Commit Graph

1804 Commits

Author SHA1 Message Date
Roel Janssen 1fd904fb38
gnu: Update r-mutationalpatterns to 1.4.1.
* gnu/packages/bioinformatics.scm (r-mutationalpatterns): Update to 1.4.1.
2017-11-29 14:56:28 +01:00
Roel Janssen efa6a1ddb5
gnu: Add r-copynumber.
* gnu/packages/bioinformatics.scm (r-copynumber): New variable.
2017-11-29 12:46:17 +01:00
Ricardo Wurmus d7f24778de
gnu: Add java-picard-1.113.
* gnu/packages/bioinformatics.scm (java-picard-1.113): New variable.
2017-11-27 12:12:41 +01:00
Ricardo Wurmus d7fed31ad2
gnu: Add java-picard.
* gnu/packages/bioinformatics.scm (java-picard): New variable.
2017-11-27 12:12:40 +01:00
Ricardo Wurmus bd94b6f850
gnu: java-htsjdk: Update to 2.3.0.
* gnu/packages/bioinformatics.scm (java-htsjdk): Update to 2.3.0.
[arguments]: Build with JDK 8.
[inputs]: Add java-ngs, java-snappy, java-commons-compress,
java-commons-logging-minimal, java-commons-jexl-2, and java-xz.
[native-inputs]: Add java-testng.
2017-11-27 12:12:40 +01:00
Ricardo Wurmus 35e78aaa25
gnu: r-rhdf5: Fix build phase.
* gnu/packages/bioinformatics.scm (r-rhdf5)[arguments]: Fix "unpack-smallhdf5"
phase.
2017-11-27 12:11:52 +01:00
Ricardo Wurmus e6debcaf02
gnu: subread: Update to 1.6.0.
* gnu/packages/bioinformatics.scm (subread): Update to 1.6.0.
2017-11-23 13:16:12 +01:00
Ricardo Wurmus aa33cc29ca
gnu: idr: Update to 2.0.3.
* gnu/packages/bioinformatics.scm (idr): Update to 2.0.3.
[source]: Add snippet to remove generated code.
2017-11-21 23:17:43 +01:00
Ricardo Wurmus 40590caf3b
gnu: idr: Correct license.
* gnu/packages/bioinformatics.scm (idr)[license]: Change to GPLv2+.
2017-11-21 23:17:43 +01:00
Ricardo Wurmus 261b38a978
gnu: r-genomeinfodbdata: Update to 0.99.1.
* gnu/packages/bioinformatics.scm (r-genomeinfodbdata): Update to 0.99.1.
2017-11-18 11:18:41 +01:00
Ricardo Wurmus 592f4a9434
gnu: r-go-db: Update to 3.5.0.
* gnu/packages/bioinformatics.scm (r-go-db): Update to 3.5.0.
2017-11-18 11:18:41 +01:00
Ricardo Wurmus e4664290ce
gnu: r-org-ce-eg-db: Update to 3.5.0.
* gnu/packages/bioinformatics.scm (r-org-ce-eg-db): Update to 3.5.0.
2017-11-18 11:18:40 +01:00
Ricardo Wurmus 19fc299f68
gnu: r-org-dm-eg-db: Update to 3.5.0.
* gnu/packages/bioinformatics.scm (r-org-dm-eg-db): Update to 3.5.0.
2017-11-18 11:18:40 +01:00
Ricardo Wurmus f3569f5218
gnu: r-org-mm-eg-db: Update to 3.5.0.
* gnu/packages/bioinformatics.scm (r-org-mm-eg-db): Update to 3.5.0.
2017-11-18 11:18:40 +01:00
Ricardo Wurmus 57dc9b58db
gnu: r-genomationdata: Update to 1.10.0.
* gnu/packages/bioinformatics.scm (r-genomationdata): Update to 1.10.0.
2017-11-18 11:18:39 +01:00
Ricardo Wurmus 90dbd984f8
gnu: Remove duplicate from (gnu packages bioinformatics).
* gnu/packages/bioinformatics.scm (r-annotationfilter): Remove duplicate.
2017-11-18 11:18:39 +01:00
Ricardo Wurmus 676507e388
gnu: r-org-hs-eg-db: Clarify description.
* gnu/packages/bioinformatics.scm (r-org-hs-eg-db)[description]: Clarify.
2017-11-18 11:18:38 +01:00
Ricardo Wurmus d595fed33d
gnu: r-org-hs-eg-db: Update to 3.5.0.
* gnu/packages/bioinformatics.scm (r-org-hs-eg-db): Update to 3.5.0.
2017-11-18 11:18:37 +01:00
Ricardo Wurmus ccedfd3a43
gnu: r-org-hs-eg-db: Remove duplicate package definition.
* gnu/packages/bioinformatics.scm (r-org-hs-eg-db): Remove duplicate variable.
2017-11-18 11:18:37 +01:00
Ricardo Wurmus ac257f127a
gnu: Move testing packages from python.scm to check.scm.
* gnu/packages/python.scm (python-behave-web-api, python2-behave-web-api,
python-mock, python2-mock, python-mock-2, python-nose, python2-nose,
python-nose2, python2-nose2, python-unittest2, python2-unittest2,
python-pytest, python2-pytest, python-pytest-3.0, python2-pytest-3.0,
python-pytest-cov, python2-pytest-cov, python-pytest-runner,
python2-pytest-runner, python-pytest-mock, python2-pytest-mock,
python-pytest-xdist, python2-pytest-xdist, python-scripttest,
python2-scripttest, python-testtools, python2-testtools, python-testscenarios,
python2-testscenarios, python-testresources, python2-testresources,
python-subunit, python2-subunit, python-fixtures, python2-fixtures,
python-testrepository, python2-testrepository, python-coverage,
python2-coverage, python-cov-core, python2-cov-core, python-testpath,
python2-testpath, python-testlib, python2-testlib, python-pytest-cache,
python2-pytest-cache, python-pytest-localserver, python-pytest-xprocess,
python-pytest-subtesthack, python2-pytest-subtesthack, python-hypothesis,
python2-hypothesis, python-lit, python2-lit, python-pytest-pep8,
python2-pytest-pep8, python-pytest-flakes, python2-pytest-flakes,
python2-coverage-test-runner, python-pylint, python2-pylint,
python-paramunittest, python2-python-paramunittest, python-pytest-warnings,
python2-pytest-warnings, python-pytest-capturelog, python2-pytest-capturelog,
python-pytest-catchlog, python2-pytest-catchlog, python-nosexcover,
python2-nosexcover, python-discover, python2-discover, behave, python-rednose,
python2-rednose, python-nose-randomly, python2-nose-randomly,
python-nose-timer, python2-nose-timer): Move from here...
