325c039c1d
gnu: Add r-sparql.
...
* gnu/packages/bioinformatics.scm (r-sparql): New variable.
2017-09-05 11:02:03 +02:00
d10092b849
gnu: Put autoconf-related phases immediately after the 'unpack phase.
...
* gnu/packages/audio.scm (audacity, rtmidi)[arguments]: Correct phases
accordingly.
* gnu/packages/bioinformatics.scm (mash, seek, vsearch, emboss,
htslib-for-sambamba)[arguments]: Likewise.
* gnu/packages/ci.scm (cuirass)[arguments]: Likewise.
* gnu/packages/compression.scm (minizip, xdelta)[arguments]: Likewise.
* gnu/packages/cpp.scm (libzen)[arguments]: Likewise.
* gnu/packages/crypto.scm (opendht)[arguments]: Likewise.
* gnu/packages/databases.scm (4store, mdbtools)[arguments]: Likewise.
* gnu/packages/debug.scm (stress-make)[arguments]: Likewise.
* gnu/packages/dns.scm (dnscrypt-proxy, dnscrypt-wrapper)[arguments]:
Likewise.
* gnu/packages/emacs.scm (emacs-pdf-tools)[arguments]: Likewise.
* gnu/packages/embedded.scm (libjaylink, openocd)[arguments]: Likewise.
* gnu/packages/engineering.scm (gerbv)[arguments]: Likewise.
* gnu/packages/erlang.scm (erlang)[arguments]: Likewise.
* gnu/packages/ftp.scm (weex)[arguments]: Likewise.
* gnu/packages/gnome.scm (dia)[arguments]: Likewise.
* gnu/packages/gnunet.scm (gnurl, guile-gnunet)[arguments]: Likewise.
* gnu/packages/gtk.scm (guile-rsvg, graphene)[arguments]: Likewise.
* gnu/packages/guile.scm (guildhall, guile-ics, guile-sqlite3)[arguments]:
Likewise.
* gnu/packages/ibus.scm (ibus-libpinyin)[arguments]: Likewise.
* gnu/packages/irc.scm (weechat)[arguments]: Likewise.
* gnu/packages/java.scm (classpath-devel)[arguments]: Likewise.
* gnu/packages/libreoffice.scm (libetonyek)[arguments]: Likewise.
* gnu/packages/libusb.scm (hidapi)[arguments]: Likewise.
* gnu/packages/linux.scm (gpm)[arguments]: Likewise.
* gnu/packages/logging.scm (glog)[arguments]: Likewise.
* gnu/packages/machine-learning.scm (ghmm)[arguments]: Likewise.
* gnu/packages/mail.scm (dovecot-trees, dovecot-libsodium-plugin, esmtp)
[arguments]: Likewise.
* gnu/packages/messaging.scm (freetalk, libmesode, libstrophe)[arguments]:
Likewise.
* gnu/packages/microcom.scm (microcom)[arguments]: Likewise.
* gnu/packages/ocaml.scm (ocaml-ssl)[arguments]: Likewise.
* gnu/packages/parallel.scm (slurm)[arguments]: Likewise.
* gnu/packages/pdf.scm (libharu)[arguments]: Likewise.
* gnu/packages/samba.scm (cifs-utils)[arguments]: Likewise.
* gnu/packages/serialization.scm (msgpack)[arguments]: Likewise.
* gnu/packages/shells.scm (scsh)[arguments]: Likewise.
* gnu/packages/telephony.scm (libiax2)[arguments]: Likewise.
* gnu/packages/textutils.scm (dotconf)[arguments]: Likewise.
* gnu/packages/version-control.scm (findnewest)[arguments]: Likewise.
* gnu/packages/video.scm (libmediainfo, mediainfo)[arguments]: Likewise.
2017-09-04 00:10:59 -04:00
81195d139f
gnu: r-genomicalignments: Update to 1.12.2.
...
* gnu/packages/bioinformatics.scm (r-genomicalignments): Update to 1.12.2.
2017-09-01 15:11:58 +02:00
db2e43863c
gnu: r-vegan: Update to 2.4-4.
...
* gnu/packages/bioinformatics.scm (r-vegan): Update to 2.4-4.
[native-inputs]: Remove r-knitr.
2017-09-01 15:11:57 +02:00
7b92acdf52
gnu: r-maldiquant: Update to 1.16.4.
...
* gnu/packages/bioinformatics.scm (r-maldiquant): Update to 1.16.4.
2017-09-01 15:11:57 +02:00
6bd27981f6
gnu: r-bookdown: Update to 0.5.
...
* gnu/packages/bioinformatics.scm (r-bookdown): Update to 0.5.
2017-09-01 15:11:56 +02:00
75690c9f6b
gnu: r-rcas: Correct license.
...
* gnu/packages/bioinformatics.scm (r-rcas)[license]: Use correct license.
2017-09-01 10:26:31 +02:00
eda8f36cd6
gnu: r-rcas: Update to 1.3.3.
...
* gnu/packages/bioinformatics.scm (r-rcas): Update to 1.3.3.
2017-09-01 10:26:30 +02:00
f4bf420c84
gnu: vsearch: Update to 2.4.4.
...
* gnu/packages/bioinformatics.scm (vsearch): Update to 2.4.4.
2017-09-01 14:45:57 +08:00
25bd1fc1c1
gnu: metabat: Update to 2.12.1.
...
* gnu/packages/patches/metabat-remove-compilation-date.patch: Delete file.
* gnu/local.mk (dist_patch_DATA): Remove it.
* gnu/packages/bioinformatics.scm (metabat): Update to 2.12.1.
[source]: Remove it. Use url-fetch.
2017-09-01 14:45:57 +08:00
0691851a64
gnu: bioinformatics: Work around more "dotless @INC" build failures.
...
* gnu/packages/bioinformatics.scm (ncbi-vdb, sra-tools)[arguments]: Add
'set-perl-search-path' phase.
2017-08-31 12:37:05 +08:00
690a904ad7
gnu: metabat: Update to 2.11.3.
...
* gnu/packages/bioinformatics.scm (metabat): Update to 2.11.3.
[source]: Use git-fetch. Remove boost-related patch.
* gnu/packages/patches/metabat-fix-boost-issue.patch: Delete file.
* gnu/local.mk (dist_patch_DATA): Remove it.
2017-08-31 10:43:18 +08:00
799247d2d9
gnu: multiqc: Update to 1.2.
...
* gnu/packages/bioinformatics.scm (multiqc): Update to 1.2.
[source]: Remove patches.
[arguments]: Remove to enable tests.
[propagated-inputs]: Add python-spectra, python-requests, python-markdown,
python-lzstring.
* gnu/packages/patches/multiqc-fix-git-subprocess-error.patch: Delete file.
* gnu/local.mk (dist_patch_DATA): Remove it.
2017-08-30 17:32:00 +02:00
2718a9cd09
Merge branch 'master' into core-updates
2017-08-21 02:40:37 +02:00
17cddc1714
gnu: Add r-annotationfilter.
...
* gnu/packages/bioinformatics.scm (r-annotationfilter): New variable.
2017-08-20 14:00:04 +02:00
bf3fa99654
gnu: Add r-methylkit.
...
* gnu/packages/bioinformatics.scm (r-methylkit): New variable.
2017-08-17 18:00:17 +02:00
212f612040
gnu: Add r-qvalue.
...
* gnu/packages/bioinformatics.scm (r-qvalue): New variable.
2017-08-17 17:26:12 +02:00
d4a1e918cb
gnu: Add r-fastseg.
...
* gnu/packages/bioinformatics.scm (r-fastseg): New variable.
2017-08-17 17:26:11 +02:00
4a007ffafe
gnu: Add r-annotationhub.
...
* gnu/packages/bioinformatics.scm (r-annotationhub): New variable.
2017-08-17 17:25:47 +02:00
5f96f30f5d
gnu: Add r-interactivedisplaybase.
...
* gnu/packages/bioinformatics.scm (r-interactivedisplaybase): New variable.
2017-08-17 17:25:46 +02:00
d534f3a4d3
gnu: r-mzr: Fix building on aarch64 and armhf.
...
* gnu/packages/bioinformatics.scm (r-mzr)[inputs]: Add boost.
2017-08-16 12:36:25 +03:00
06f31e50b1
gnu: diamond: Update to 0.9.10.
...
* gnu/packages/bioinformatics.scm (diamond): Update to 0.9.10.
2017-08-15 18:49:33 +10:00
3837108e40
gnu: bcftools: Fix building on aarch64.
...
* gnu/packages/patches/bcftools-regidx-unsigned-char.patch: New file.
* gnu/packages/bioinformatics.scm (bcftools)[source]: Use it.
* gnu/local.mk (dist_patch_DATA): Register it.
2017-08-15 10:31:20 +03:00
09ec5a0f0c
Merge branch 'master' into core-updates
2017-08-15 03:10:14 -04:00
9634804890
gnu: Add bismark.
...
* gnu/packages/bioinformatics.scm (bismark): New variable.
2017-08-14 12:00:56 +02:00
86763fdd70
gnu: Add r-dexseq.
...
* gnu/packages/bioinformatics.scm (r-dexseq): New variable.
2017-08-14 12:00:51 +02:00
cc294bcee6
Merge branch 'master' into core-updates
2017-08-09 17:25:31 -04:00
1b22ecdac4
gnu: r-wgcna: Update to 1.61.
...
* gnu/packages/bioinformatics.scm (r-wgcna): Update to 1.61.
[propagated-inputs]: Add r-rcpp, r-robust, r-survival.
2017-08-09 20:08:13 +02:00
18f5d2a70a
gnu: Add reference to (gnu packages graph).
...
This is a follow-up to 1738138cb3
2017-08-09 15:43:35 +02:00
2d9495da23
Merge branch 'master' into core-updates
2017-08-07 16:45:16 -04:00
9d217d277e
gnu: r-bsgenome-hsapiens-ucsc-hg19: Restore original hash.
...
* gnu/packages/bioinformatics.scm (r-bsgenome-hsapiens-ucsc-hg19)[source]:
Restore hash from before the tarball changed in place. It changed back.
This reverts commit fd40857938
2017-08-07 01:58:39 +02:00
f167595ba1
Merge branch 'master' into core-updates
2017-08-06 00:23:20 -04:00
a56bf101c6
gnu: perl: Work around more "dotless @INC" build issues.
...
* gnu/packages/web.scm (perl-www-curl)[arguments]: Add 'set-search-path'
phase.
* gnu/packages/bioinformatics.scm (ngs-sdk)[arguments]: Augment
'configure' phase to set PERL5LIB.
* gnu/packages/image.scm (steghide)[arguments]: Add #:phases argument.
2017-08-05 00:31:26 +02:00
7cb6155088
gnu: bioinformatics.scm: Use (gnu packages cran) module.
...
This is a follow up to a8cba9dd11
2017-08-03 21:39:12 +03:00
5e0de29892
gnu: r-seqminer: Update to 6.0.
...
* gnu/packages/bioinformatics.scm (r-seqminer): Update to 6.0.
2017-08-03 17:53:54 +02:00
4e0c847d59
gnu: r-wgcna: Update to 1.60.
...
* gnu/packages/bioinformatics.scm (r-wgcna): Update to 1.60.
2017-08-03 17:53:54 +02:00
c8a9b2bcbf
gnu: r-qtl: Update to 1.41-6.
...
* gnu/packages/bioinformatics.scm (r-qtl): Update to 1.41-6.
2017-08-03 17:53:54 +02:00
023aa8ff58
gnu: r-seqinr: Update to 3.4-5.
...
* gnu/packages/bioinformatics.scm (r-seqinr): Update to 3.4-5.
2017-08-03 17:53:54 +02:00
7150f1c30c
gnu: r-optparse: Update to 1.4.4.
...
* gnu/packages/bioinformatics.scm (r-optparse): Update to 1.4.4.
2017-08-03 17:53:53 +02:00
3f6ec083ec
gnu: r-bookdown: Update to 0.4.
...
* gnu/packages/bioinformatics.scm (r-bookdown): Update to 0.4.
2017-08-03 17:53:53 +02:00
75e6639f36
gnu: htseq: Use PyPI URI.
...
This is a follow-up to 92971d68ac
2017-08-03 21:08:13 +10:00
92971d68ac
gnu: htseq: Update to 0.9.1.
...
* gnu/packages/bioinformatics.scm (htseq): Update to 0.9.1.
[arguments]: Use python-3 by removing field.
[native-inputs]: Add 'python-cython'.
[propagated-inputs]: Use python3 numpy package.
[inputs]: Use python3 pysam package. Add 'python-matplotlib'.
(python2-htseq): New variable.
(clipper)[inputs]: Use it.
2017-08-03 21:02:30 +10:00
f1915a5dd0
gnu: r-deseq2: Update to 1.16.1.
...
* gnu/packages/bioinformatics.scm (r-deseq2): Update to 1.16.1.
2017-08-02 00:33:23 +02:00
fd215c2978
gnu: r-annotationforge: Update to 1.18.1.
...
* gnu/packages/bioinformatics.scm (r-annotationforge): Update to 1.18.1.
2017-08-02 00:33:07 +02:00
bd4a0bab5f
gnu: r-category: Update to 2.42.1.
...
* gnu/packages/bioinformatics.scm (r-category): Update to 2.42.1.
2017-08-02 00:32:46 +02:00
0ff478344b
gnu: r-biocstyle: Update to 2.4.1.
...
* gnu/packages/bioinformatics.scm (r-biocstyle): Update to 2.4.1.
2017-08-02 00:32:31 +02:00
9c4348d8c4
gnu: r-dnacopy: Update to 1.50.1.
...
* gnu/packages/bioinformatics.scm (r-dnacopy): Update to 1.50.1.
2017-08-02 00:32:11 +02:00
3ec25eb2a8
gnu: r-iranges: Update to 2.10.2.
...
* gnu/packages/bioinformatics.scm (r-iranges): Update to 2.10.2.
2017-08-02 00:31:46 +02:00
6252dd0f15
gnu: r-genomeinfodb: Update to 1.12.2.
...
* gnu/packages/bioinformatics.scm (r-genomeinfodb): Update to 1.12.2.
