch from git.
...
* gnu/packages/bioinformatics.scm (bwa-pssm)[source]: Fetch from git.
2018-10-21 23:06:45 +02:00
9a6808e0c0
gnu: tophat: Update to 2.1.1.
...
* gnu/packages/bioinformatics.scm (tophat): Update to 2.1.1.
* gnu/packages/patches/tophat-build-with-later-seqan.patch: Delete file.
* gnu/local.mk (dist_patch_DATA): Remove patch.
2018-10-21 23:06:45 +02:00
617c478506
gnu: python2-dendropy: Disable failing test.
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* gnu/packages/bioinformatics.scm (python2-dendropy)[arguments]: Disable
failing test.
2018-10-21 22:31:56 +10:00
21c837405a
gnu: bowtie: Update to 2.3.4.3.
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* gnu/packages/bioinformatics.scm (bowtie): Update to 2.3.4.3.
[source]: Fetch from git.
[inputs]: Replace python-2 with python-wrapper; move perl, perl-clone,
perl-test-deep, and perl-test-simple from here...
[native-inputs]: ...to here.
[arguments]: Simplify check phase.
2018-10-20 23:37:34 +02:00
f45093429c
gnu: blast+: Use INVOKE and return #T unconditionally.
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* gnu/packages/bioinformatics.scm (blast+)[arguments]: Use INVOKE and
return #T unconditionally.
2018-10-20 23:37:34 +02:00
f8b697a385
gnu: bedops: Update to 2.4.35.
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* gnu/packages/bioinformatics.scm (bedops): Update to 2.4.35.
[source]: Fetch from git.
2018-10-20 23:37:34 +02:00
337d72fb44
gnu: bedops: Use INVOKE.
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* gnu/packages/bioinformatics.scm (bedops)[arguments]: Use INVOKE.
2018-10-20 23:37:34 +02:00
c793f4d8fb
gnu: bamm: Fetch from git and use INVOKE.
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* gnu/packages/bioinformatics.scm (bamm)[source]: Fetch from git.
[arguments]: Use INVOKE and return #T unconditionally.
2018-10-20 23:37:34 +02:00
95758e2faf
gnu: aragorn: Use invoke and simplify.
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* gnu/packages/bioinformatics.scm (aragorn)[arguments]: Use INVOKE in build
phase; simplify install phase.
2018-10-20 23:37:33 +02:00
8b4102b903
gnu: clipper: Update to 1.2.1.
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* gnu/packages/bioinformatics.scm (clipper): Update to 1.2.1.
[source]: Fetch from git.
[arguments]: Add fix-typo phase.
2018-10-20 23:37:33 +02:00
895cf8278a
gnu: python-pybedtools: Update to 0.7.10.
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* gnu/packages/bioinformatics.scm (python2-pybedtools): Update to 0.7.10.
[arguments]: Disable broken tests.
[propagated-inputs]: Replace bedtools with bedtools-2.26; add
python-matplotlib, python-pysam, and python-pyyaml.
[native-inputs]: Remove python-pyyaml; add kentutils, python-numpy,
python-pandas, and python-six.
(python-pybedtools): New variable.
2018-10-20 23:37:33 +02:00
129363b762
gnu: Add bedtools-2.26.
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* gnu/packages/bioinformatics.scm (bedtools-2.26): New variable.
2018-10-20 23:37:28 +02:00
e8a7eab169
gnu: kallisto: Update to 0.44.0.
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* gnu/packages/bioinformatics.scm (kallisto): Update to 0.44.0.
[source]: Fetch from git.
[arguments]: Add build phase to use htslib from Guix.
[inputs]: Add htslib.
2018-10-11 16:12:11 +02:00
b6bd8b108a
gnu: Add filtlong.
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* gnu/packages/bioinformatics.scm (filtlong): New variable.
Co-authored-by: Ludovic Courtès <ludo@gnu.org>
2018-10-08 18:32:42 +02:00
d71078bc75
gnu: Add ngless.
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* gnu/packages/bioinformatics.scm (ngless): New variable.
2018-10-05 23:59:27 +02:00
357450dca0
gnu: bioruby: Update to 1.5.2.