* gnu/packages/check.scm: ...to here.
* gnu/packages/admin.scm,
gnu/packages/android.scm,
gnu/packages/backup.scm,
gnu/packages/bioinformatics.scm,
gnu/packages/calendar.scm,
gnu/packages/dav.scm,
gnu/packages/django.scm,
gnu/packages/freedesktop.scm,
gnu/packages/haskell.scm,
gnu/packages/image.scm,
gnu/packages/irc.scm,
gnu/packages/jrnl.scm,
gnu/packages/ldc.scm,
gnu/packages/libffi.scm,
gnu/packages/mail.scm,
gnu/packages/mpd.scm,
gnu/packages/openstack.scm,
gnu/packages/package-management.scm,
gnu/packages/password-utils.scm,
gnu/packages/python-crypto.scm,
gnu/packages/python-web.scm,
gnu/packages/rdf.scm,
gnu/packages/statistics.scm,
gnu/packages/storage.scm,
gnu/packages/time.scm,
gnu/packages/tls.scm,
gnu/packages/tor.scm,
gnu/packages/tryton.scm: Adjust accordingly.
2017-11-17 22:36:26 +01:00
Ludovic Courtès 589e3f4e70
gnu: Move more packages from python to python-web.
* gnu/packages/python.scm (python-requests, python2-requests)
(python-requests-2.7, python-oauthlib, python2-oauthlib)
(python-furl, python2-furl, python-wsgi-intercept)
(python-publicsuffix, python2-publicsuffix)
(python-publicsuffix2, python2-publicsuffix2): Move to...
* gnu/packages/python-web.scm: ... here.
* gnu/packages/bioinformatics.scm, gnu/packages/finance.scm:
gnu/packages/maths.scm, gnu/packages/terminals.scm,
gnu/packages/video.scm, gnu/packages/virtualization.scm: Adjust
accordingly.
2017-11-16 08:45:15 +01:00
Ben Woodcroft a68e586097
gnu: diamond: Update to 0.9.13.
* gnu/packages/bioinformatics.scm (diamond): Update to 0.9.13.
2017-11-14 08:25:43 +10:00
Ricardo Wurmus 5ccde2079e
gnu: Move test packages from perl to perl-check.
* gnu/packages/perl.scm (perl-test2-bundle-extended,
perl-test2-plugin-nowarnings, perl-test-base, perl-test-class,
perl-test-class-most, perl-test-cleannamespaces, perl-test-command,
perl-test-cpan-meta, perl-test-cpan-meta-json, perl-test-deep,
perl-test-differences, perl-test-directory, perl-test-eol,
perl-test-exception, perl-test-fatal, perl-test-file-sharedir-dist,
perl-test-files, perl-test-harness, perl-test-leaktrace,
perl-test-longstring, perl-test-manifest, perl-test-memory-cycle,
perl-test-mockobject, perl-test-mocktime, perl-test-most, perl-test-needs,
perl-test-notabs, perl-test-nowarnings, perl-test-number-delta,
perl-test-output, perl-test-pod, perl-test-pod-coverage, perl-test-requires,
perl-test-script, perl-test-sharedfork, perl-test-simple, perl-test-taint,
perl-test-tester, perl-test-trap, perl-test-utf8, perl-test-warn,
perl-test-warnings, perl-test-without-module, perl-test-writevariants,
perl-test-yaml, perl-test-trailingspace): Move variables to ...
* gnu/packages/perl-check.scm: ... this new file.
* gnu/local.mk (GNU_SYSTEM_MODULES): Add it.
* gnu/packages/admin.scm,
gnu/packages/bioinformatics.scm,
gnu/packages/crypto.scm,
gnu/packages/databases.scm,
gnu/packages/glib.scm,
gnu/packages/gnupg.scm,
gnu/packages/image-viewers.scm,
gnu/packages/language.scm,
gnu/packages/networking.scm,
gnu/packages/package-management.scm,
gnu/packages/perl.scm,
gnu/packages/terminals.scm,
gnu/packages/tex.scm,
gnu/packages/version-control.scm,
gnu/packages/web.scm,
gnu/packages/xml.scm,
gnu/packages/xorg.scm: Use perl-check module.
2017-11-13 23:03:01 +01:00
Ricardo Wurmus d4735e8c65
gnu: cd-hit: Update source tarball hash.
* gnu/packages/bioinformatics.scm (cd-hit)[source]: Update hash.
2017-11-13 16:02:35 +01:00
Tobias Geerinckx-Rice 11ed4108fb
gnu: methylkit: Use new home page.
* gnu/packages/bioinformatics.scm (methylkit)[home-page]: Update.
2017-11-11 05:17:58 +01:00
Ben Woodcroft 7c087150ec
gnu: vsearch: Update to 2.6.0.
* gnu/packages/bioinformatics.scm (vsearch): Update to 2.6.0.
2017-11-11 09:33:16 +10:00
Ricardo Wurmus 0af4df7e61
gnu: cutadapt: Update to 1.14.
* gnu/packages/bioinformatics.scm (cutadapt): Update to 1.14.
2017-11-10 15:32:42 +01:00
Ben Woodcroft da4a707c88
gnu: roary: Update to 3.11.0.