2017-08-02 00:31:28 +02:00
48f5d283b2
gnu: r-variantannotation: Update to 1.22.3.
...
* gnu/packages/bioinformatics.scm (r-variantannotation): Update to 1.22.3.
2017-08-02 00:31:08 +02:00
1b4738e23c
gnu: r-limma: Update to 3.32.5.
...
* gnu/packages/bioinformatics.scm (r-limma): Update to 3.32.5.
2017-08-02 00:30:49 +02:00
1898a7832f
gnu: r-biobase: Update to 2.36.2.
...
* gnu/packages/bioinformatics.scm (r-biobase): Update to 2.36.2.
2017-08-02 00:30:27 +02:00
62eb93a7d0
gnu: r-annotationdbi: Update to 1.38.2.
...
* gnu/packages/bioinformatics.scm (r-annotationdbi): Update to 1.38.2.
2017-08-02 00:28:32 +02:00
0c6494a1db
gnu: r-biomart: Update to 2.32.1.
...
* gnu/packages/bioinformatics.scm (r-biomart): Update to 2.32.1.
2017-08-02 00:28:16 +02:00
1ff74d074e
gnu: r-biocparallel: Update to 1.10.1.
...
* gnu/packages/bioinformatics.scm (r-biocparallel): Update to 1.10.1.
2017-08-02 00:27:57 +02:00
5077bc3e2e
gnu: r-biostrings: Update to 2.44.2.
...
* gnu/packages/bioinformatics.scm (r-biostrings): Update to 2.44.2.
2017-08-02 00:27:35 +02:00
adf5d0a0bc
gnu: r-delayedarray: Update to 0.2.7.
...
* gnu/packages/bioinformatics.scm (r-delayedarray): Update to 0.2.7.
2017-08-02 00:27:16 +02:00
f41150f13d
gnu: r-summarizedexperiment: Update to 1.6.3.
...
* gnu/packages/bioinformatics.scm (r-summarizedexperiment): Update to 1.6.3.
2017-08-02 00:26:55 +02:00
26760c80cd
gnu: r-genomicalignments: Update to 1.12.1.
...
* gnu/packages/bioinformatics.scm (r-genomicalignments): Update to 1.12.1.
2017-08-02 00:26:33 +02:00
15afa9bf8f
gnu: r-rtracklayer: Update to 1.36.4.
...
* gnu/packages/bioinformatics.scm (r-rtracklayer): Update to 1.36.4.
2017-08-02 00:26:00 +02:00
8cfaa9ab4e
gnu: r-genomicfeatures: Update to 1.28.4.
...
* gnu/packages/bioinformatics.scm (r-genomicfeatures): Update to 1.28.4.
2017-08-02 00:25:26 +02:00
9eb2714625
gnu: r-copywriter: Update to 2.8.1.
...
* gnu/packages/bioinformatics.scm (r-copywriter): Update to 2.8.1.
2017-08-02 00:25:00 +02:00
bfa0d1e773
gnu: r-sva: Update to 3.24.4.
...
* gnu/packages/bioinformatics.scm (r-sva): Update to 3.24.4.
2017-08-02 00:24:27 +02:00
aa9780daf9
Merge branch 'master' into core-updates
2017-08-01 23:42:28 +02:00
d931a4bbeb
gnu: metabat: Limit to x86_64 and i686 only.
...
* gnu/packages/bioinformatics.scm (metabat)[supported-systems]: New field.
2017-08-01 17:28:35 +03:00
a9085f0c5c
gnu: metabat: Update to 2.11.2.
...
* gnu/packages/bioinformatics.scm (metabat): Update to 2.11.2.
2017-07-29 22:37:47 +10:00
d3dce32216
gnu: metabat: Fix boost-related compilation issue.
...
Reported by Leo Famulari.
* gnu/packages/patches/metabat-fix-boost-issue.patch: New file.
* gnu/packages/bioinformatics.scm (metabat): Use it.
* gnu/local.mk (dist_patch_DATA): Add it.
2017-07-23 22:35:52 +10:00
f3f68a442c
gnu: metabat: Update to 2.11.1.
...
* gnu/packages/bioinformatics.scm (metabat): Update to 2.11.1.
[source]: Add patch to fix compilation.
[arguments]: Adjust regular expressions modifying 'SConstruct'.
* gnu/packages/patches/metabat-fix-compilation.patch: New file.
* gnu/local.mk (dist_patch_DATA): Add it.
2017-07-23 10:29:36 +10:00
897ab082b2
gnu: python-plastid: Update to 0.4.8.
...
* gnu/packages/bioinformatics.scm (python-plastid): Update to 0.4.8.
2017-07-23 10:29:36 +10:00
0620387a59
gnu: bcftools: Update to 1.5.
...
* gnu/packages/bioinformatics.scm (bcftools): Update to 1.5.
[origin]: Remove fix-makefile patch.
[arguments]: Add configure flags, add LIBS make flag. Do not delete
configure phase.
* gnu/packages/patches/bcftools-fix-makefile.patch: Remove file.
* gnu/local.mk (dist_patch_DATA): Remove it.
2017-07-23 10:29:36 +10:00
63fa0ffcd4
gnu: samtools: Update to 1.5.
...
* gnu/packages/bioinformatics.scm (samtools): Update to 1.5.
2017-07-23 10:29:36 +10:00
4fb6d1280e
gnu: htslib: Update to 1.5.
...
* gnu/packages/bioinformatics.scm (htslib): Update to 1.5.
2017-07-23 10:29:35 +10:00
60739965da
gnu: python-pysam: Update to 0.11.2.2.
...
* gnu/packages/bioinformatics.scm (python-pysam): Update to 0.11.2.2.
2017-07-23 10:29:35 +10:00
bca2c57658
gnu: bamm: Use htslib-1.3.
...
* gnu/packages/bioinformatics (htslib-1.3): New variable.
(bamm)[inputs]: Replace htslib with htslib-1.3.
2017-07-23 10:29:35 +10:00
98593f9f51
gnu: bcftools: Update to 1.4.1.
...
* gnu/packages/bioinformatics.scm (bcftools): Update to 1.4.1.
[arguments]: Move Makefile modifications from here ...
[source]: ... to added patch. Adjust patch for update to 1.4.
* gnu/packages/patches/bcftools-fix-makefile.patch: New file.
* gnu/local.mk (dist_patch_DATA): Register it.
2017-07-23 10:29:35 +10:00
4ab1644049
gnu: samtools: Update to 1.4.1.
...
* gnu/packages/bioinformatics.scm (samtools): Update to 1.4.1.
[arguments]: Add '--with-htslib=system' configure flag.
[inputs]: Add htslib.
2017-07-23 10:29:34 +10:00
a9e4a1e641
gnu: htslib: Update to 1.4.1.
...
* gnu/packages/bioinformatics.scm (htslib): Update to 1.4.1.
[inputs]: Add curl, openssl.
2017-07-23 10:29:34 +10:00
c842d42593
gnu: samtools: Use "modify-phases" syntax.
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* gnu/packages/bioinformatics.scm (samtools)[arguments]: Use "modify-phases"
syntax.
2017-07-23 10:29:34 +10:00
3a4b0b126b
gnu: r-s4vectors: Update to 0.14.3.
...
* gnu/packages/bioinformatics.scm (r-s4vectors): Update to 0.14.3.
2017-07-22 17:31:19 +02:00
a35a1e9c13
gnu: r-genomicranges: Update to 1.28.4.
...
* gnu/packages/bioinformatics.scm (r-genomicranges): Update to 1.28.4.
2017-07-22 17:22:07 +02:00
fd40857938
gnu: r-bsgenome-hsapiens-ucsc-hg19: Update hash.
...
* gnu/packages/bioinformatics.scm (r-bsgenome-hsapiens-ucsc-hg19)[source]:
Update hash because the tarball changed in place.
2017-07-19 14:39:37 +02:00
2324541bd0
gnu: sortmerna: Limit support to x86_64 and i686 only.
...
* gnu/packages/bioinformatics.scm (sortmerna)[supported-systems]: New field.
2017-07-19 14:37:47 +03:00
2805f9b2a0
gnu: raxml: Limit to x86_64 and i686 only.
...
* gnu/packages/bioinformatics.scm (raxml)[supported-systems]: New field.
2017-07-18 09:00:10 +03:00
06e372360e
gnu: bowtie: Use 'modify-phases'.
...
* gnu/packages/bioinformatics.scm (bowtie)[arguments]: Use 'modify-phases'
syntax.
2017-07-14 19:23:37 +10:00
d6e63cf31c
gnu: bowtie: Update to 2.3.2.
...
* gnu/packages/bioinformatics.scm (bowtie): Update to 2.3.2.
[inputs]: Add zlib.
2017-07-14 18:54:10 +10:00
fed7200862
gnu: deeptools: Update to 2.5.1.
...
* gnu/packages/bioinformatics.scm (deeptools): Update to 2.5.1.
[arguments]: Remove.
[native-inputs]: Use "python-" instead of "python2-" variants.
[inputs]: Likewise; add python-py2bit.
2017-07-09 17:07:27 +02:00
eb2200f3bd
gnu: Add python-py2bit.
...
* gnu/packages/bioinformatics.scm (python-py2bit): New variable.
2017-07-09 17:07:23 +02:00
4732e6ee84
gnu: blast+: Update to 2.6.0.
...
* gnu/packages/bioinformatics.scm (blast+): Update to 2.6.0.
[origin]: Remove bundled pcre. Add patch.
[arguments]: Replace paths in run_with_lock.c. Configure with pcre.
[inputs]: Add pcre, perl, python.
* gnu/packages/patches/blast+-fix-makefile.patch: New file.
* gnu/local.mk (dist_patch_DATA): Add it.
2017-07-08 12:05:59 +10:00
0a66c38764
Revert "gnu: blast+: Update to 2.6.0."
...
This reverts commit 18dea67dc3
2017-07-06 19:38:55 -04:00
ce7e361fa3
gnu: gemma: Fix building on non-Intel architectures.
...
* gnu/packages/patches/gemma-intel-compat.patch: New file.
* gnu/packages/bioinformatics.scm (gemma)[source]: Add patch.
[arguments]: Add NO_INTEL_COMPAT flag on non-Intel architectures.
* gnu/local.mk (dist_patch_DATA): Register patch.
2017-07-04 22:55:44 +03:00
a522517cdb
gnu: diamond: Update to 0.9.9.
...
* gnu/packages/bioinformatics.scm (diamond): Update to 0.9.9.
2017-07-04 19:59:01 +10:00
18dea67dc3
gnu: blast+: Update to 2.6.0.
...
* gnu/packages/bioinformatics.scm (blast+): Update to 2.6.0.
[origin]: Remove bundled pcre.
[arguments]: Replace paths in run_with_lock.c. Configure with pcre.
[inputs]: Add pcre, perl, python.
2017-07-04 19:58:42 +10:00
ba773f65f0
gnu: cd-hit: Update to 4.6.8.
...
* gnu/packages/bioinformatics.scm (cd-hit): Update to 4.6.8.
2017-07-01 10:49:37 +10:00
fd99d95b3f
gnu: bwa: Update to 0.7.15.
...
* gnu/packages/bioinformatics.scm (bwa): Update to 0.7.15.
2017-07-01 09:48:20 +10:00
7ceb0a83e3
gnu: Add f-seq.
...
* gnu/packages/bioinformatics.scm (f-seq): New variable.
2017-06-25 22:26:07 +02:00
dfc83eadaf
gnu: orfm: Update to 0.7.1.
...
* gnu/packages/bioinformatics.scm (orfm): Update to 0.7.1.
2017-06-24 14:46:46 +10:00
ab8d728144
gnu: orfm: Update to 0.7.0.
...
* gnu/packages/bioinformatics.scm (orfm): Update to 0.7.0.
2017-06-23 22:22:50 +10:00
94820951d6
gnu: Add kentutils.
...
* gnu/packages/bioinformatics.scm (kentutils): New variable.
2017-06-23 08:09:33 +02:00
c1dfe8c30b
gnu: python2-bx-python: Update to 0.7.3.
...
* gnu/packages/bioinformatics.scm (python2-bx-python): Update to 0.7.3.
2017-06-22 17:25:40 +02:00
148585c240
gnu: Move contents of zip module into compression module.
...
* gnu/packages/zip.scm (zip, unzip, zziplib, perl-zip): Move to...
* gnu/packages/compression.scm: ...here.
* gnu/packages/zip.scm: Delete file.
* gnu/local.mk (GNU_SYSTEM_MODULES): Unregister deleted file.
* po/packages/POTFILES.in: Unregister deleted file.
* gnu/packages/{audio, avr, bioinformatics, busybox, cdrom, ci, compression,
docbook, documentation, fonts, fpga, game-development, games, gl, gnome,
gnuzilla, graphics, guile, haskell, image, java, kodi, ldc, libreoffice,
markup, maths, mc, monitoring, music, php, pretty-print, python, scheme,
smalltalk, statistics, synergy, tex, textutils, video, web-browsers, xml,
zip}.scm, guix/build-system/{ant, font}.scm, guix/{download, packages}.scm:
Adapt module import.
2017-06-20 18:10:35 +05:30
0002be1d0b
gnu: diamond: Update to 0.9.8.
...
* gnu/packages/bioinformatics.scm (diamond): Update to 0.9.8.
2017-06-17 13:05:08 +10:00
a147fadd3b
gnu: tadbit: Fix typo in description.
...
* gnu/packages/bioinformatics.scm (tadbit)[description]: Fix typo.
2017-06-16 00:29:21 +02:00
07bf6929b9
gnu: gemma: Fix indentation.
...
* gnu/packages/bioinformatics.scm (gemma)[arguments]: Fix indentation.
2017-06-15 10:32:03 +03:00
2c9232ae69
gnu: gemma: Fix building on 32-bit architectures.
...
* gnu/packages/bioinformatics.scm (gemma)[arguments]: On 32-bit
architectures add 'FORCE_32BIT' flag.
2017-06-15 10:31:44 +03:00
8befd0940b
gnu: Add tadbit.
...
* gnu/packages/bioinformatics.scm (tadbit): New variable.