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This works with Ruby 2.5.
* gnu/packages/bioinformatics.scm (bioruby): Update to 1.5.2.
2018-10-05 21:25:39 +01:00
a6798218be
gnu: samtools-0.1: Adjust to match changes in samtools.
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* gnu/packages/bioinformatics.scm (samtools-0.1)[arguments]: Override make
flags.
2018-10-05 09:21:54 +02:00
8e72f0f319
gnu: deeptools: Update to 3.1.2.
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* gnu/packages/bioinformatics.scm (deeptools): Update to 3.1.2.
[source]: Fetch from git.
[arguments]: Delete reset-gzip-timestamps phase.
[inputs]: Add python-plotly.
2018-10-05 09:21:54 +02:00
939882f734
gnu: python-pysam: Update to 0.15.1.
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* gnu/packages/bioinformatics.scm (python-pysam): Update to 0.15.1.
[source]: Fetch from git.
[arguments]: Delete tests requiring internet access; use "invoke".
[inputs]: Add curl.
2018-10-05 09:21:54 +02:00
f79b59e311
gnu: bcftools: Update to 1.9.
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* gnu/packages/bioinformatics.scm (bcftools): Update to 1.9.
[arguments]: Remove obsolete make flags.
2018-10-05 09:21:54 +02:00
4ae4a15232
gnu: samtools: Update to 1.9.
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* gnu/packages/bioinformatics.scm (samtools): Update to 1.9.
[origin]: Remove bundled htslib sources.
[arguments]: Remove obsolete make-flags.
2018-10-05 09:21:54 +02:00
bd5f5eece9
gnu: htslib: Update to 1.9.
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* gnu/packages/bioinformatics.scm (htslib): Update to 1.9.
2018-10-05 09:21:50 +02:00
0f1622220a
gnu: Add r-absfiltergsea.
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* gnu/packages/bioinformatics.scm (r-absfiltergsea): New variable.
2018-10-02 16:23:49 -04:00
3f0f49d708
gnu: Add poretools.
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* gnu/packages/bioinformatics.scm (poretools): New variable.
2018-10-02 16:05:14 -04:00
f2bc53af70
gnu: Add porechop.
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* gnu/packages/bioinformatics.scm (porechop): New variable.
2018-09-30 14:09:48 -04:00
e72702475d
gnu: Add r-bseqsc.
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* gnu/packages/bioinformatics.scm (r-bseqsc): New variable.
2018-09-24 13:31:20 +02:00
28829c040f
gnu: Add r-cssam.
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* gnu/packages/bioinformatics.scm (r-cssam): New variable.
2018-09-24 13:31:20 +02:00
a434730f2e
gnu: Add r-xbioc.
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* gnu/packages/bioinformatics.scm (r-xbioc): New variable.
2018-09-24 13:31:20 +02:00
05fb1e0017
gnu: hmmer: Update to 3.2.1.
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* gnu/packages/bioinformatics.scm (hmmer): Update to 3.2.1.
[origin]: Remove patch.
[license]: Change to BSD-3.
[supported-systems]: New field.
* gnu/packages/patches/hmmer-remove-cpu-specificity.patch: Delete file.
* gnu/local.mk (dist_patch_DATA): Remove it.
2018-09-22 09:16:47 +10:00
7e27393f82
gnu: Add r-pore.
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* gnu/packages/bioinformatics.scm (r-pore): New variable.
Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2018-09-21 17:04:37 +02:00
89ee8a6edf
gnu: rsem: Update to 1.3.1.
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* gnu/packages/bioinformatics.scm (rsem): Update to 1.3.1.
[source]: Fetch from git; remove patch; delete bundled samtools.
[arguments]: Pass make flags; adjust phases.
[inputs]: Remove ncurses and samtools-0.1; add htslib-1.3.
* gnu/packages/patches/rsem-makefile.patch: Remove patch.
* gnu/local.mk (dist_patch_DATA): Remove it.
2018-09-20 17:55:26 +02:00
1dd153b3aa
gnu: Add python-hic2cool.