* gnu/packages/bioinformatics.scm (roary): Update to 3.11.0.
[inputs]: Add perl-digest-md5-file.
2017-11-09 18:12:32 +10:00
Ricardo Wurmus 34260a10d7
gnu: miso: Use pypi-uri.
* gnu/packages/bioinformatics.scm (miso)[source]: Use pypi-uri.
2017-11-08 17:41:08 +01:00
Ricardo Wurmus c49102ecca
gnu: Add r-hitc.
* gnu/packages/bioinformatics.scm (r-hitc): New variable.
2017-11-07 23:32:45 +01:00
Ricardo Wurmus 30eb4e37c8
gnu: Add r-fithic.
* gnu/packages/bioinformatics.scm (r-fithic): New variable.
2017-11-07 23:32:45 +01:00
Ricardo Wurmus fbf5440637
gnu: Add r-sushi.
* gnu/packages/bioinformatics.scm (r-sushi): New variable.
2017-11-07 23:32:45 +01:00
Ricardo Wurmus 2e4ce60e7c
gnu: Add r-gwascat.
* gnu/packages/bioinformatics.scm (r-gwascat): New variable.
2017-11-07 23:32:44 +01:00
Ricardo Wurmus 4272000661
gnu: Add r-gviz.
* gnu/packages/bioinformatics.scm (r-gviz): New variable.
2017-11-07 23:32:44 +01:00
Ricardo Wurmus 794ff347a9
gnu: Add r-gqtlstats.
* gnu/packages/bioinformatics.scm (r-gqtlstats): New variable.
2017-11-07 23:32:44 +01:00
Ricardo Wurmus 66c39102e5
gnu: Add r-ldblock.
* gnu/packages/bioinformatics.scm (r-ldblock): New variable.
2017-11-07 23:32:44 +01:00
Ricardo Wurmus 15f98b0d23
gnu: Add r-erma.
* gnu/packages/bioinformatics.scm (r-erma): New variable.
2017-11-07 23:32:43 +01:00
Ricardo Wurmus 421c68e3f7
gnu: Add r-homo-sapiens.
* gnu/packages/bioinformatics.scm (r-homo-sapiens): New variable.
2017-11-07 23:32:43 +01:00
Ricardo Wurmus b52a866d14
gnu: Add r-org-hs-eg-db.
* gnu/packages/bioinformatics.scm (r-org-hs-eg-db): New variable.
2017-11-07 23:32:43 +01:00
Ricardo Wurmus dd5fc8b78e
gnu: Add r-snpstats.
* gnu/packages/bioinformatics.scm (r-snpstats): New variable.
2017-11-07 23:32:43 +01:00
Ricardo Wurmus e2b927993e
gnu: Add r-gqtlbase.
* gnu/packages/bioinformatics.scm (r-gqtlbase): New variable.
2017-11-07 23:32:43 +01:00
Ricardo Wurmus 96a392a0b2
gnu: Add r-gprofiler.
* gnu/packages/bioinformatics.scm (r-gprofiler): New variable.
2017-11-07 23:32:42 +01:00
Ricardo Wurmus 60faf94597
gnu: Add r-ggbio.
* gnu/packages/bioinformatics.scm (r-ggbio): New variable.
2017-11-07 23:32:42 +01:00
Ricardo Wurmus 7af1f40373
gnu: Add r-biovizbase.
* gnu/packages/bioinformatics.scm (r-biovizbase): New variable.
2017-11-07 23:32:42 +01:00
Ricardo Wurmus 2f6f61fd8e
gnu: Add r-organismdbi.
* gnu/packages/bioinformatics.scm (r-organismdbi): New variable.
2017-11-07 23:32:42 +01:00
Ricardo Wurmus aa30ab5aee
gnu: Add r-ensembldb.
* gnu/packages/bioinformatics.scm (r-ensembldb): New variable.
2017-11-07 23:32:42 +01:00
Ricardo Wurmus 763e98103a
gnu: Add r-annotationfilter.
* gnu/packages/bioinformatics.scm (r-annotationfilter): New variable.
2017-11-07 23:32:42 +01:00
Ricardo Wurmus 04e2a2e969
gnu: Add r-dirichletmultinomial.
* gnu/packages/bioinformatics.scm (r-dirichletmultinomial): New variable.
2017-11-07 23:32:41 +01:00
Ricardo Wurmus 3af149f524
gnu: Add r-complexheatmap.
* gnu/packages/bioinformatics.scm (r-complexheatmap): New variable.
2017-11-07 23:32:41 +01:00
Ricardo Wurmus 902fb15d92
gnu: Add r-genomicfiles.
* gnu/packages/bioinformatics.scm (r-genomicfiles): New variable.
2017-11-07 23:32:41 +01:00
Ricardo Wurmus e160aa1f81
gnu: Add r-gage.
* gnu/packages/bioinformatics.scm (r-gage): New variable.
2017-11-07 12:39:51 +01:00
Ricardo Wurmus 3121814ef1
gnu: Add r-keggrest.
* gnu/packages/bioinformatics.scm (r-keggrest): New variable.
2017-11-07 12:39:51 +01:00
Ricardo Wurmus baa00ee90d
gnu: r-msnbase: Update to 2.4.0.
* gnu/packages/bioinformatics.scm (r-msnbase): Update to 2.4.0.
[propagated-inputs]: Add r-lattice; remove r-reshape2.
2017-11-07 08:15:44 +01:00
Ricardo Wurmus 39d9098def
gnu: r-mutationalpatterns: Update to 1.4.0.
* gnu/packages/bioinformatics.scm (r-mutationalpatterns): Update to 1.4.0.
[propagated-inputs]: Add r-cowplot, r-ggdendro, and r-s4vectors.
2017-11-07 08:15:44 +01:00
Ricardo Wurmus 14b3c71911
gnu: r-annotationhub: Update to 2.10.0.
* gnu/packages/bioinformatics.scm (r-annotationhub): Update to 2.10.0.