2017-06-09 03:32:23 +02:00
aa163424b2
gnu: Add imp.
...
* gnu/packages/bioinformatics.scm (imp): New variable.
2017-06-09 03:31:51 +02:00
282b01515b
gnu: Add phylip.
...
* gnu/packages/bioinformatics.scm (phylip): New variable.
2017-06-09 03:31:50 +02:00
3420c905cd
gnu: Add gess.
...
* gnu/packages/bioinformatics.scm (gess): New variable.
2017-06-09 03:31:50 +02:00
44f6c88909
gnu: Add trim-galore.
...
* gnu/packages/bioinformatics.scm (trim-galore): New variable.
2017-06-09 03:31:50 +02:00
b8fffd3a53
gnu: Add ritornello.
...
* gnu/packages/bioinformatics.scm (ritornello): New variable.
2017-06-09 03:31:50 +02:00
f69ff11af7
gnu: diamond: Update to 0.9.6.
...
* gnu/packages/bioinformatics.scm (diamond): Update to 0.9.6.
2017-06-08 09:39:23 +10:00
b9a601d9db
gnu: Add kaiju.
...
* gnu/packages/bioinformatics.scm (kaiju): New variable.
2017-06-02 12:38:23 +02:00
0d2b2fd4f4
gnu: diamond: Update to 0.9.3.
...
* gnu/packages/bioinformatics.scm (diamond): Update to 0.9.3.
2017-05-28 21:06:06 -04:00
ca40d4e7c5
gnu: diamond: Update to 0.9.2.
...
* gnu/packages/bioinformatics.scm (diamond): Update to 0.9.2.
2017-05-27 22:03:00 -04:00
b608765a2c
gnu: diamond: Update to 0.9.1.
...
* gnu/packages/bioinformatics.scm (diamond): Update to 0.9.1.
2017-05-22 21:17:41 +01:00
296b3c631c
gnu: Add r-edaseq.
...
* gnu/packages/bioinformatics.scm (r-edaseq): New variable.
2017-05-22 18:54:59 +02:00
7b46532779
gnu: Add r-deseq.
...
* gnu/packages/bioinformatics.scm (r-deseq): New variable.
2017-05-22 18:54:59 +02:00
d4b83651d1
gnu: Add r-aroma-light.
...
* gnu/packages/bioinformatics.scm (r-aroma-light): New variable.
2017-05-22 18:54:58 +02:00
74297231be
gnu: fraggenescan: Update to 1.30.
...
* gnu/packages/bioinformatics.scm (fraggenescan): Update to 1.30.
[arguments]: Update patching of paths, install procedure. Add new test
case.
2017-05-22 11:44:20 +01:00
7569613076
gnu: roary: Update to 3.8.2.
...
* gnu/packages/bioinformatics.scm (roary): Update to 3.8.2.
2017-05-22 11:44:20 +01:00
3cbfc149c3
gnu: taxtastic: Update to 0.6.4.
...
* gnu/packages/bioinformatics.scm (taxtastic): Update to 0.6.4.
[source]: Use PyPI URI.
2017-05-22 11:44:19 +01:00
b458413721
gnu: r-mutationalpatterns: Update to 1.2.1.
...
* gnu/packages/bioinformatics.scm (r-mutationalpatterns): Update to 1.2.1.
2017-05-22 09:44:08 +02:00
ef81341f0e
gnu: diamond: Update to 0.9.0.
...
* gnu/packages/bioinformatics.scm (diamond): Update to 0.9.0.
[license]: Change to AGPL3+.
2017-05-21 16:08:03 +01:00
88682c9a72
gnu: fasttree: Update to 2.1.10.
...
* gnu/packages/bioinformatics.scm (fasttree): Update to 2.1.10.
2017-05-21 15:42:08 +01:00
abc08cbae6
gnu: python-biom-format: Update to 2.1.6.
...
* gnu/packages/bioinformatics.scm (python-biom-format): Update to 2.1.6.
[propagated-inputs]: Add python-pandas.
2017-05-21 15:42:08 +01:00
2b18ad054c
gnu: Add gemma.
...
* gnu/packages/bioinformatics.scm (gemma): New variable.
Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2017-05-18 14:22:03 +02:00
2252f087d4
gnu: guile-json: Rename "guile2.2-json" to "guile-json".
...
* gnu/packages/guile.scm (guile-json)[native-inputs]: Change GUILE-2.0
to GUILE-2.2.
(guile2.2-json): Define using 'deprecated-package'.
(guile2.0-json): New variable.
* gnu/packages/bioinformatics.scm (rcas-web)[inputs]: Update accordingly.
* gnu/packages/ci.scm (cuirass)[inputs]: Likewise.
* gnu/packages/package-management.scm (guix)[inputs]: Likewise.
2017-05-13 22:25:22 +02:00
c033f5d6b5
gnu: Add pplacer.
...
* gnu/packages/bioinformatics.scm (pplacer, pplacer-scripts): New
variables.
2017-05-10 22:13:55 +02:00
ad0ae297d4
gnu: Add taxtastic.
...
* gnu/packages/bioinformatics.scm (taxtastic): New variable.
2017-05-10 22:13:55 +02:00
2f3108ad03
gnu: Avoid circular dependencies by Perl license.
...
* guix/licenses.scm (perl-license): New variable.
* gnu/packages/bioinformatics.scm: Change (package-license perl) to perl-license.
* gnu/packages/compression.scm: Same.
* gnu/packages/databases.scm: Same.
* gnu/packages/gd.scm: Same.
* gnu/packages/language.scm: Same.
* gnu/packages/libevent.scm: Same.
* gnu/packages/mail.scm: Same.
* gnu/packages/messaging.scm: Same.
* gnu/packages/ncurses.scm: Same.
* gnu/packages/networking.scm: Same.
* gnu/packages/photo.scm: Same.
* gnu/packages/tcl.scm: Same.
* gnu/packages/tex.scm: Same.
* gnu/packages/tls.scm: Same.
* gnu/packages/web.scm: Same.
* gnu/packages/wm.scm: Same.
* gnu/packages/xml.scm: Same.
* gnu/packages/xorg.scm: Same.
* gnu/packages/zip.scm: Same.
Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2017-05-02 23:41:14 +02:00
f432254237
gnu: vcftools: Update to 0.1.15.
...
* gnu/packages/bioinformatics.scm (vcftools): Update to 0.1.15.
2017-05-01 16:18:39 +02:00
90f83099e8
gnu: r-genomeinfodbdata: Fix source url.
...
* gnu/packages/bioinformatics.scm (r-genomeinfodbdata)[source]: Use
source uri and not bioconductor-uri shortener.
2017-04-29 22:53:43 +03:00
524bfe2dbf
gnu: r-msnid: Update to 1.10.0.
...
* gnu/packages/bioinformatics.scm (r-msnid): Update to 1.10.0.
2017-04-28 11:05:42 +02:00
82359c72cb
gnu: r-msnbase: Update to 2.2.0.
...
* gnu/packages/bioinformatics.scm (r-msnbase): Update to 2.2.0.
2017-04-28 11:05:41 +02:00
5bfa6e090d
gnu: r-pcamethods: Update to 1.68.0.
...
* gnu/packages/bioinformatics.scm (r-pcamethods): Update to 1.68.0.
2017-04-28 11:05:40 +02:00
63bf2102cd
gnu: r-mzid: Update to 1.14.0.
...
* gnu/packages/bioinformatics.scm (r-mzid): Update to 1.14.0.
2017-04-28 11:05:38 +02:00
60c08b2ff4
gnu: r-vsn: Update to 3.44.0.
...
* gnu/packages/bioinformatics.scm (r-vsn):
[source]: Update to 3.44.0,
[propagated-inputs]: Add r-hexbin.
2017-04-28 11:05:37 +02:00
bd3cc4cc52
gnu: r-affy: Update to 1.54.0.
...
* gnu/packages/bioinformatics.scm (r-affy): Update to 1.54.0.
2017-04-28 11:05:37 +02:00
71abcc4cbf
gnu: r-affyio: Update to 1.46.0.
...
* gnu/packages/bioinformatics.scm (r-affyio): Update to 1.46.0.
2017-04-28 11:05:36 +02:00
e440ad6d4f
gnu: r-mzr: Update to 2.10.0.
...
* gnu/packages/bioinformatics.scm (r-mzr): Update to 2.10.0.
2017-04-28 11:05:35 +02:00
5b1337cc60
gnu: r-protgenerics: Update to 1.8.0.
...
* gnu/packages/bioinformatics.scm (r-protgenerics): Update to 1.8.0.
2017-04-28 11:05:33 +02:00
1d09d017db
gnu: r-sva: Update to 3.24.0.
...
* gnu/packages/bioinformatics.scm (r-sva): Update to 3.24.0.
2017-04-28 11:05:20 +02:00
d52d2d623a
gnu: r-copywriter: Update to 2.8.0.
...
* gnu/packages/bioinformatics.scm (r-copywriter): Update to 2.8.0.
2017-04-28 11:05:19 +02:00
7d72f2a803
gnu: r-chipseq: Update to 1.26.0.
...
* gnu/packages/bioinformatics.scm (r-chipseq): Update to 1.26.0.
2017-04-28 11:05:18 +02:00
04049a5f2c
gnu: r-rhdf5: Update to 2.20.0.
...
* gnu/packages/bioinformatics.scm (r-rhdf5): Update to 2.20.0.
2017-04-28 11:05:18 +02:00
ff58a1af98
gnu: r-tximport: Update to 1.4.0.
...
* gnu/packages/bioinformatics.scm (r-tximport): Update to 1.4.0.
2017-04-28 11:05:16 +02:00
cf4ac4e465
gnu: r-mutationalpatterns: Update to 1.2.0.
...
* gnu/packages/bioinformatics.scm (r-mutationalpatterns):
[source]: Update to 1.2.0,
[propagated-inputs]: Add r-bsgenome-hsapiens-1000genomes-hs37d5,
r-bsgenome-hsapiens-ucsc-hg19.
2017-04-28 11:05:13 +02:00
ccd2aade98
gnu: r-bamsignals: Update to 1.8.0.
...
* gnu/packages/bioinformatics.scm (r-bamsignals): Update to 1.8.0.
2017-04-28 11:05:12 +02:00
37631ddc28
gnu: r-rhtslib: Update to 1.8.0.
...
* gnu/packages/bioinformatics.scm (r-rhtslib): Update to 1.8.0.
2017-04-28 11:05:11 +02:00
8444f6067a
gnu: r-zlibbioc: Update to 1.22.0.
...
* gnu/packages/bioinformatics.scm (r-zlibbioc): Update to 1.22.0.
2017-04-28 11:05:10 +02:00
a7b90ea990
gnu: r-motifrg: Update to 1.20.0.
...
* gnu/packages/bioinformatics.scm (r-motifrg): Update to 1.20.0.
2017-04-28 11:05:09 +02:00
0fce7d9be5
gnu: r-seqlogo: Update to 1.42.0.
...
* gnu/packages/bioinformatics.scm (r-seqlogo): Update to 1.42.0.
2017-04-28 11:05:08 +02:00
3ae82c8dfe
gnu: r-genomation: Update to 1.8.0.
...
* gnu/packages/bioinformatics.scm (r-genomation): Update to 1.8.0.
2017-04-28 11:05:07 +02:00
08b9224d2d
gnu: r-seqpattern: Update to 1.8.0.
...
* gnu/packages/bioinformatics.scm (r-seqpattern): Update to 1.8.0.
2017-04-28 11:05:06 +02:00
5999359f56
gnu: r-impute: Update to 1.50.0.
...
* gnu/packages/bioinformatics.scm (r-impute): Update to 1.50.0.
2017-04-28 11:05:06 +02:00
c54a702a28
gnu: r-bsgenome: Update to 1.44.0.
...
* gnu/packages/bioinformatics.scm (r-bsgenome): Update to 1.44.0.
2017-04-28 11:05:04 +02:00
6e70b6d63c
gnu: r-topgo: Update to 2.28.0.
...
* gnu/packages/bioinformatics.scm (r-topgo): Update to 2.28.0.
2017-04-28 11:05:03 +02:00
56373771b3
gnu: r-graph: Update to 1.54.0.
...
* gnu/packages/bioinformatics.scm (r-graph): Update to 1.54.0.
2017-04-28 11:05:02 +02:00
5d0301a339
gnu: r-genomicfeatures: Update to 1.28.0.
...
* gnu/packages/bioinformatics.scm (r-genomicfeatures): Update to 1.28.0.
2017-04-28 11:05:01 +02:00
2ea7155b04
gnu: r-rtracklayer: Update to 1.36.0.
...
* gnu/packages/bioinformatics.scm (r-rtracklayer): Update to 1.36.0.
2017-04-28 11:05:00 +02:00
5f16d1e47d
gnu: r-genomicalignments: Update to 1.12.0.
...
* gnu/packages/bioinformatics.scm (r-genomicalignments): Update to 1.12.0.
2017-04-28 11:04:59 +02:00
d006ee31af
gnu: r-summarizedexperiment: Update to 1.6.0.
...
* gnu/packages/bioinformatics.scm (r-summarizedexperiment):
[source]: Update to 1.6.0,
[propagated-inputs]: Add r-delayedarray.
2017-04-28 11:04:58 +02:00
6bf5543be8
gnu: r-rsamtools: Update to 1.28.0.
...
* gnu/packages/bioinformatics.scm (r-rsamtools): Update to 1.28.0.
2017-04-28 11:04:57 +02:00
3ed41af6b5
gnu: r-biostrings: Update to 2.44.0.
...
* gnu/packages/bioinformatics.scm (r-biostrings): Update to 2.44.0.
2017-04-28 11:04:56 +02:00
502da6ffc7
gnu: r-biocparallel: Update to 1.10.0.
...
* gnu/packages/bioinformatics.scm (r-biocparallel): Update to 1.10.0.
2017-04-28 11:04:55 +02:00
78e7a589c9
gnu: r-biomart: Update to 2.32.0.
...
* gnu/packages/bioinformatics.scm (r-biomart): Update to 2.32.0.
2017-04-28 11:04:47 +02:00
aafaab22d3
gnu: r-annotationdbi: Update to 1.38.0.