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* gnu/packages/bioinformatics.scm (python-hic2cool): New variable.
2018-09-14 09:15:49 +02:00
875d068176
Adjust all users of (gnu packages ldc) to use (gnu packages dlang).
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This is a followup to commit 98d6543f86
2018-09-10 15:44:32 -04:00
5bfa7510d1
gnu: Add python-pygenometracks.
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* gnu/packages/bioinformatics.scm (python-pygenometracks): New variable.
2018-09-10 16:50:26 +02:00
1189c7f1b0
gnu: Add python-hicexplorer.
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* gnu/packages/bioinformatics.scm (python-hicexplorer): New variable.
2018-09-10 16:50:26 +02:00
5bb9e0af8d
gnu: Add python-cooler.
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* gnu/packages/bioinformatics.scm (python-cooler): New variable.
2018-09-10 16:50:26 +02:00
80f4db91b1
gnu: Add python-pyfaidx.
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* gnu/packages/bioinformatics.scm (python-pyfaidx): New variable.
2018-09-10 16:50:26 +02:00
1f41f01c14
gnu: Add python-pypairix.
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* gnu/packages/bioinformatics.scm (python-pypairix): New variable.
2018-09-10 16:50:26 +02:00
a9d496b353
gnu: Add python-intervaltree.
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* gnu/packages/bioinformatics.scm (python-intervaltree): New variable.
2018-09-10 16:50:26 +02:00
ab50580a9d
gnu: r-annotationhub: Update to 2.12.1.
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* gnu/packages/bioinformatics.scm (r-annotationhub): Update to 2.12.1.
2018-09-09 22:26:02 +02:00
d53aeeafcc
Add missing use-modules clause.
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This is a follow-up to commit 5dfe491290
2018-09-06 04:53:32 +02:00
00a43cb81c
gnu: pigx-scrnaseq: Use latest version of Pandoc.
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* gnu/packages/bioinformatics.scm (pigx-scrnaseq)[inputs]: Replace
"ghc-pandoc-citeproc-with-pandoc-1" with "ghc-pandoc-citeproc", and
"ghc-pandoc-1" with "ghc-pandoc".
2018-09-05 20:03:09 +02:00
c2b4f81e51
gnu: pigx-bsseq: Use latest version of Pandoc.
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* gnu/packages/bioinformatics.scm (pigx-bsseq)[inputs]: Replace
"ghc-pandoc-citeproc-with-pandoc-1" with "ghc-pandoc-citeproc", and
"ghc-pandoc-1" with "ghc-pandoc".
2018-09-05 20:03:09 +02:00
7cd40c8c5d
gnu: pigx-chipseq: Use latest version of Pandoc.
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* gnu/packages/bioinformatics.scm (pigx-chipseq)[inputs]: Replace
"ghc-pandoc-citeproc-with-pandoc-1" with "ghc-pandoc-citeproc", and
"ghc-pandoc-1" with "ghc-pandoc".
2018-09-05 20:03:09 +02:00
ca248f1db9
gnu: pigx-rnaseq: Use latest version of Pandoc.
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* gnu/packages/bioinformatics.scm (pigx-rnaseq)[inputs]: Replace
"ghc-pandoc-citeproc-with-pandoc-1" with "ghc-pandoc-citeproc", and
"ghc-pandoc-1" with "ghc-pandoc".
2018-09-05 20:03:09 +02:00
dff5640a59
gnu: r-rcas: Use standard version of ghc-pandoc-citeproc.
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* gnu/packages/bioinformatics.scm (r-rcas)[native-inputs]: Replace
"ghc-pandoc-citeproc-with-pandoc-1" with "ghc-pandoc-citeproc".
2018-09-05 20:03:09 +02:00
5dfe491290
gnu: r-graph: Move from bioinformatics to bioconductor.
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* gnu/packages/bioinformatics.scm (r-graph): Move from here...
* gnu/packages/bioconductor.scm (r-graph): ...to here.
2018-09-05 20:03:08 +02:00
Ricardo Wurmus
Ben Woodcroft
pimi
Ricardo Wurmus
Christopher Baines
Leo Famulari