[propagated-inputs]: Add r-curl.
2017-11-07 08:15:44 +01:00
Ricardo Wurmus 15ca195979
gnu: r-mzr: Remove bundled copy of boost.
* gnu/packages/bioinformatics.scm (r-mzr)[source]: Remove boost source.
[arguments]: Add build phase "use-system-boost" to link with our boost
package and avoid building the bundled sources.
2017-11-07 08:15:44 +01:00
Ricardo Wurmus 34b9675449
gnu: r-mzr: Update to 2.12.0.
* gnu/packages/bioinformatics.scm (r-mzr): Update to 2.12.0.
2017-11-07 08:15:43 +01:00
Ricardo Wurmus b500dbcdef
gnu: r-mzid: Update to 1.16.0.
* gnu/packages/bioinformatics.scm (r-mzid): Update to 1.16.0.
2017-11-07 08:15:43 +01:00
Ricardo Wurmus eeaa6967f9
gnu: r-chipseq: Update to 1.28.0.
* gnu/packages/bioinformatics.scm (r-chipseq): Update to 1.28.0.
[propagated-inputs]: Add r-lattice.
2017-11-07 08:15:43 +01:00
Ricardo Wurmus 158b6743dc
gnu: r-genomicfeatures: Update to 1.30.0.
* gnu/packages/bioinformatics.scm (r-genomicfeatures): Update to 1.30.0.
[propagated-inputs]: Add r-rmysql.
2017-11-07 08:15:43 +01:00
Ricardo Wurmus 4dd469ef6d
gnu: r-rtracklayer: Update to 1.38.0.
* gnu/packages/bioinformatics.scm (r-rtracklayer): Update to 1.38.0.
[arguments]: Adjust patch to use system zlib.
2017-11-07 08:15:42 +01:00
Ricardo Wurmus a044c7f4c4
gnu: r-biocparallel: Update to 1.12.0.
* gnu/packages/bioinformatics.scm (r-biocparallel): Update to 1.12.0.
[propagated-inputs]: Add r-bh.
2017-11-07 08:15:42 +01:00
Ricardo Wurmus 42e11d3301
gnu: r-biomart: Update to 2.34.0.
* gnu/packages/bioinformatics.scm (r-biomart): Update to 2.34.0.
[propagated-inputs]: Add r-progress and r-stringr.
2017-11-07 08:15:42 +01:00
Ricardo Wurmus 010ab2ffd2
gnu: r-edger: Update to 3.20.1.
* gnu/packages/bioinformatics.scm (r-edger): Update to 3.20.1.
[propagated-inputs]: Add r-rcpp.
2017-11-07 08:15:42 +01:00
Ricardo Wurmus eb3f5cc76a
gnu: r-gostats: Update to 2.44.0.
* gnu/packages/bioinformatics.scm (r-gostats): Update to 2.44.0.
[propagated-inputs]: Add r-rgraphviz.
2017-11-07 08:15:41 +01:00
Ricardo Wurmus 2404cc4283
gnu: r-category: Update to 2.44.0.
* gnu/packages/bioinformatics.scm (r-category): Update to 2.44.0.
[propagated-inputs]: Remove r-rsqlite; add r-dbi.
2017-11-07 08:15:41 +01:00
Ricardo Wurmus 1be0f53664
gnu: r-vsn: Update to 3.46.0.
* gnu/packages/bioinformatics.scm (r-vsn): Update to 3.46.0.
[propagated-inputs]: Remove r-hexbin.
2017-11-07 08:15:40 +01:00
Ricardo Wurmus 007424b5a5
gnu: r-motifrg: Rename input label.
* gnu/packages/bioinformatics.scm (r-motifrg)[propagated-inputs]:
Rename label of r-bsgenome-hsapiens-ucsc-hg19.
2017-11-07 08:15:40 +01:00
Ricardo Wurmus ce59d62519
gnu: r-motifrg: Update to 1.22.0.
* gnu/packages/bioinformatics.scm (r-motifrg): Update to 1.22.0.
2017-11-07 08:15:40 +01:00
Ricardo Wurmus 98791c25c8
gnu: r-qvalue: Update to 2.10.0.
* gnu/packages/bioinformatics.scm (r-qvalue): Update to 2.10.0.
2017-11-07 08:15:39 +01:00
Ricardo Wurmus 87fa5aface
gnu: r-fastseq: Update to 1.24.0.
* gnu/packages/bioinformatics.scm (r-fastseq): Update to 1.24.0.
2017-11-07 08:15:39 +01:00
Ricardo Wurmus 1567c8d91b
gnu: r-interactivedisplaybase: Update to 1.16.0.
* gnu/packages/bioinformatics.scm (r-interactivedisplaybase): Update to
1.16.0.
2017-11-07 08:15:39 +01:00
Ricardo Wurmus 0096127974
gnu: r-edaseq: Update to 2.12.0.
* gnu/packages/bioinformatics.scm (r-edaseq): Update to 2.12.0.
2017-11-07 08:15:39 +01:00
Ricardo Wurmus 22752bef3b
gnu: r-msnid: Update to 1.11.0.
* gnu/packages/bioinformatics.scm (r-msnid): Update to 1.11.0.
2017-11-07 08:15:38 +01:00
Ricardo Wurmus 8140f680ad
gnu: r-deseq: Update to 1.30.0.
* gnu/packages/bioinformatics.scm (r-deseq): Update to 1.30.0.
2017-11-07 08:15:38 +01:00
Ricardo Wurmus 531e80903f
gnu: r-aroma-light: Update to 3.8.0.
* gnu/packages/bioinformatics.scm (r-aroma-light): Update to 3.8.0.
2017-11-07 08:15:38 +01:00
Ricardo Wurmus a998c9a464
gnu: r-pcamethods: Update to 1.70.0.
* gnu/packages/bioinformatics.scm (r-pcamethods): Update to 1.70.0.