...
* gnu/packages/bioinformatics.scm (r-annotationdbi): Update to 1.38.0.
2017-04-28 11:04:46 +02:00
b2fff403c8
gnu: r-biobase: Update to 2.36.0.
...
* gnu/packages/bioinformatics.scm (r-biobase): Update to 2.36.0.
2017-04-28 11:04:44 +02:00
1859712bef
gnu: r-genomicranges: Update to 1.28.0.
...
* gnu/packages/bioinformatics.scm (r-genomicranges): Update to 1.28.0.
2017-04-28 11:04:42 +02:00
17a02f5149
gnu: r-xvector: Update to 0.16.0.
...
* gnu/packages/bioinformatics.scm (r-xvector): Update to 0.16.0.
2017-04-28 11:04:42 +02:00
abf5a14e11
gnu: r-limma: Update to 3.32.0.
...
* gnu/packages/bioinformatics.scm (r-limma): Update to 3.32.0.
2017-04-28 11:04:41 +02:00
d2d7af9832
gnu: r-variantannotation: Update to 1.22.0.
...
* gnu/packages/bioinformatics.scm (r-variantannotation): Update to 1.22.0.
2017-04-28 11:04:40 +02:00
00ffd55fa1
gnu: r-edger: Update to 3.18.0.
...
* gnu/packages/bioinformatics.scm (r-edger): Update to 3.18.0.
2017-04-28 11:04:39 +02:00
38b99ccc57
gnu: r-genomeinfodb: Update to 1.12.0.
...
* gnu/packages/bioinformatics.scm (r-genomeinfodb): [source] Update to 1.12.0,
[propagated-inputs]: Add r-genomeinfodbdata.
2017-04-28 11:04:37 +02:00
7d9ab5d920
gnu: r-iranges: Update to 2.10.0.
...
* gnu/packages/bioinformatics.scm (r-iranges): Update to 2.10.0.
2017-04-28 11:04:36 +02:00
f1f380185b
gnu: r-s4vectors: Update to 0.14.0.
...
* gnu/packages/bioinformatics.scm (r-s4vectors): Update to 0.14.0.
2017-04-28 11:04:34 +02:00
9b02d49cb0
gnu: r-dnacopy: Update to 1.50.0.
...
* gnu/packages/bioinformatics.scm (r-dnacopy): Update to 1.50.0.
2017-04-28 11:04:33 +02:00
2e11beec48
gnu: r-bioccheck: Update to 1.12.0.
...
* gnu/packages/bioinformatics.scm (r-bioccheck): Update to 1.12.0.
2017-04-28 11:04:32 +02:00
3bef24c968
gnu: r-biocstyle: Update to 2.4.0.
...
* gnu/packages/bioinformatics.scm (r-biocstyle): [source] Update to 2.4.0.
[propagated-inputs]: Add r-bookdown, r-knitr, r-rmarkdown, r-yaml.
2017-04-28 11:04:31 +02:00
68eac34974
gnu: r-biocviews: Update to 1.44.0.
...
* gnu/packages/bioinformatics.scm (r-biocviews): Update to 1.44.0.
2017-04-28 11:04:30 +02:00
3bef15286a
gnu: r-biocinstaller: Update to 1.26.0.
...
* gnu/packages/bioinformatics.scm (r-biocinstaller): Update to 1.26.0.
2017-04-28 11:04:28 +02:00
28a5b3f2c6
gnu: r-biocgenerics: Update to 0.22.0.
...
* gnu/packages/bioinformatics.scm (r-biocgenerics): Update to 0.22.0.
2017-04-28 11:04:26 +02:00
795a604526
gnu: r-grohmm: Update to 1.10.0.
...
* gnu/packages/bioinformatics.scm (r-grohmm): Update to 1.10.0.
2017-04-28 11:04:25 +02:00
026dc7e4fc
gnu: r-systempiper: Update to 1.10.0.
...
* gnu/packages/bioinformatics.scm (r-systempiper): Update to 1.10.0.
2017-04-28 11:04:24 +02:00
34c276f761
gnu: r-shortread: Update to 1.34.0.
...
* gnu/packages/bioinformatics.scm (r-shortread): Update to 1.34.0.
2017-04-28 11:04:22 +02:00
9511773423
gnu: r-gostats: Update to 2.42.0.
...
* gnu/packages/bioinformatics.scm (r-gostats): Update to 2.42.0.
2017-04-28 11:04:21 +02:00
ca0289aee7
gnu: r-category: Update to 2.42.0.
...
* gnu/packages/bioinformatics.scm (r-category): Update to 2.42.0.
2017-04-28 11:04:20 +02:00
c584a07ffd
gnu: r-gseabase: Update to 1.38.0.
...
* gnu/packages/bioinformatics.scm (r-gseabase): Update to 1.38.0.
2017-04-28 11:04:19 +02:00
8ab6f241ea
gnu: r-rbgl: Update to 1.52.0.
...
* gnu/packages/bioinformatics.scm (r-rbgl): Update to 1.52.0.
2017-04-28 11:04:16 +02:00
46972a4427
gnu: r-annotationforge: Update to 1.18.0.
...
* gnu/packages/bioinformatics.scm (r-annotationforge): Update to 1.18.0.
2017-04-28 11:04:12 +02:00
3ae74e451c
gnu: r-deseq2: Update to 1.16.0.
...
* gnu/packages/bioinformatics.scm (r-deseq2): Update to 1.16.0.
2017-04-28 11:04:09 +02:00
b5bc3a3963
gnu: r-genefilter: Update to 1.58.0.
...
* gnu/packages/bioinformatics.scm (r-genefilter): Update to 1.58.0.
2017-04-28 11:04:06 +02:00
97a50e4f34
gnu: r-geneplotter: Update to 1.54.0.
...
* gnu/packages/bioinformatics.scm (r-geneplotter): Update to 1.54.0.
2017-04-28 11:03:59 +02:00
dbab99b6d2
gnu: r-annotate: Update to 1.54.0.
...
* gnu/packages/bioinformatics.scm (r-annotate): Update to 1.54.0.
2017-04-28 11:03:47 +02:00
ffef27f3d2
gnu: Add r-genomeinfodbdata.
...
* gnu/packages/bioinformatics.scm (r-genomeinfodbdata): New variable.
2017-04-28 10:17:06 +02:00
71e34e6b5b
gnu: Add r-delayedarray.
...
* gnu/packages/bioinformatics.scm (r-delayedarray): New variable.
2017-04-28 10:15:12 +02:00
2abfc5b827
gnu: Add r-bookdown.
...
* gnu/packages/bioinformatics.scm (r-bookdown): New variable.
2017-04-28 10:09:31 +02:00
31c374e081
gnu: python-pysam: Disable tests.
...
* gnu/packages/bioinformatics.scm (python-pysam): Disable tests.
2017-04-25 14:05:59 +02:00
b2955e224e
gnu: python-pysam: Fix tests, again.
...
* gnu/packages/bioinformatics.scm (python-pysam)[arguments]: Run nosetests
explicitly with a single process.
2017-04-24 18:46:28 +02:00
c136240efc
gnu: diamond: Enable building on all architectures.
...
* gnu/packages/bioinformatics.scm (diamond)[supported-systems]: Remove
field.
2017-04-24 19:30:10 +03:00
1a84edeb0b
gnu: r-seqminer: Update to 5.9.
...
* gnu/packages/bioinformatics.scm (r-seqminer): Update to 5.9.
2017-04-22 23:30:31 +02:00
a7d12a9e71
gnu: proteinortho: Update to 5.16.
...
* gnu/packages/bioinformatics.scm (proteinortho): Update to 5.16.
2017-04-21 23:03:56 +10:00
37199768e8
gnu: diamond: Update to 0.8.38.
...
* gnu/packages/bioinformatics.scm (diamond): Update to 0.8.38.
2017-04-21 23:03:55 +10:00
d1e4ad1b02
gnu: Fix typos in descriptions.
...
* gnu/packages/admin.scm (di)[description]: Likewise.
* gnu/packages/bioinformatics.scm (r-annotate)[description]: Likewise.
* gnu/packages/datastructures.scm (sparsehash)[description]: Likewise.
* gnu/packages/dns.scm (knot)[description]: Likewise.
* gnu/packages/emacs.scm (emacs-idle-highlight)[synopsis, description]:
Likewise.
* gnu/packages/gnome.scm (libpeas)[description]: Likewise.
* gnu/packages/gtk.scm (python2-pygtk)[description]: Likewise.
* gnu/packages/kde-frameworks.scm (kactivities)[description]: Fix typo.
* gnu/packages/libevent.scm (perl-anyevent)[description]: Likewise.
* gnu/packages/machine-learning.scm (ghmm)[description]: Likewise.
* gnu/packages/mail.scm (mlmmj)[description]: Likewise.
* gnu/packages/maths.scm (vc)[description]: Likewise.
* gnu/packages/music.scm (gx-super-fuzz-lv2)[description]: Likewise.
* gnu/packages/networking.scm (nload)[description]: Likewise.
* gnu/packages/python.scm (python-execnet)[description]: Likewise.
* gnu/packages/terminals.scm (tilda)[description]: Likewise.
* gnu/packages/python.scm (python-execnet, python-tables)
(python2-coverage-test-runner, python2-rope)[description]: Likewise.
2017-04-17 02:04:08 +02:00
88eb119f95
gnu: mafft: Update to 7.310.
...
* gnu/packages/bioinformatics.scm (mafft): Update to 7.310.
2017-04-14 15:19:37 +10:00
e9e0fab079
gnu: raxml: Update to 8.2.10.
...
* gnu/packages/bioinformatics.scm (raxml): Update to 8.2.10.
2017-04-09 21:44:14 +10:00
6acdff5875
gnu: r-rsamtools: Update to 1.26.2.
...
* gnu/packages/bioinformatics.scm (r-rsamtools): Update to 1.26.2.
2017-04-09 13:34:53 +02:00
dc8ebe43af
gnu: r-biocparallel: Update to 1.8.2.
...
* gnu/packages/bioinformatics.scm (r-biocparallel): Update to 1.8.2.
2017-04-09 13:34:53 +02:00
1d65b5379b
gnu: r-vegan: Update to 2.4-3.
...
* gnu/packages/bioinformatics.scm (r-vegan): Update to 2.4-3.
[arguments]: Remove build phase "revert-test-deletion".
[native-inputs]: Remove "r-vegan-delete-tests-patch".
2017-04-08 10:25:50 +02:00
37982693ca
gnu: vsearch: Update to 2.4.3.
...
* gnu/packages/bioinformatics.scm (vsearch): Update to 2.4.3.
2017-04-07 21:35:07 +10:00
e18c731ba0
gnu: r-seqinr: Update to 3.3-6.
...
* gnu/packages/bioinformatics.scm (r-seqinr): Update to 3.3-6.
2017-04-06 14:39:22 +02:00
0685fe3c86
gnu: r-rcpparmadillo: Update to 0.7.700.0.0.
...
* gnu/packages/statistics.scm (r-rcpparmadillo): Update to 0.7.700.0.0.
[source]: Do not delete bundled armadillo sources, because upstream no longer
hosts previous versions.
[propagated-inputs]: Remove "armadillo-for-rcpparmadillo".
[arguments]: Remove because we no longer need to link with the armadillo
library.
* gnu/packages/bioinformatics.scm (r-deseq2)[arguments]: Remove because we no
longer need to link with armadillo library.
2017-04-06 14:39:22 +02:00
a3656b11d2
gnu: r-annotationforge: Update to 1.16.1.
...
* gnu/packages/bioinformatics.scm (r-annotationforge): Update to 1.16.1.
2017-04-06 14:39:22 +02:00
e0d7b31820
gnu: r-shortread: Update to 1.32.1.
...
* gnu/packages/bioinformatics.scm (r-shortread): Update to 1.32.1.
2017-04-06 14:39:21 +02:00
2cea968e41
gnu: r-s4vectors: Update to 0.12.2.
...
* gnu/packages/bioinformatics.scm (r-s4vectors): Update to 0.12.2.
2017-04-06 14:39:21 +02:00
7d05eb2dcc
gnu: r-iranges: Update to 2.8.2.
...
* gnu/packages/bioinformatics.scm (r-iranges): Update to 2.8.2.
2017-04-06 14:39:21 +02:00
e89cf15091
gnu: r-variantannotation: Update to 1.20.3.
...
* gnu/packages/bioinformatics.scm (r-variantannotation): Update to 1.20.3.
2017-04-06 14:39:21 +02:00
3506a62762
gnu: r-limma: Update to 3.30.13.
...
* gnu/packages/bioinformatics.scm (r-limma): Update to 3.30.13.
2017-04-06 14:39:21 +02:00
4cd4721dbb
gnu: r-genomicranges: Update to 1.26.4.
...
* gnu/packages/bioinformatics.scm (r-genomicranges): Update to 1.26.4.
2017-04-06 14:39:20 +02:00
69b356efce
gnu: r-annotationdbi: Update to 1.36.2.
...
* gnu/packages/bioinformatics.scm (r-annotationdbi): Update to 1.36.2.
2017-04-06 14:39:20 +02:00
5cc3b7a548
gnu: r-genomicalignments: Update to 1.10.1.
...
* gnu/packages/bioinformatics.scm (r-genomicalignments): Update to 1.10.1.
2017-04-06 14:39:20 +02:00
25d8854723
gnu: r-rtracklayer: Update to 1.34.2.
...
* gnu/packages/bioinformatics.scm (r-rtracklayer): Update to 1.34.2.
2017-04-06 14:39:20 +02:00
9ce6cb082e
gnu: r-genomicfeatures: Update to 1.26.4.
...
* gnu/packages/bioinformatics.scm (r-genomicfeatures): Update to 1.26.4.
2017-04-06 14:39:20 +02:00
57ac1d2f03
gnu: r-seqminer: Update to 5.7.
...
* gnu/packages/bioinformatics.scm (r-seqminer): Update to 5.7.
2017-04-06 14:39:19 +02:00
e8bec95e69
gnu: r-maldiquant: Update to 1.16.2.
...
