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.
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* 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.
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* 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.
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* 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.
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* gnu/packages/bioinformatics.scm (r-variantannotation): Update to 1.22.3.
2017-08-02 00:31:08 +02:00
Roel Janssen