2017-11-07 08:15:38 +01:00
Ricardo Wurmus 8a8138d248
gnu: r-affyio: Update to 1.48.0.
* gnu/packages/bioinformatics.scm (r-affyio): Update to 1.48.0.
2017-11-07 08:15:38 +01:00
Ricardo Wurmus dad5f83817
gnu: r-affy: Update to 1.56.0.
* gnu/packages/bioinformatics.scm (r-affy): Update to 1.56.0.
2017-11-07 08:15:37 +01:00
Ricardo Wurmus 9a665dfb6f
gnu: r-protgenerics: Update to 1.10.0.
* gnu/packages/bioinformatics.scm (r-protgenerics): Update to 1.10.0.
2017-11-07 08:15:37 +01:00
Ricardo Wurmus 617700895b
gnu: r-seqlogo: Update to 1.44.0.
* gnu/packages/bioinformatics.scm (r-seqlogo): Update to 1.44.0.
2017-11-07 08:15:37 +01:00
Ricardo Wurmus e127c918f8
gnu: r-genomation: Update to 1.10.0.
* gnu/packages/bioinformatics.scm (r-genomation): Update to 1.10.0.
[propagated-inputs]: Remove r-rhtslib.
[inputs]: Remove zlib.
2017-11-07 08:15:37 +01:00
Ricardo Wurmus e6ce4bf00d
gnu: r-impute: Update to 1.52.0.
* gnu/packages/bioinformatics.scm (r-impute): Update to 1.52.0.
2017-11-07 08:15:37 +01:00
Ricardo Wurmus 0f948b116b
gnu: r-seqpattern: Update to 1.10.0.
* gnu/packages/bioinformatics.scm (r-seqpattern): Update to 1.10.0.
2017-11-07 08:15:36 +01:00
Ricardo Wurmus e67850b40d
gnu: r-bsgenome: Update to 1.46.0.
* gnu/packages/bioinformatics.scm (r-bsgenome): Update to 1.46.0.
2017-11-07 08:15:36 +01:00
Ricardo Wurmus d13a3fea7e
gnu: r-topgo: Update to 2.30.0.
* gnu/packages/bioinformatics.scm (r-topgo): Update to 2.30.0.
2017-11-07 08:15:36 +01:00
Ricardo Wurmus aeb73879f6
gnu: r-graph: Update to 1.56.0.
* gnu/packages/bioinformatics.scm (r-graph): Update to 1.56.0.
2017-11-07 08:15:36 +01:00
Ricardo Wurmus 96fb465174
gnu: r-genomicalignments: Update to 1.14.0.
* gnu/packages/bioinformatics.scm (r-genomicalignments): Update to 1.14.0.
2017-11-07 08:15:35 +01:00
Ricardo Wurmus 6fcbed7329
gnu: r-summarizedexperiment: Update to 1.8.0.
* gnu/packages/bioinformatics.scm (r-summarizedexperiment): Update to 1.8.0.
2017-11-07 08:15:35 +01:00
Ricardo Wurmus cb0a9a7493
gnu: r-delayedarray: Update to 0.4.1.
* gnu/packages/bioinformatics.scm (r-delayedarray): Update to 0.4.1.
2017-11-07 08:15:35 +01:00
Ricardo Wurmus f8068419a6
gnu: r-rsamtools: Update to 1.30.0.
* gnu/packages/bioinformatics.scm (r-rsamtools): Update to 1.30.0.
2017-11-07 08:15:35 +01:00
Ricardo Wurmus b719435ebb
gnu: r-biostrings: Update to 2.46.0.
* gnu/packages/bioinformatics.scm (r-biostrings): Update to 2.46.0.
2017-11-07 08:15:35 +01:00
Ricardo Wurmus 0f8d98f294
gnu: r-annotationdbi: Update to 1.40.0.
* gnu/packages/bioinformatics.scm (r-annotationdbi): Update to 1.40.0.
2017-11-07 08:15:34 +01:00
Ricardo Wurmus ca52123611
gnu: r-biobase: Update to 2.38.0.
* gnu/packages/bioinformatics.scm (r-biobase): Update to 2.38.0.
2017-11-07 08:15:34 +01:00
Ricardo Wurmus aa5c1f61f1
gnu: r-genomicranges: Update to 1.30.0.
* gnu/packages/bioinformatics.scm (r-genomicranges): Update to 1.30.0.
2017-11-07 08:15:34 +01:00
Ricardo Wurmus 2b6ae8bfd5
gnu: r-xvector: Update to 0.18.0.
* gnu/packages/bioinformatics.scm (r-xvector): Update to 0.18.0.
2017-11-07 08:15:34 +01:00
Ricardo Wurmus f642c0e4c7
gnu: r-limma: Update to 3.34.0.
* gnu/packages/bioinformatics.scm (r-limma): Update to 3.34.0.
2017-11-07 08:15:33 +01:00
Ricardo Wurmus 7f1bac3528
gnu: r-variantannotation: Update to 1.24.0.
* gnu/packages/bioinformatics.scm (r-variantannotation): Update to 1.24.0.
2017-11-07 08:15:33 +01:00
Ricardo Wurmus 8aab0235e0
gnu: r-genomeinfodb: Update to 1.14.0.
* gnu/packages/bioinformatics.scm (r-genomeinfodb): Update to 1.14.0.
2017-11-07 08:15:33 +01:00
Ricardo Wurmus 9e482c2069
gnu: r-iranges: Update to 2.12.0.
* gnu/packages/bioinformatics.scm (r-iranges): Update to 2.12.0.
2017-11-07 08:15:33 +01:00
Ricardo Wurmus 41f0f94976
gnu: r-s4vectors: Update to 0.16.0.
* gnu/packages/bioinformatics.scm (r-s4vectors): Update to 0.16.0.
2017-11-07 08:15:33 +01:00
Ricardo Wurmus 2167eafc1d
gnu: r-biocstyle: Update to 2.6.0.
* gnu/packages/bioinformatics.scm (r-biocstyle): Update to 2.6.0.