* gnu/packages/bioinformatics.scm (r-maldiquant): Update to 1.16.2.
2017-04-06 14:39:19 +02:00
4cd07e487e
gnu: r-genomeinfodb: Update to 1.10.3.
...
* gnu/packages/bioinformatics.scm (r-genomeinfodb): Update to 1.10.3.
[propagated-inputs]: Add "r-rcurl".
2017-04-06 14:39:11 +02:00
acbeb2d56b
gnu: r-xvector: Update to 0.14.1.
...
* gnu/packages/bioinformatics.scm (r-xvector): Update to 0.14.1.
2017-04-06 14:39:11 +02:00
da250f733a
gnu: r-bioccheck: Update to 1.10.1.
...
* gnu/packages/bioinformatics.scm (r-bioccheck): Update to 1.10.1.
[propagated-inputs]: Remove "r-knitr" and "r-devtools".
2017-04-06 14:39:11 +02:00
1108a920bd
gnu: sra-tools: Fix glibc naming conflict.
...
* gnu/packages/bioinformatics.scm (sra-tools)[arguments]: Add build phase
"patch-away-glibc-conflict" to fix a definition conflict with glibc 2.25.
2017-04-05 18:06:51 +02:00
beebe43176
gnu: sra-tools: Use "modify-phases" syntax.
...
* gnu/packages/bioinformatics.scm (sra-tools)[arguments]: Use "modify-phases"
syntax.
2017-04-05 18:06:51 +02:00
fc5b12879f
gnu: diamond: Update to 0.8.37.
...
* gnu/packages/bioinformatics.scm (diamond): Update to 0.8.37.
2017-04-05 22:49:01 +10:00
7bf837fd43
gnu: Use HTTPS URLs for GitHub home-pages.
...
* gnu/packages/bioinformatics.scm, gnu/packages/emacs.scm,
gnu/packages/haskell.scm, gnu/packages/libffi.scm, gnu/packages/lisp.scm,
gnu/packages/ocaml.scm, gnu/packages/openstack.scm, gnu/packages/python.scm,
gnu/packages/ruby.scm, gnu/packages/shells.scm, gnu/packages/statistics.scm,
gnu/packages/xdisorg.scm: Use HTTPS URLs for all packages with a home-page on
GitHub.
2017-04-02 20:00:51 -04:00
cf1d581464
gnu: khmer: Build with gcc-4.
...
* gnu/packages/bioinformatics.scm (khmer)[inputs]: Add gcc-4.9.
2017-04-02 10:14:17 +10:00
84157bb8bf
Merge branch 'master' into core-updates
...
Most conflicts are from 6fd52309b8
2017-03-30 22:59:53 +02:00
fa702e1a29
gnu: discrover: Add missing includes.
...
* gnu/packages/bioinformatics.scm (discrover)[arguments]: Add build phase
"add-missing-includes" to include "random" headers.
2017-03-30 10:35:54 +02:00
0d2c0562b8
gnu: stringtie: Remove typedef conflict.
...
* gnu/packages/bioinformatics.scm (stringtie)[arguments]: Remove conflicting
typedef in a new build phase "remove-duplicate-typedef".
2017-03-30 10:35:53 +02:00
e1f02f92e9
Replace (compose not PROC) with simpler idioms.
...
* gnu/packages/bioinformatics.scm (python-pysam)[arguments] <check>:
Use (negate proc) instead of (compose not proc).
* guix/import/cran.scm (recursive-import): Likewise.
* guix/import/elpa.scm (filter-dependencies): Use 'remove' instead of
'(filter (compose not proc) ...)'.
2017-03-28 22:15:44 +02:00
939b6b113b
gnu: star: Update to 2.5.3a.
...
* gnu/packages/bioinformatics.scm (star): Update to 2.5.3a.
2017-03-23 11:21:08 +01:00
54262c5435
gnu: python-pysam: Run tests in parallel.
...
* gnu/packages/bioinformatics.scm (python-pysam)[arguments]: Run nose tests in
parallel.
2017-03-22 12:33:28 +01:00
71dbf592c4
gnu: python-pysam: Run tests before installation.
...
* gnu/packages/bioinformatics.scm (python-pysam)[arguments]: Adjust check
phase to be run before installation.
2017-03-22 12:33:28 +01:00
879b521cd0
gnu: python-pysam: Update to 0.10.0.
...
* gnu/packages/bioinformatics.scm (python-pysam): Update to 0.10.0.
2017-03-22 12:33:24 +01:00
f6396d862f
gnu: Rename "guile-next" to "guile".
...
* gnu/packages/guile.scm (guile-next): Rename to...
(guile-2.2): ... this. Update users.
[name]: Change to "guile".
[synopsis]: Remove.
[properties]: Remove 'upstream-name', 'ftp-server', and
'ftp-directory'.
* gnu/packages/bioinformatics.scm (rcas-web): Update accordingly.
* gnu/packages/tls.scm (gnutls/guile-2.2): Likewise.
* tests/guix-build.sh: Use 'guile@2.2' instead of 'guile-next'.
* doc/guix.texi (Package Transformation Options): Update examples that
referred to "guile-next".
2017-03-19 18:14:22 +01:00
2d7c4ae3ee
gnu: r: Rename to r-minimal.
...
* gnu/packages/statistics.scm (r): Rename to...
(r-minimal): ...this new variable.
(r-with-recommended-packages): Rename to...
(r): ...this.
* guix/build-system/r.scm (default-r): Reference r-minimal.
* gnu/packages/emacs.scm (emacs-ess)[inputs],
gnu/packages/machine-learning.scm (shogun)[inputs],
gnu/packages/python.scm (python-rpy2)[inputs],
gnu/packages/bioinformatics.scm (ribotaper)[inputs],
(couger)[propagated-inputs],
(roary)[inputs],
(rsem)[inputs],
(rcas-web)[inputs]: Change "r" to "r-minimal".
2017-03-17 10:14:02 +01:00
aeb64f3cb2
gnu: r: Do not build recommended packages.
...
* gnu/packages/statistics.scm (r)[arguments]: Rename phase
"build-recommended-packages-reproducibly" to "build-reproducibly"; add
configure flag "--without-recommended-packages".
* guix/import/cran.scm (default-r-packages): Remove recommended packages.
* gnu/packages/python.scm (python-rpy2)[inputs]: Add r-survival.
* gnu/packages/bioinformatics.scm (r-ape)[propagated-inputs]: Add r-lattice
and r-nlme.
(r-vegan)[propagated-inputs]: Add r-mass.
(r-genefilter)[propagated-inputs]: Add r-survival.
(r-grohmm)[propagated-inputs]: Add r-mass.
(r-bioccheck)[propagated-inputs]: Add r-codetools.
(r-summarizedexperiment)[propagated-inputs]: Add r-matrix.
(r-topgo)[propagated-inputs]: Add r-lattice.
(r-sva)[propagated-inputs]: Add r-mgcv.
(r-raremetals2)[propagated-inputs]: Add r-mass.
(r-vsn)[propagated-inputs]: Add r-lattice.
(r-pcamethods)[propagated-inputs]: Add r-mass.
* gnu/packages/bioinformatics.scm (r-ggplot2)[propagated-inputs]: Add r-mass.
(r-locfit)[propagated-inputs]: Add r-lattice.
(r-coda)[propagated-inputs]: Add r-lattice.
(r-irlba)[propagated-inputs]: Add r-matrix.
(r-glmnet)[propagated-inputs]: Add r-matrix.
(r-e1071)[propagated-inputs]: Add r-class.
(r-spams)[propagated-inputs]: Add r-lattice and r-matrix.
(r-hmisc)[propagated-inputs]: Add r-cluster, r-foreign, r-lattice, r-nnet, and
r-rpart.
(r-zoo)[propagated-inputs]: Add r-lattice.
(r-mixtools)[propagated-inputs]: Add r-boot and r-mass.
(r-flexmix)[propagated-inputs]: Add r-lattice and r-nnet.
(r-prabclus)[propagated-inputs]: Add r-mass.
(r-fpc)[propagated-inputs]: Add r-class, r-cluster, and r-mass.
(r-rcppeigen)[propagated-inputs]: Add r-matrix.
(r-matrixmodels)[propagated-inputs]: Add r-matrix.
(r-lme4)[propagated-inputs]: Add r-mass and r-nlme.
(r-pbkrtest)[propagated-inputs]: Add r-mass and r-matrix.
(r-car)[propagated-inputs]: Add r-mass, r-mgcv, and r-nnet.
(r-tclust)[propagated-inputs]: Add r-cluster.
2017-03-17 10:14:02 +01:00
2441c28414
gnu: Add r-seurat.
...
* gnu/packages/bioinformatics.scm (r-seurat): New variable.
Co-authored-by: Ricardo Wurmus <rekado@elephly.net>
2017-03-16 14:54:58 +01:00
79849358f8
gnu: sra-tools: Update to 2.8.2-1.
...
* gnu/packages/bioinformatics.scm (sra-tools): Update to 2.8.2-1.
[arguments]: Add DEFAULT_CRT and DEFAULT_KFG to make flags.
2017-03-16 13:40:36 +01:00
d5e1716239
gnu: ncbi-vdb: Install configuration files.
...
* gnu/packages/bioinformatics.scm (ncbi-vdb)[arguments]: Add phase
"install-configuration-files".
2017-03-16 13:39:53 +01:00
558e23074e
gnu: ncbi-vdb: Override search path for java-ngs.
...
* gnu/packages/bioinformatics.scm (ncbi-vdb)[arguments]: Patch "package.prl"
to ensure that java-ngs is found by the configure script; remove configure
flag "--with-ngs-java-prefix".
2017-03-16 13:38:39 +01:00
701111989e
gnu: ncbi-vdb: Use modify-phases syntax.
...
* gnu/packages/bioinformatics.scm (ncbi-vdb)[arguments]: Use modify-phases
syntax.
2017-03-16 10:20:56 +01:00
5021f54787
gnu: ncbi-vdb: Update to 2.8.2.
...
* gnu/packages/bioinformatics.scm (ncbi-vdb): Update to 2.8.2.
2017-03-16 10:19:25 +01:00
6c4ccf3228
gnu: ngs-sdk: Update to 1.3.0.
...
* gnu/packages/bioinformatics.scm (ngs-sdk): Update to 1.3.0.
2017-03-16 10:18:48 +01:00
f38607536e
gnu: Use INSTALL-FILE where appropriate.
...
* gnu/packages/admin.scm (wpa-supplicant-minimal): Substitute the simpler
INSTALL-FILE for COPY-FILE when invoked with redundant arguments.
* gnu/packages/bioinformatics.scm (couger, aragorn, express-beta-diversity,
edirect, fasttree, rsem, samtools-0.1): Likewise.
* gnu/packages/code.scm (withershins): Likewise.
* gnu/packages/conky.scm (conky): Likewise.
* gnu/packages/debug.scm (delta, american-fuzzy-lop): Likewise.
* gnu/packages/emacs.scm (emacs-mit-scheme-doc): Likewise.
* gnu/packages/engineering.scm (librecad): Likewise.
2017-03-15 22:19:39 +01:00
b2d748edff
gnu: samtools: End installation phases with truth.
...
* gnu/packages/bioinformatics.scm (samtools, samtools-0.1)[arguments]:
Return #T instead of the undefined results of COPY-FILE or INSTALL-FILE.
2017-03-15 01:10:30 +01:00
fbf45d6ea7
gnu: vsearch: Update to 2.4.2.
...
* gnu/packages/bioinformatics.scm (vsearch): Update to 2.4.2.
2017-03-11 11:37:15 +10:00
036cd0cb8b
gnu: Add r-ape.
...
* gnu/packages/bioinformatics.scm (r-ape): New variable.
Co-authored-by: Ben Woodcroft <donttrustben@gmail.com>
2017-03-11 10:43:26 +10:00
79f09fa239
gnu: hmmer: Build reproducibly.
...
* gnu/packages/patches/hmmer-remove-cpu-specificity.patch: New file.
* gnu/packages/bioinformatics.scm (hmmer): Use it.
2017-03-10 20:31:30 +10:00
5ded35d89d
gnu: Add sambamba.
...
* gnu/packages/bioinformatics.scm (htslib-for-sambamba, sambamba): New
variables.
2017-03-10 10:13:59 +01:00
3f98071ac5
Merge branch 'python-tests'
2017-03-03 16:55:43 +01:00
a9f754d733
gnu: diamond: Update to 0.8.36.
...
* gnu/packages/bioinformatics.scm (diamond): Update to 0.8.36.
2017-03-02 21:19:26 +10:00
48d66a9c99
gnu: bamtools: Update to 2.4.1.
...
* gnu/packages/bioinformatics.scm (bamtools): Update to 2.4.1.
2017-02-28 12:10:02 +01:00
2bb12f5a68
gnu: ribodiff: Fix test failure.
...
* gnu/packages/bioinformatics.scm (ribodiff)[native-inputs]: Add PYTHON2-MOCK
and PYTHON2-NOSE.
2017-02-27 15:32:17 +01:00
1885bb0c08
gnu: python-dendropy: Fix failing tests.
...
* gnu/packages/patches/python-dendropy-fix-tests.patch: New file.
* gnu/local.mk (dist_patch_DATA): Add it.
* gnu/packages/bioinformatics.scm (python-dendropy)[source]: Add patch.
2017-02-24 23:44:31 +01:00
424b1ae769
Merge branch 'master' into python-tests
2017-02-13 22:35:05 +01:00
206af46fe1
gnu: vsearch: Update to 2.4.0.
...
* gnu/packages/bioinformatics.scm (vsearch): Update to 2.4.0.
[source]: Convert most operations in the snippet to patch form and adjust
for 2.4.0.
* gnu/packages/patches/vsearch-unbundle-cityhash.patch: New file.
* gnu/local.mk (dist_patch_DATA): Add it.
2017-02-09 21:21:29 +10:00
47055b273a
gnu: r-edger: Add r-statmod to inputs.
...
* gnu/packages/bioinformatics.scm (r-edger)[propagated-inputs]: Add r-statmod.
2017-02-01 22:12:01 +01:00
58f91e4d03
download: url-fetch/tarball: Make ‘name’ truly optional.