2017-11-07 08:15:32 +01:00
Ricardo Wurmus 3241461670
gnu: r-biocinstaller: Update to 1.28.0.
* gnu/packages/bioinformatics.scm (r-biocinstaller): Update to 1.28.0.
2017-11-07 08:15:32 +01:00
Ricardo Wurmus d61fc4e104
gnu: r-biocgenerics: Update to 0.24.0.
* gnu/packages/bioinformatics.scm (r-biocgenerics): Update to 0.24.0.
2017-11-07 08:15:32 +01:00
Ricardo Wurmus 704fe4d115
gnu: r-grohmm: Update to 1.12.0.
* gnu/packages/bioinformatics.scm (r-grohmm): Update to 1.12.0.
2017-11-07 08:15:32 +01:00
Ricardo Wurmus 843826e262
gnu: r-shortread: Update to 1.36.0.
* gnu/packages/bioinformatics.scm (r-shortread): Update to 1.36.0.
2017-11-07 08:15:31 +01:00
Ricardo Wurmus b53755258a
gnu: r-systempiper: Update to 1.12.0.
* gnu/packages/bioinformatics.scm (r-systempiper): Update to 1.12.0.
2017-11-07 08:15:31 +01:00
Ricardo Wurmus 9f52e53d5d
gnu: r-gseabase: Update to 1.40.0.
* gnu/packages/bioinformatics.scm (r-gseabase): Update to 1.40.0.
2017-11-07 08:15:31 +01:00
Ricardo Wurmus fad7c0c7bd
gnu: r-sva: Update to 3.26.0.
* gnu/packages/bioinformatics.scm (r-sva): Update to 3.26.0.
2017-11-07 08:15:31 +01:00
Ricardo Wurmus 91e1867972
gnu: r-methylkit: Update to 1.4.0.
* gnu/packages/bioinformatics.scm (r-methylkit): Update to 1.4.0.
2017-11-07 08:15:31 +01:00
Ricardo Wurmus c126ba69db
gnu: r-copywriter: Update to 2.10.0.
* gnu/packages/bioinformatics.scm (r-copywriter): Update to 2.10.0.
2017-11-07 08:15:30 +01:00
Ricardo Wurmus 598dacf657
gnu: r-annotationfilter: Update to 1.2.0.
* gnu/packages/bioinformatics.scm (r-annotationfilter): Update to 1.2.0.
2017-11-07 08:15:30 +01:00
Ricardo Wurmus e6b332d43b
gnu: r-rhdf5: Update to 2.22.0.
* gnu/packages/bioinformatics.scm (r-rhdf5): Update to 2.22.0.
2017-11-07 08:15:30 +01:00
Ricardo Wurmus 19e8929cbd
gnu: r-tximport: Update to 1.6.0.
* gnu/packages/bioinformatics.scm (r-tximport): Update to 1.6.0.
2017-11-07 08:15:30 +01:00
Ricardo Wurmus da153b7f94
gnu: r-bamsignals: Update to 1.10.0.
* gnu/packages/bioinformatics.scm (r-bamsignals): Update to 1.10.0.
2017-11-07 08:15:30 +01:00
Ricardo Wurmus 5c18470008
gnu: r-zlibbioc: Update to 1.24.0.
* gnu/packages/bioinformatics.scm (r-zlibbioc): Update to 1.24.0.
2017-11-07 08:15:29 +01:00
Ricardo Wurmus 1d0263b44e
gnu: r-rhtslib: Update to 1.10.0.
* gnu/packages/bioinformatics.scm (r-rhtslib): Update to 1.10.0.
2017-11-07 08:15:29 +01:00
Ricardo Wurmus c25154e5cb
gnu: r-rbgl: Update to 1.54.0.
* gnu/packages/bioinformatics.scm (r-rbgl): Update to 1.54.0.
2017-11-07 08:15:29 +01:00
Ricardo Wurmus 727706ad38
gnu: r-annotationforge: Update to 1.20.0.
* gnu/packages/bioinformatics.scm (r-annotationforge): Update to 1.20.0.
2017-11-07 08:15:29 +01:00
Ricardo Wurmus 3fd010ff30
gnu: r-dexseq: Update to 1.24.0.
* gnu/packages/bioinformatics.scm (r-dexseq): Update to 1.24.0.
2017-11-07 08:15:28 +01:00
Ricardo Wurmus 0166dc07ef
gnu: r-deseq2: Update to 1.18.0.
* gnu/packages/bioinformatics.scm (r-deseq2): Update to 1.18.0.
2017-11-07 08:15:28 +01:00
Ricardo Wurmus 554fac74aa
gnu: r-genefilter: Update to 1.60.0.
* gnu/packages/bioinformatics.scm (r-genefilter): Update to 1.60.0.
2017-11-07 08:15:28 +01:00
Ricardo Wurmus cb4d3ff2c4
gnu: r-geneplotter: Update to 1.56.0.
* gnu/packages/bioinformatics.scm (r-geneplotter): Update to 1.56.0.
2017-11-07 08:15:28 +01:00
Ricardo Wurmus 2d4e887dc0
gnu: r-annotate: Update to 1.56.0.
* gnu/packages/bioinformatics.scm (r-annotate): Update to 1.56.0.
2017-11-07 08:15:28 +01:00
Ricardo Wurmus 94fd86e5e1
gnu: r-dnacopy: Update to 1.52.0.
* gnu/packages/bioinformatics.scm (r-dnacopy): Update to 1.52.0.
2017-11-07 08:15:27 +01:00
Ricardo Wurmus c7782c3f1f
gnu: r-biocviews: Update to 1.46.0.
* gnu/packages/bioinformatics.scm (r-biocviews): Update to 1.46.0.
[propagated-inputs]: Remove r-knitr.
2017-11-07 08:15:27 +01:00
Ricardo Wurmus 7373b4167a
gnu: r-bioccheck: Update to 1.14.0.