...
* guix/download.scm (url-fetch/tarbomb): Fall back to ‘file-name’ if
‘name’ is #f, like the regular ‘url-fetch’ does.
* gnu/packages/bioinformatics.scm (muscle)[source]: Remove ‘file-name’.
* gnu/packages/engineering.scm (fastcap)[source]: Likewise.
* gnu/packages/scheme.scm (scmutils)[source]: Likewise.
2017-02-01 15:53:32 +01:00
69f2b3bdf9
gnu: Add r-rhdf5.
2017-01-31 22:35:11 +01:00
d4af25b51b
gnu: Add r-tximport.
2017-01-31 22:35:08 +01:00
aa3eeeb542
gnu: Add r-bsgenome-hsapiens-1000genomes-hs37d5.
...
* gnu/packages/bioinformatics.scm (r-bsgenome-hsapiens-1000genomes-hs37d5):
New variable.
2017-01-30 12:11:04 +01:00
c0dee46c85
gnu: r-vegan: Update to 2.4-2.
...
* gnu/packages/bioinformatics.scm (r-vegan): Update to 2.4-2.
2017-01-21 18:17:16 +10:00
cda0f9a4a9
gnu: diamond: Update to 0.8.34.
...
* gnu/packages/bioinformatics.scm (diamond): Update to 0.8.34.
2017-01-21 17:28:11 +10:00
2923f3e5b9
gnu: r-msnid: Expand abbreviation in description.
...
* gnu/packages/bioinformatics.scm (r-msnid)[description]: Expand "MS/MS"
to "tandem mass spectrometry".
2017-01-20 15:38:03 +01:00
e614d6398a
gnu: r-msnbase: Expand abbreviation in description.
...
* gnu/packages/bioinformatics.scm (r-msnbase)[description]: Expand "MS"
to "mass spectrometry".
2017-01-20 15:38:03 +01:00
1778ea740e
gnu: multiqc: Add python-nose to inputs.
...
* gnu/packages/bioinformatics.scm (multiqc)[propagated-inputs]: Add
python-nose.
2017-01-18 16:09:49 +01:00
66da3a9f31
gnu: Add r-msnid.
...
* gnu/packages/bioinformatics.scm (r-msnid): New variable.
2017-01-17 21:46:50 +01:00
11879284cb
gnu: Add r-msnbase.
...
* gnu/packages/bioinformatics.scm (r-msnbase): New variable.
2017-01-17 21:46:50 +01:00
6a67e181ac
gnu: Add r-pcamethods.
...
* gnu/packages/bioinformatics.scm (r-pcamethods): New variable.
2017-01-17 21:46:50 +01:00
4aa7d592f1
gnu: Add r-mzid.
...
* gnu/packages/bioinformatics.scm (r-mzid): New variable.
2017-01-17 21:46:50 +01:00
7c08afaf7b
gnu: Add r-vsn.
...
* gnu/packages/bioinformatics.scm (r-vsn): New variable.
2017-01-17 21:46:50 +01:00
05c7e5fb76
gnu: Add r-affy.
...
* gnu/packages/bioinformatics.scm (r-affy): New variable.
2017-01-17 21:46:49 +01:00
5c9d15055f
gnu: Add r-affyio.
...
* gnu/packages/bioinformatics.scm (r-affyio): New variable.
2017-01-17 21:46:49 +01:00
71676a1f4c
gnu: Add r-mzr.
...
* gnu/packages/bioinformatics.scm (r-mzr): New variable.
2017-01-17 21:46:49 +01:00
ae26217430
gnu: Add r-protgenerics.
...
* gnu/packages/bioinformatics.scm (r-protgenerics): New variable.
2017-01-17 21:46:49 +01:00
0e7d058e44
gnu: Add r-maldiquant.
...
* gnu/packages/bioinformatics.scm (r-maldiquant): New variable.
2017-01-17 21:46:49 +01:00
1f40e73cb5
gnu: Add r-raremetals2.
...
* gnu/packages/bioinformatics.scm (r-raremetals2): New variable.
2017-01-17 21:46:48 +01:00
fb1e528ef1
gnu: Add r-seqminer.
...
* gnu/packages/bioinformatics.scm (r-seqminer): New variable.
2017-01-17 21:46:48 +01:00
769fc6bb18
gnu: Add ribodiff.
...
* gnu/packages/bioinformatics.scm (ribodiff): New variable.
2017-01-17 21:46:48 +01:00
e84efc50d7
gnu: Add hisat2.
...
* gnu/packages/bioinformatics.scm (hisat2): New variable.
2017-01-17 21:46:48 +01:00
b91cfa22e1
gnu: Add r-centipede.
...
* gnu/packages/bioinformatics.scm (r-centipede): New variable.
2017-01-16 23:18:27 +01:00
dd42a330d1
gnu: Add r-sva.
...
* gnu/packages/bioinformatics.scm (r-sva): New variable.
2017-01-14 11:15:18 +01:00
cc0725914e
Merge branch 'master' into python-tests
2017-01-13 10:21:17 -05:00
c5173d74d6
gnu: Add r-txdb-mmusculus-ucsc-mm10-knowngene.
...
* gnu/packages/bioinformatics.scm (r-txdb-mmusculus-ucsc-mm10-knowngene): New variable.
2017-01-12 10:02:57 +01:00
3a3bf2f819
gnu: Add r-copywriter.
...
* gnu/packages/bioinformatics.scm (r-copywriter): New variable.
2017-01-06 16:31:19 +01:00
d407bdb931
gnu: Add r-copyhelper.
...
* gnu/packages/bioinformatics.scm (r-copyhelper): New variable.
2017-01-06 16:31:14 +01:00
6193563a36
gnu: Add r-chipseq.
...
* gnu/packages/bioinformatics.scm (r-chipseq): New variable.
2017-01-06 16:31:02 +01:00
dbf9d37114
gnu: bioruby: Update to 1.5.1.
...
* gnu/packages/bioinformatics.scm (bioruby): Update to 1.5.1.
2017-01-06 19:06:07 +10:00
0c37e2a3d2
gnu: cd-hit: Update to 4.6.6.
...
* gnu/packages/bioinformatics.scm (cd-hit): Update to 4.6.6.
2017-01-06 19:06:03 +10:00
3b3b60d037
gnu: Use HTTPS for all sourceforge.net home pages.
...
* gnu/packages/admin.scm (mingetty, clusterssh)[home-page]: Use HTTPS.
* gnu/packages/audio.scm (libbs2b, soxr)[home-page]: Likewise.
* gnu/packages/bioinformatics.scm (bless)[home-page]: Likewise.
* gnu/packages/display-managers.scm (slim)[home-page]: Likewise.
* gnu/packages/games.scm (extremetuxracer)[home-page]: Likewise.
* gnu/packages/ghostscript.scm (gs-fonts)[home-page]: Likewise.
* gnu/packages/haskell.scm (ghc-regex-base, ghc-regex-posix,
ghc-regex-compat)[home-page]: Likewise.
* gnu/packages/image.scm (imlib2)[home-page]: Likewise.
* gnu/packages/libreoffice.scm (librevenge, libcmis, libodfgen, libmwaw)
[home-page]: Likewise.
* gnu/packages/linux.scm (hdparm, acpid, libavc1394, rng-tools)
[home-page]: Likewise.
* gnu/packages/mail.scm (esmtp)[home-page]: Likewise.
* gnu/packages/mp3.scm (ripperx)[home-page]: Likewise.
* gnu/packages/onc-rpc.scm (libtirpc)[home-page]: Likewise.
* gnu/packages/perl.scm (perl-czplib)[home-page]: Likewise.
* gnu/packages/python.scm (python-pyasn1-modules)[home-page]: Likewise.
* gnu/packages/xdisorg.scm (xosd)[home-page]: Likewise.
2017-01-04 05:14:22 +01:00
407a280103
gnu: r-genomicranges: Update to 1.26.2.
...
* gnu/packages/bioinformatics.scm (r-genomicranges): Update to 1.26.2.
2017-01-03 13:28:35 +01:00
ac370a3397
gnu: r-genomeinfodb: Update to 1.10.2.
...
* gnu/packages/bioinformatics.scm (r-genomeinfodb): Update to 1.10.2.
2017-01-03 12:47:36 +01:00
25d84d3122
gnu: python-dendropy: Update to 4.2.0.
...
* gnu/packages/bioinformatics.scm (python-dendropy): Update to 4.2.0.
[source]: Remove patch.
(python2-dendropy)[source]: Use the same source as python-dendropy.
* gnu/packages/patches/python-dendropy-exclude-failing-tests.patch: Remove
file.
* gnu/local.mk (dist_patch_DATA): Remove it.
2017-01-01 16:47:47 +10:00
322a583fcf
gnu: diamond: Update to 0.8.31.
...
* gnu/packages/bioinformatics.scm (diamond): Update to 0.8.31.
2017-01-01 16:47:47 +10:00
a29929b32c
gnu: multiqc: Update to 0.9.
...
Suggested by Raoul Bonnal <ilpuccio.febo@gmail.com>.
* gnu/packages/bioinformatics.scm (multiqc): Update to 0.9.
[origin]: Add patch.
* gnu/packages/patches/multiqc-fix-git-subprocess-error.patch: New file.
* gnu/local.mk (dist_patch_DATA): Add it.
2016-12-30 17:22:43 +10:00
76b64381cb
gnu: r-genomicfeatures: Update to 1.26.2.
...
* gnu/packages/bioinformatics.scm (r-genomicfeatures): Update to 1.26.2.
2016-12-29 22:24:12 +01:00
2f642e5229
gnu: r-biostrings: Update to 2.42.1.
...
* gnu/packages/bioinformatics.scm (r-biostrings): Update to 2.42.1.
2016-12-29 22:24:11 +01:00
72c2693b9e
gnu: r-limma: Update to 3.30.7.
...
* gnu/packages/bioinformatics.scm (r-limma): Update to 3.30.7.
2016-12-29 22:24:11 +01:00
5796af9981
gnu: r-variantannotation: Update to 1.20.2.
...
* gnu/packages/bioinformatics.scm (r-variantannotation): Update to 1.20.2.
2016-12-29 22:24:11 +01:00
5d3acc0b36
gnu: r-edger: Update to 3.16.5.
...
* gnu/packages/bioinformatics.scm (r-edger): Update to 3.16.5.
2016-12-29 22:24:11 +01:00
81a17b61e7
gnu: r-genomeinfodb: Update to 1.10.1.
...
* gnu/packages/bioinformatics.scm (r-genomeinfodb): Update to 1.10.1.
2016-12-29 22:24:11 +01:00
54d9b568fc
gnu: r-iranges: Update to 2.8.1.
...
* gnu/packages/bioinformatics.scm (r-iranges): Update to 2.8.1.
2016-12-29 22:24:11 +01:00
86fc9c4a2c
gnu: r-s4vectors: Update to 0.12.1.
...
* gnu/packages/bioinformatics.scm (r-s4vectors): Update to 0.12.1.
2016-12-29 22:24:11 +01:00
c8ad8b6976
gnu: r-biocstyle: Update to 2.2.1.
...
* gnu/packages/bioinformatics.scm (r-biocstyle): Update to 2.2.1.
2016-12-29 22:24:10 +01:00
007ee80277
gnu: r-deseq2: Update to 1.14.1.
...
* gnu/packages/bioinformatics.scm (r-deseq2): Update to 1.14.1.
2016-12-29 22:24:10 +01:00
d0f0579e6f
gnu: r-annotate: Update to 1.52.1.
...
* gnu/packages/bioinformatics.scm (r-annotate): Update to 1.52.1.
[propagated-inputs]: Add r-rcurl.
2016-12-29 22:24:10 +01:00
421f7772b4
gnu: r-qtl: Update to 1.40-8.
...
* gnu/packages/bioinformatics.scm (r-qtl): Update to 1.40-8.
2016-12-29 21:49:09 +01:00
2c8d6c0be4
gnu: r-rcas: Update to 1.1.1.
...
* gnu/packages/bioinformatics.scm (r-rcas): Update to 1.1.1.
[propagated-inputs]: Add plotrix.
2016-12-27 14:50:55 +01:00
9916ef8bb6
gnu: diamond: Update to 0.8.30.
...
* gnu/packages/bioinformatics.scm (diamond): Update to 0.8.30.
2016-12-27 09:18:05 +10:00
33d5b2464d
gnu: cutadapt: Use ‘modify-phases’ syntax.
...
* gnu/packages/bioinformatics.scm (cutadapt)[arguments]: Use
‘modify-phases’.
2016-12-20 05:36:55 +01:00
1f94bff2d4
gnu: cutadapt: Update to 1.12.
...
* gnu/packages/bioinformatics.scm (cutadapt): Update to 1.12.
[inputs]: Add python-xopen.
2016-12-19 20:33:32 +01:00
3fffabce2a
gnu: Add attribution line for Raoul Bonnal.
...
This is a follow-up commit to c9e9154e99
2016-12-18 10:01:04 +10:00
c9e9154e99
gnu: star: Update to 2.5.2b.
...
* gnu/packages/bioinformatics (star): Update to 2.5.2b.
[source]: Delete precompiled binary.
Co-authored-by: Ben Woodcroft <donttrustben@gmail.com>
2016-12-17 23:26:35 +10:00
cdc2bb50b2
gnu: pbtranscript-tofu: Disable tests.
...
* gnu/packages/bioinformatics.scm (pbtranscript-tofu)[arguments]: Set #:tests? #f.
2016-12-16 18:15:47 +01:00
0d90875974
gnu: multiqc: Fix test dependencies.
...
* gnu/packages/bioinformatics.scm (multiqc)[native-inputs]: Add python-nose.
2016-12-16 13:28:49 +01:00
14386fc7d9
gnu: idr: Remove explicit wrapper. This is now done implicitly.
...
* gnu/packages/bioinformatics.scm (idr)[arguments]: Remove #:phases.
2016-12-16 13:16:39 +01:00
b7a820fc97
gnu: idr: Correct inputs.
...
* gnu/packages/bioinformatics.scm (idr)[inputs]: Move everything from here ...
[propagated-inputs]: ... to here. Add python-sympy.