* gnu/packages/bioinformatics.scm (r-bioccheck): Update to 1.14.0.
[native-inputs]: Remove which.
[propagated-inputs]: Add r-stringdist.
2017-11-07 08:15:27 +01:00
Ben Woodcroft 171ba2480f
gnu: diamond: Update to 0.9.12.
* gnu/packages/bioinformatics.scm (diamond): Update to 0.9.12.
2017-11-04 10:51:44 +10:00
Ricardo Wurmus 66865ab8ac
gnu: multiqc: Update to 1.3.
* gnu/packages/bioinformatics.scm (multiqc): Update to 1.3.
[propagated-inputs]: Add python-enum34.
[license]: The license was changed to "GPLv3 or later" with this release.
2017-11-03 17:18:52 +01:00
Ricardo Wurmus b12c6a664d
gnu: r-ape: Update to 5.0.
* gnu/packages/bioinformatics.scm (r-ape): Update to 5.0.
[propagated-inputs]: Add r-rcpp.
2017-11-03 14:14:38 +01:00
Ben Woodcroft 03d6e9dd08
gnu: vsearch: Update to 2.5.2.
* gnu/packages/bioinformatics.scm (vsearch): Update to 2.5.2.
2017-11-01 10:57:05 +10:00
Ben Woodcroft e126b79736
gnu: diamond: Update to 0.9.11.
* gnu/packages/bioinformatics.scm (diamond): Update to 0.9.11.
2017-11-01 10:57:03 +10:00
Ricardo Wurmus 7bf59f7021
gnu: Remove cufflinks.
Cufflinks includes essential non-free code.
Fixes <https://bugs.gnu.org/28946>.

* gnu/packages/bioinformatics.scm (cufflinks): Remove variable.
2017-10-31 08:17:06 +01:00
Ben Woodcroft ed5e9a33f8
gnu: vsearch: Update to 2.5.1.
* gnu/packages/bioinformatics.scm (vsearch): Update to 2.5.1.
2017-10-26 19:55:29 +10:00
Ben Woodcroft 6f141eff47
gnu: bwa: Update to 0.7.17.
* gnu/packages/bioinformatics.scm (bwa): Update to 0.7.17.
2017-10-25 09:29:22 +10:00
Ben Woodcroft ae6e00f6f9
gnu: bwa: Change source URL to GitHub.
* gnu/packages/bioinformatics.scm (bwa)[source]: Change source URL to
GitHub.
2017-10-25 09:29:22 +10:00
Tobias Geerinckx-Rice ce4dfde0d8
gnu: miso: Update to 0.5.4.
* gnu/packages/bioinformatics.scm (miso): Update to 0.5.4.
2017-10-23 14:49:29 +02:00
Tobias Geerinckx-Rice 5713bbf157
Use HTTPS for bioconductor.org.
* doc/guix.texi (Invoking guix import, Invoking guix refresh): Use HTTPS for
bioconductor.org URLs.
* gnu/packages/bioinformatics.scm (r-annotate, r-geneplotter, r-genefilter)
(r-deseq2, r-dexseq, r-annotationforge, r-rbgl, r-gseabase, r-category)
(r-gostats, r-shortread, r-biocgenerics, r-biocinstaller, r-biocviews)
(r-biocstyle, r-bioccheck, r-s4vectors, r-iranges, r-genomeinfodbdata)
(r-genomeinfodb, r-xvector, r-genomicranges, r-biobase, r-annotationdbi)
(r-biomart, r-biocparallel, r-biostrings, r-rsamtools, r-delayedarray)
(r-summarizedexperiment, r-genomicalignments, r-rtracklayer)
(r-genomicfeatures, r-graph, r-topgo, r-bsgenome, r-impute, r-seqpattern)
(r-seqlogo, r-motifrg, r-bamsignals, r-mutationalpatterns, r-tximport)
(r-rhdf5, r-chipseq, r-sva, r-affy, r-vsn, r-mzid, r-msnid)
(r-interactivedisplaybase, r-annotationhub)[home-page]: Likewise.
* gnu/packages/bioinformatics.scm (r-txdb-hsapiens-ucsc-hg19-knowngene)
(r-go-db, r-bsgenome-hsapiens-1000genomes-hs37d5, r-org-hs-eg-db)
(r-org-ce-eg-db, r-org-dm-eg-db, r-org-mm-eg-db)
(r-bsgenome-hsapiens-ucsc-hg19, r-bsgenome-mmusculus-ucsc-mm9)
(r-bsgenome-mmusculus-ucsc-mm10, r-txdb-mmusculus-ucsc-mm10-knowngene)
(r-bsgenome-celegans-ucsc-ce6, r-bsgenome-celegans-ucsc-ce10)
(r-bsgenome-dmelanogaster-ucsc-dm3, r-copyhelper)[source, home-page]:
Likewise.
* gnu/packages/statistics.scm (r-rcurl)[source]: Likewise.
* guix/build-system/r.scm (bioconductor-uri): Likewise.
* guix/import/cran.scm (%cran-url, bioconductor-package?)
(bioconductor-data-package?, bioconductor-experiment-package?): Likewise.
2017-10-21 17:43:40 +02:00
Ricardo Wurmus c0770feedd
gnu: f-seq: Fix location of commons-cli.jar.
* gnu/packages/bioinformatics.scm (f-seq)[arguments]: Fix location of
commons-cli.jar in the wrapper script.
2017-10-18 23:54:16 +02:00
Cyril Roelandt af6ce61088
gnu: python-biopython: Update to 1.70.
* gnu/packages/python.scm (python-biopython, python2-biopython): Update to 1.70.
2017-10-14 03:17:50 +02:00
Ricardo Wurmus dad66da493
gnu: Add plink-ng.
* gnu/packages/bioinformatics.scm (plink-ng): New variable.
2017-10-13 11:14:00 +02:00
Ricardo Wurmus dc8ddbfb07
gnu: Add paml.
* gnu/packages/bioinformatics.scm (paml): New variable.