2016-12-16 13:11:20 +01:00
1c10a1d75c
gnu: idr: Disable tests.
...
* gnu/packages/bioinformatics.scm (idr)[arguments]: Set #:tests? #f.
2016-12-16 13:08:57 +01:00
aaffb9c97b
gnu: deeptools: Fix test dependency.
...
* gnu/packages/bioinformatics.scm (deeptools)[native-inputs]: Add python-nose.
2016-12-16 04:27:35 +01:00
d281be18bc
gnu: clipper: Fix test dependency.
...
* gnu/packages/bioinformatics.scm (clipper)[native-inputs]: Add python2-nose.
2016-12-16 04:26:32 +01:00
0c6c9c00ab
gnu: Update more dead Google Code home pages.
...
* gnu/packages/bioinformatics.scm (cutadapt, mosaik, pepr)[home-page]:
Update to their respective replacements.
2016-12-14 22:08:51 +01:00
da5ebd1007
gnu: python-biom-format: Fix tests.
...
* gnu/packages/bioinformatics.scm (python-biom-format,
python2-biom-format)[native-inputs]: Add python-nose.
2016-12-14 19:18:26 +01:00
991e143d25
gnu: diamond: Update to 0.8.29.
...
* gnu/packages/bioinformatics.scm (diamond): Update to 0.8.29.
2016-12-13 20:01:56 +10:00
ced1c496aa
gnu: orfm: Update to 0.6.1.
...
* gnu/packages/bioinformatics.scm (orfm): Update to 0.6.1.
2016-12-13 20:00:50 +10:00
2df3d147ef
gnu: orfm: Update to 0.6.0.
...
* gnu/packages/bioinformatics.scm (orfm): Update to 0.6.0.
2016-12-12 20:49:31 +10:00
a225db5293
gnu: vsearch: Update to 2.3.4.
...
* gnu/packages/bioinformatics.scm (vsearch): Update to 2.3.4.
2016-12-10 10:45:13 +10:00
7922ab8fe8
gnu: pardre: Update to 1.1.5-1.
...
* gnu/packages/bioinformatics.scm (pardre): update to 1.1.5-1.
[source]: Update source hash.
2016-12-10 10:45:12 +10:00
1b7f17ef90
gnu: vsearch: Update to 2.3.3.
...
* gnu/packages/bioinformatics.scm (vsearch): Update to 2.3.3.
2016-12-08 22:39:10 +10:00
e990c81d38
gnu: aragorn: Update to 1.2.38.
...
* gnu/packages/bioinformatics.scm (aragorn): Update to 1.2.38.
2016-12-04 10:51:54 +10:00
3bf4280659
Merge branch 'master' into python-build-system
2016-11-29 18:47:16 +01:00
bd3be46e7f
gnu: Add r-gkmsvm.
...
* gnu/packages/bioinformatics.scm (r-gkmsvm): New variable.
2016-11-28 22:43:18 +01:00
2d9fb1702f
gnu: Add r-seqgl.
...
* gnu/packages/bioinformatics.scm (r-seqgl): New variable.
2016-11-28 22:43:17 +01:00
c827f20286
gnu: Add r-chipkernels.
...
* gnu/packages/bioinformatics.scm (r-chipkernels): New variable.
2016-11-28 22:43:17 +01:00
d71605294f
gnu: Add r-wgcna.
...
* gnu/packages/bioinformatics.scm (r-wgcna): New variable.
2016-11-28 22:43:17 +01:00
e619a5c245
gnu: Add r-r4rna.
...
* gnu/packages/bioinformatics.scm (r-r4rna): New variable.
2016-11-28 22:43:16 +01:00
9926875572
gnu: Add newick-utils.
...
* gnu/packages/bioinformatics.scm (newick-utils): New variable.
2016-11-28 09:00:41 +10:00
5e0a0f4226
gnu: roary: Update to 3.7.0.
...
* gnu/packages/bioinformatics.scm (roary): Update to 3.7.0.
2016-11-26 20:15:39 +10:00
31a9d653ad
gnu: Add proteinortho.
...
* gnu/packages/bioinformatics.scm (proteinortho): New variable.
2016-11-26 20:15:37 +10:00
de32aa74b4
Merge branch 'master' into python-build-system
2016-11-25 11:20:21 -05:00
8e5f8c98e2
gnu: diamond: Update to 0.8.27.
...
* gnu/packages/bioinformatics.scm (diamond): Update to 0.8.27.
2016-11-22 21:01:21 +10:00
daf72603eb
gnu: Remove redundancy where mkdir-p <dir> is followed by install-file <file> <dir>.
...
* gnu/packages/bioinformatics.scm (bwa)[arguments]: Remove redundant mkdir-p.
(eigensoft)[arguments]: Likewise.
(snap-aligner)[arguments]: Likewise.
(pardre)[arguments]: Likewise.
(piranha)[arguments]: Likewise.
* gnu/packages/maths.scm (hypre)[arguments]: Likewise.
* gnu/packages/mp3.scm (mpc123)[arguments]: Likewise.
* gnu/packages/music.scm (tuxguitar)[arguments]: Likewise.
* gnu/packages/pdf.scm (impressive)[arguments]: Likewise.
* gnu/packages/qemu.scm (qemu)[arguments]: Likewise.
Signed-off-by: Leo Famulari <leo@famulari.name>
2016-11-21 14:39:54 -05:00
de5bc89093
gnu: python2-pbcore: Fix inputs:
...
* gnu/packages/bioinformatics.scm (python2-pbcore) [inputs] change to
[propagated-inputs]. [native-inputs]: Remove python-docutils, which
comes with sphinx. [former propagated-inputs]: move all (which is only
pyxb) to [inputs].
2016-11-15 22:32:01 +01:00
54c85e12fd
gnu: python2-warpedlmm: Remove phase remove-bin-directory.
...
This directory did contain contain wrappers for `nose`, which should not
be there anyway (since nose already was a native-input). The new
python build system no longer creates this directory, while the old one
did. (This difference is due to the bloody details of how packages are
installed.)
* gnu/packages/bioinformatics.scm (python2-warpedlmm)
[modify-phases] Remove, since remove-bin-directory was the only
modification here.
2016-11-15 22:32:00 +01:00
f2516de2fc
gnu: Fix python inputs, part 7: Ensure python-cython is a native-input.
...
* gnu/packages/audio.scm (python-pyliblo): [inputs] Move python-cyton to
[native-inputs].
* gnu/packages/bioinformatics.scm (python2-pybedtools): dito.
* gnu/packages/music.scm (beast, python-pyportmidi): dito.
* gnu/packages/python.scm (python2-fastlmm, python-kivy): dito.
2016-11-15 22:31:07 +01:00
f22efa0152
gnu: Fix python inputs, part 1: all inputs become propagated-inputs.
...
This patch contains the changes where all [inputs] are changed to
[propagated-inputs]
* gnu/packages/python.scm (python-passlib, python-paramiko, python-ccm,
python-babel, python-keyring python-pandas, python-tzlocal,
python-parse-type, python-nose2, python-pytest, python-pytest-mock,
python-pytest-xdist, python-scripttest, python-testtools, python-pytest-cov,
python-testscenarios, python-pbr-0.11, python-oauthlib, python-jinja2,
python-sphinx, python-tzlocal, python-bugz, python2-pytest-mock, behave,
pelican, sqlalchemy-utils, python-pygridtools, python-urwidtrees,
python-tornado, python2-tornado, python-debian, python-execnet,
python-pytest-cache, pytest-localserver, python-clint, python-rply,
python-hy, python-rauth, python-rsa, python-celery, python-vobject, s3cmd,
python-prompt-toolkit, ptpython, python-requests-oauthlib, python-stem,
python-binaryornot, python2-binaryornot, python-nltk, python-pymongo,
python-schematics, python-url, python2-url, python-freezegun,
python-glances, python-graphql-core, python-graphql-relay, python-graphene,
python-nautilus, python-s3transfer): All [inputs] become
[propagated-inputs].
* gnu/packages/bioinformatics.scm (python-biopython): Likewise.
* gnu/packages/django.scm (pytest-django): Likewise.
* gnu/packages/mail.scm (python-mailmanclient): Likewise.
* gnu/packages/password-utils.scm (python-bcrypt): Likewise.
* gnu/packages/propbuf.scm (python-protobuf): Likewise.
* gnu/packages/rdf.scm (python-rdflib): Likewise.
SQACH all become propagated
2016-11-15 22:31:03 +01:00
b41a05ce49
gnu: Remove work-arounds for bug 20765 (ensure uncompressed eggs).
...
Bug 20765 is solved since we build all Python packages using
option "--single-version-externally-managed".
* gnu/packages/bioinformatics.scm (pbtranscript-tofu): Remove
configure-flags. (pepr): remove phase "disable-egg-generation".
* gnu/packages/pdf.scm (reportlab): Remove configure-flags.
* gnu/packages/python.scm (python-sphinx-rtd-theme, python2-elib.intl,
python-pkgconfig, python-pytest-pep8, python-pytest-flakes): Remove
configure-flags. (python-pillow) remove phase
"disable-egg-generation". (python-libarchive-c) Remove patching
setup.cfg.
* gnu/packages/statistics.scm (python-patsy): remove phase
"prevent-generation-of-egg-archive".
* gnu/packages/tls.scm (python-acme): remove phase
"disable-egg-compression".
* gnu/packages/tor.scm (onionshare): Remove configure-flags.
2016-11-15 22:31:02 +01:00
5c31f4aa7c
gnu: Remove python-setuptools and python2-setuptools from inputs (part 4a)
...
This patch contains the changes for all modules beside python.scm where
setuptools are used in an inherited package and removing this input also
removes the need for inheriting the package. This is the case if adding
setuptools in the inherited package was the only change.
Change this to not inherit and remove the new needless call to
"strip-python2-variant (if applicable).
* gnu/packages/bioinformatics.scm (python-biopython, python2-biopython,
python-twobitreader, python2-twobitreader,
python-plastid, python2-plastid,
python2-pybigwig,
python2-screed,
sra-tools): No longer "inherit" Python 2 packages
inheriting from a Python 3 package if the sole reason for inheriting was
adding python-setuptools respective python2-setuptools to [inputs],
[native-inputs] or [propagated-inputs]. Remove now needless [properties]
"python2-variant" where applicable.
* gnu/packages/django.scm (python-pytest-django, python2-pytest-django,
python-django-filter, python2-django-filter): Likewise.
* gnu/packages/gnupg.scm (python2-pygpgme): Likewise.
* gnu/packages/mail.scm (python-mailmanclient, python2-mailmanclient):
Likewise.
* gnu/packages/mpd.scm (python-msp, python2-mpd2): Likewise.
* gnu/packages/music.scm (python-pylast, python2-pylast): Likewise.
* gnu/packages/openstack.scm (python-requests-mock, python2-requests-mock,
python2-git-review): Likewise.
* gnu/packages/password-utils.scm (python2-bcrypt): Likewise.
* gnu/packages/protobuf.scm (python-protobuf, python2-protobuf): Likewise.
* gnu/packages/statistics.scm (python-patsy, python2-patsy): Likewise.
* gnu/packages/web.scm (python2-feedparser): Likewise.
2016-11-15 22:28:59 +01:00
00e10c6e67
gnu: Remove python-setuptools and python2-setuptools from inputs (part 3)
...
This patch contains the changes where setuptools are used in an inherited
package and removing this input keeps the need for inheriting the package.
* gnu/packages/bioinformatics.scm (python2-biom-format): Remove
python-setuptools respective python2-setuptools from [inputs],
[native-inputs] and [propagated-inputs] in Python 2 packages inheriting from
a Python 3 package.
* gnu/packages/python.scm (python2-pytest-mock,
python2-oauthlib,
python2-seaborn,
python2-tornado,
python2-terminado,
python2-rauth,
python2-anyjson,
python2-amqp,
python2-kombu,
python2-billiard,
python2-celery,
python2-jellyfish,
python2-binaryornot,
python2-natsort,
python2-graphene): Likewise.
* gnu/packages/statistics.scm (python2-statsmodels): Likewise.
2016-11-15 22:28:38 +01:00
f3b98f4fec
gnu: Remove python-setuptools and python2-setuptools from inputs (part 2)
...
This patch contains the changes where removing setuptools from the inputs
affected some code-lines beside.
* gnu/packages/admin.scm (ansible): Remove all [inputs], [native-inputs] and
[propagated-inputs] where python-setuptools or python2-setuptools are the
sole entries. Remove python-setuptools and python2-setuptools listed on a
line by its own from [inputs], [native-inputs] and [propagated-inputs].
* gnu/packages/backup.scm (duplicity): Likewise.
* gnu/packages/bioinformatics.scm (bamm, python2-pybedtools,
python2-bx-python, python2-dendropy, python-pysam, python2-pysam, clipper,
crossmap, cutadapt, deeptools, grit, idr, python2-warpedlmm,
pbtranscript-tofu, seqmagick): Likewise.
* gnu/packages/docbook.scm (dblatex): Likewise.
* gnu/packages/freedesktop.scm (python-pyxdg, python2-pyxdg): Likewise.
* gnu/packages/lirc.scm (python2-lirc): Likewise.
* gnu/packages/mp3.scm (eyed3): Likewise.
* gnu/packages/nutrition.scm (gourmet): Likewise.
* gnu/packages/openstack.scm (python-hacking, python2-hacking,
python-os-testr, python2-os-testr,
python-stevedore, python2-stevedore,
python-tempest-lib, python2-tempest-lib,
python-oslo.log, python2-oslo.log,
python-keystoneclient, python2-keystoneclient): Likewise.
* gnu/packages/password-utils.scm (assword): Likewise.
* gnu/packages/python.scm (python-passlib, python2-passlib,
python-babel, python2-babel,
python-parse-type,
python-pytest, python2-pytest,
python-scripttest, python2-scripttest,
python-testtools, python2-testtools,
python-testscenarios, python2-testscenarios,
python-subunit, python2-subunit,
python-pbr-0.11,
python-pbr, python2-pbr,
python-testrepository, python2-testrepository,
behave,
python-wheel, python2-wheel,
python-requests, python2-requests,
python-jsonschema, python2-jsonschema,
python-pyjwt, python2-pyjwt,
python-virtualenv, python2-virtualenv,
python-jinja2, python2-jinja2,
python-joblib, python2-joblib,
python-sphinx, python2-sphinx,
python-feedgenerator, python2-feedgenerator,
python-scikit-image, python2-scikit-image,
python-redis, python2-redis,
python2-fastlmm,
python-numpydoc, python2-numpydoc,
python-matplotlib, python2-matplotlib,
python2-pysnptools,
python-rpy2, python2-rpy2,
python-pillow, python2-pillow,
python-pycparser, python2-pycparser,
python-cffi, python2-cffi,
python-cairocffi, python2-cairocffi,
python-drmaa, python2-drmaa,
python-pathpy, python2-pathpy,
python-simplegeneric, python2-simplegeneric,
python-ipython, python2-ipython,
python-apsw, python2-apsw,
python-lxml, python2-lxml,
python-networkx, python2-networkx,
python-pyzmq, python2-pyzmq,
python-mccabe, python2-mccabe,
python-mccabe-0.2.1,
python-flake8, python2-flake8,
python-flake8-2.2.4,
python-mistune, python2-mistune,
python-ptyprocess, python2-ptyprocess,
python-llfuse, python2-llfuse,
python-webob, python2-webob,
python-xlrd, python2-xlrd,
python-tables, python2-tables,
python-pip, python2-pip,
python-libarchive-c, python2-libarchive-c,
python-docopt, python2-docopt,
python-pyrfc3339, python2-pyrfc3339,
python-configobj, python2-configobj,
python-clint, python2-clint,
python-rply, python2-rply,
python2-rpython,
python-widgetsnbextension, python2-widgetsnbextension
jupyter,
python-jupyter-console, python2-jupyter-console,
python-hy, python2-hy,
python-urllib3, python2-urllib3,
python-rsa, python2-rsa,
python-tox, python2-tox,
python2-hypothesis,
python-paste, python2-paste,
python-pastescript, python2-pastescript,
python2-unicodecsv,
python-pkgconfig, python2-pkgconfig,
python2-rope,
python-sqlparse, python2-sqlparse,
python-gevent, python2-gevent,
python-tabulate, python2-tabulate,
python-arrow, python2-arrow,
python-cleo, python2-cleo,
python-fake-factory, python2-fake-factory,
ptpython): Likewise.
* gnu/packages/rdf.scm (python-rdflib, python2-rdflib): Likewise.
* gnu/packages/terminals.scm (asciinema): Likewise.
* gnu/packages/version-control.scm (git-annex-remote-hubic): Likewise.
* gnu/packages/xdisorg.scm (arandr): Likewise.
2016-11-15 22:27:31 +01:00
5d85493284
gnu: Remove python-setuptools and python2-setuptools from inputs (part 1b)
...
This patch contains the changes in all modules beside python.scm where
removing setuptools from the inputs could be achieved by removing complete
lines.
* gnu/packages/admin.scm (graphios, thefuck): Remove all [inputs],
[native-inputs] and [propagated-inputs] where python-setuptools or
python2-setuptools are the sole entries. Remove python-setuptools and
python2-setuptools listed on a line by its own from [inputs],
[native-inputs] and [propagated-inputs].
* gnu/packages/backup.scm (rdiff-backup): Likewise.
* gnu/packages/bioinformatics.scm (htseq, macs, python2-pbcore, rseqc,
multiqc): Likewise.
* gnu/packages/django.scm (python-django, python2-django,
python-django-simple-math-captcha, python2-django-simple-math-captcha):
Likewise.
* gnu/packages/docker.scm (python-docker-py, docker-compose): Likewise.
* gnu/packages/game-development.scm (python-pygame): Likewise.
* gnu/packages/key-mon.scm (key-mon): Likewise.
* gnu/packages/mail.scm (khard): Likewise.
* gnu/packages/music.scm (beets, python2-pyechonest): Likewise.
* gnu/packages/openstack.scm (python-bandit, python2-bandit,
python-debtcollector, python2-debtcollector,
python-mox3, python2-mox3,
python-os-client-config, python2-os-client-config,
python-oslo.config, python2-oslo.config,
python-oslo.context, python2-oslo.context,
python-oslo.i18n, python2-oslo.i18n,
python-oslo.serialization, python2-oslo.serialization,
python-oslosphinx, python2-oslosphinx,
python-oslotest, python2-oslotest,
python-oslo.utils, python2-oslo.utils,
python-swiftclient, python2-swiftclient): Likewise.
* gnu/packages/pdf.scm (pdfposter): Likewise.
* gnu/packages/tls.scm (python-acme, python2-acme): Likewise.
2016-11-15 21:58:44 +01:00
84590149e6
gnu: hisat: Fix typo.
...
* gnu/packages/bioinformatics.scm (hisat)[arguments]: Fix directory
name in install phase.
2016-11-15 20:21:08 +01:00
7c45670b32
gnu: r-org-mm-eg-db: Update to 3.4.0.
...
* gnu/packages/bioinformatics.scm (r-org-mm-eg-db): Update to 3.4.0.
2016-11-11 09:08:08 +01:00
0cfac6f270
gnu: r-org-dm-eg-db: Update to 3.4.0.
...
* gnu/packages/bioinformatics.scm (r-org-dm-eg-db): Update to 3.4.0.
2016-11-11 09:08:08 +01:00
f04a3eff98
gnu: r-org-ce-eg-db: Update to 3.4.0.
...
* gnu/packages/bioinformatics.scm (r-org-ce-eg-db): Update to 3.4.0.
2016-11-11 09:08:08 +01:00
83f9a6fb60
gnu: r-org-hs-eg-db: Update to 3.4.0.
...
* gnu/packages/bioinformatics.scm (r-org-hs-eg-db): Update to 3.4.0.
2016-11-11 09:08:07 +01:00
3cf7c31720
gnu: diamond: Update to 0.8.26.
...
* gnu/packages/bioinformatics.scm (diamond): Update to 0.8.26.
2016-11-07 21:31:09 +10:00
ed8fbe5e62
gnu: r-rcas: Update to 1.0.0.
...
* gnu/packages/bioinformatics.scm (r-rcas): Update to 1.0.0.
2016-11-03 19:01:46 +01:00
16a8bd3194
gnu: r-rtracklayer: Update to 1.34.1.
...
* gnu/packages/bioinformatics.scm (r-rtracklayer): Update to 1.34.1.
2016-11-03 19:01:46 +01:00
c15ae9b008
gnu: r-biocparallel: Update to 1.8.1.
...
* gnu/packages/bioinformatics.scm (r-biocparallel): Update to 1.8.1.
2016-11-03 19:01:46 +01:00
5b3b2d2f02
gnu: r-limma: Update to 3.30.2.
...
* gnu/packages/bioinformatics.scm (r-limma): Update to 3.30.2.
2016-11-03 19:01:46 +01:00
ed3054231d
gnu: r-edger: Update to 3.16.1.
...
* gnu/packages/bioinformatics.scm (r-edger): Update to 3.16.1.
2016-11-03 19:01:45 +01:00
044ac8d294
gnu: python-twobitreader: Update to 3.1.4.
...
* gnu/packages/bioinformatics.scm (python-twobitreader, python2-twobitreader):
Update to 3.1.4.
2016-10-28 13:59:11 -04:00
900fb8d005
gnu: python-twobitreader: Disable the test suite.
...
The tests were silently skipped with Python 3.4. With Python 3.5, this caused
the build of python-twobitreader to fail.
* gnu/packages/bioinformatics.scm (python-twobitreader,
python2-twobitreader)[arguments]: Disable the tests.
2016-10-28 13:59:11 -04:00
7500e42b3e
gnu: Add r-mutationalpatterns.
...
* gnu/packages/bioinformatics.scm (r-mutationalpatterns): New variable.
2016-10-27 20:07:05 +02:00
a46cc723ff
gnu: r-seqinr: Update to 3.3-3.
...
* gnu/packages/bioinformatics.scm (r-seqinr): Update to 3.3-3.
2016-10-26 16:23:26 +02:00
c70271ec48
gnu: bioperl-minimal: Update to 1.7.0.
...
* gnu/packages/bioinformatics.scm (bioperl-minimal): Update to 1.7.0.
2016-10-26 16:23:24 +02:00
59198f8fff
gnu: r-genomationdata: Update to 1.6.0.
...
* gnu/packages/bioinformatics.scm (r-genomationdata): Update to 1.6.0.
2016-10-26 09:28:23 +02:00
e357bec836
gnu: r-bamsignals: Update to 1.6.0.
...
* gnu/packages/bioinformatics.scm (r-bamsignals): Update to 1.6.0.
2016-10-26 09:28:23 +02:00
53ca52f013
gnu: r-rhtslib: Update to 1.6.0.
...
* gnu/packages/bioinformatics.scm (r-rhtslib): Update to 1.6.0.
[native-inputs]: Add autoconf.
2016-10-26 09:28:23 +02:00
da22da862b
gnu: r-zlibbioc: Update to 1.20.0.
...
* gnu/packages/bioinformatics.scm (r-zlibbioc): Update to 1.20.0.
2016-10-26 09:28:22 +02:00
809251e164
gnu: r-motifrg: Update to 1.18.0.
...
* gnu/packages/bioinformatics.scm (r-motifrg): Update to 1.18.0.
2016-10-26 09:28:22 +02:00
21d6c7a3e1
gnu: r-seqlogo: Update to 1.40.0.
...
* gnu/packages/bioinformatics.scm (r-seqlogo): Update to 1.40.0.
2016-10-26 09:28:22 +02:00
51c3c4900f
gnu: r-genomation: Update to 1.6.0.
...
* gnu/packages/bioinformatics.scm (r-genomation): Update to 1.6.0.
[propagated-inputs]: Add r-rcpp, r-htslib, r-runit, r-s4vectors.
[inputs]: Add zlib.
2016-10-26 09:28:21 +02:00
e92dd6f5e0
gnu: r-seqpattern: Update to 1.6.0.
...
* gnu/packages/bioinformatics.scm (r-seqpattern): Update to 1.6.0.
[propagated-inputs]: Add r-kernsmooth.
2016-10-26 09:28:21 +02:00
acf6f7e0c3
gnu: r-impute: Update to 1.48.0.
...
* gnu/packages/bioinformatics.scm (r-impute): Update to 1.48.0.
2016-10-26 09:28:21 +02:00
3d74c04451
gnu: r-bsgenome: Update to 1.42.0.
...
* gnu/packages/bioinformatics.scm (r-bsgenome): Update to 1.42.0.
2016-10-26 09:28:20 +02:00
30ec4de738
gnu: r-topgo: Update to 2.26.0.
...
* gnu/packages/bioinformatics.scm (r-topgo): Update to 2.26.0.
[propagated-inputs]: Add r-dbi.
2016-10-26 09:28:20 +02:00
3587b464fc
gnu: r-graph: Update to 1.52.0.
...
* gnu/packages/bioinformatics.scm (r-graph): Update to 1.52.0.
2016-10-26 09:28:19 +02:00
d1b1587cad
gnu: r-go-db: Update to 3.4.0.
...
* gnu/packages/bioinformatics.scm (r-go-db): Update to 3.4.0.
2016-10-26 09:28:19 +02:00
b17aac083e
gnu: r-genomicfeatures: Update to 1.26.0.
...
* gnu/packages/bioinformatics.scm (r-genomicfeatures): Update to 1.26.0.
2016-10-26 09:28:18 +02:00
6a45fd9aea
gnu: r-rtracklayer: Update to 1.34.0.
...
* gnu/packages/bioinformatics.scm (r-rtracklayer): Update to 1.34.0.
2016-10-26 09:28:18 +02:00
4ab32f0cd6
gnu: r-genomicalignments: Update to 1.10.0.
...
* gnu/packages/bioinformatics.scm (r-genomicalignments): Update to
1.10.0.
2016-10-26 09:28:18 +02:00
08da08d296
gnu: r-summarizedexperiment: Update to 1.4.0.
...
* gnu/packages/bioinformatics.scm (r-summarizedexperiment): Update to
1.4.0.
2016-10-26 09:28:17 +02:00
c0ccef41ae
gnu: r-rsamtools: Update to 1.26.1.
...
* gnu/packages/bioinformatics.scm (r-rsamtools): Update to 1.26.1.
2016-10-26 09:28:17 +02:00
47d39b6e7a
gnu: r-biostrings: Update to 2.42.0.
...
* gnu/packages/bioinformatics.scm (r-biostrings): Update to 2.42.0.
2016-10-26 09:28:17 +02:00
89559a124e
gnu: r-biocparallel: Update to 1.8.0.
...
* gnu/packages/bioinformatics.scm (r-biocparallel): Update to 1.8.0.
2016-10-26 09:28:16 +02:00
9405333186
gnu: r-biomart: Update to 2.30.0.
...
* gnu/packages/bioinformatics.scm (r-biomart): Update to 2.30.0.
2016-10-26 09:28:16 +02:00
e45dc05781
gnu: r-annotationdbi: Update to 1.36.0.
...
* gnu/packages/bioinformatics.scm (r-annotationdbi): Update to 1.36.0.
2016-10-26 09:28:16 +02:00
464870caf7
gnu: r-biobase: Update to 2.34.0.
...
* gnu/packages/bioinformatics.scm (r-biobase): Update to 2.34.0.
2016-10-26 09:28:15 +02:00
92a740afac
gnu: r-genomicranges: Update to 1.26.1.
...
* gnu/packages/bioinformatics.scm (r-genomicranges): Update to 1.26.1.
[propagated-inputs]: Add r-iranges, r-s4vectors.
2016-10-26 09:28:15 +02:00
1d048589ca
gnu: r-xvector: Update to 0.14.0.
...
* gnu/packages/bioinformatics.scm (r-xvector): Update to 0.14.0.
2016-10-26 09:28:14 +02:00
753bc32b8e
gnu: r-limma: Update to 3.30.0.
...
* gnu/packages/bioinformatics.scm (r-limma): Update to 3.30.0.
2016-10-26 09:28:14 +02:00
Roel Janssen