2017-10-13 11:14:00 +02:00
Ricardo Wurmus b3936f35ae
gnu: clustal-omega: Update to 1.2.4.
* gnu/packages/bioinformatics.scm (clustal-omega): Update to 1.2.4.
2017-10-12 23:54:54 +02:00
Ricardo Wurmus c6643f2d52
gnu: f-seq: Truncate version string.
* gnu/packages/bioinformatics.scm (f-seq)[version]: Truncate commit part of
the version string.
2017-10-12 08:43:54 +02:00
Ricardo Wurmus 01d87d3c18
gnu: rcas-web: Update to 0.0.4.
* gnu/packages/bioinformatics.scm (rcas-web): Update to 0.0.4.
2017-10-11 21:37:37 +02:00
Marius Bakke ad3a937dae
Merge branch 'master' into staging 2017-10-07 12:54:40 +02:00
Ben Woodcroft 3ae76f7f57
gnu: vsearch: Update to 2.5.0.
* gnu/packages/bioinformatics.scm (vsearch): Update to 2.5.0.
2017-10-07 09:42:55 +10:00
Marius Bakke ffcff27272
Merge branch 'master' into staging 2017-09-24 19:18:35 +02:00
Ben Woodcroft 8c864901b6
gnu: proteinortho: Update to 5.16b.
* gnu/packages/bioinformatics.scm (proteinortho): Update to 5.16b.
2017-09-23 18:10:14 +10:00
Ricardo Wurmus 9fc513ad10
gnu: Use xxd instead of vim.
* gnu/packages/audio.scm (faust-2)[native-inputs]: Replace vim with xxd.
* gnu/packages/avr.scm (microscheme)[native-inputs]: Likewise.
* gnu/packages/bioinformatics.scm (star)[native-inputs]: Likewise.
* gnu/packages/disk.scm (dosfstools)[native-inputs]: Likewise.
* gnu/packages/package-management.scm (diffoscope)[inputs]: Likewise.
2017-09-22 12:21:09 +02:00
Kei Kebreau dc1d3cdef7
gnu: Use 'modify-phases' syntax.
* gnu/packages/admin.scm (mingetty, clusterssh, wpa-supplicant-minimal,
wpa-supplicant, wakelan, acpica, tree, direvent, dstat)[arguments]: Use
'modify-phases' syntax.
* gnu/packages/algebra.scm (arb)[arguments]: Likewise.
* gnu/packages/apr.scm (apr-util)[arguments]: Likewise.
* gnu/packages/audio.scm (clalsadrv, fluidsynth, faad2, lv2-mda-piano,
lv2-mda-epiano, timidity++, vamp, soundtouch, portaudio, rsound,
zita-convolver, zita-alsa-pcmi)[arguments]: Likewise.
* gnu/packages/backup.scm (rdup, btar)[arguments]: Likewise.
* gnu/packages/bioinformatics.scm (bedops, bwa, crossmap, express,
flexbar, grit, hisat, ngs-sdk, subread)[arguments]: Likewise.
* gnu/packages/bittorrent.scm (transmission)[arguments]: Likewise.
* gnu/packages/cdrom.scm (cd-discid)[arguments]: Likewise.
* gnu/packages/compression.scm (sharutils)[arguments]: Likewise.
* gnu/packages/conky.scm (conky)[arguments]: Likewise.
* gnu/packages/databases.scm (bdb, bdb-5.3)[arguments]: Likewise.
* gnu/packages/debug.scm (delta, c-reduce)[arguments]: Likewise.
* gnu/packages/display-managers.scm (slim)[arguments]: Likewise.
* gnu/packages/dns.scm (dnsmasq)[arguments]: Likewise.
* gnu/packages/emacs.scm (geiser, emacs-wget, bbdb)[arguments]: Likewise.
* gnu/packages/engineering.scm (pcb)[arguments]: Likewise.
* gnu/packages/firmware.scm (ath9k-htc-firmware)[arguments]: Likewise.
* gnu/packages/flashing-tools.scm (flashrom)[arguments]: Likewise.
* gnu/packages/fltk.scm (fltk)[arguments]: Likewise.
* gnu/packages/freedesktop.scm (python-pyxdg)[arguments]: Likewise.
* gnu/packages/gd.scm (perl-gd)[arguments]: Likewise.
* gnu/packages/gkrellm.scm (gkrellm)[arguments]: Likewise.
* gnu/packages/glib.scm (glibmm)[arguments]: Likewise.
* gnu/packages/gl.scm (glew)[arguments]: Likewise.
* gnu/packages/gnome.scm (icon-naming-utils, orbit2, libbonobo, gnome-vfs,
libgnome, libbonoboui, goffice-0.8, dconf)[arguments]: Likewise.
* gnu/packages/gprolog.scm (gprolog)[arguments]: Likewise.
* gnu/packages/gps.scm (gpscorrelate)[arguments]: Likewise.
* gnu/packages/graphics.scm (agg)[arguments]: Likewise.
* gnu/packages/gtk.scm (ganv, girara, gtksourceview-2, guile-present,
python2-pycairo)[arguments]: Likewise.
* gnu/packages/guile.scm (guile-1.8)[arguments]: Likewise.
* gnu/packages/guile-wm.scm (guile-wm)[arguments]: Likewise.
* gnu/packages/hugs.scm (hugs)[arguments]: Likewise.
* gnu/packages/hurd.scm (gnumach-headers, hurd-headers, hurd-minimal)
[arguments]: Likewise.
* gnu/packages/image-viewers.scm (feh, sxiv)[arguments]: Likewise.
* gnu/packages/libcanberra.scm (libcanberra)[arguments]: Likewise.
* gnu/packages/linux.scm (bridge-utils, iw, fuse, unionfs-fuse/static,
lm-sensors, i2c-tools, xsensors, perf, mdadm, libaio, module-init-tools)
[arguments]: Likewise.
* gnu/packages/lisp.scm (ccl)[arguments]: Likewise.
* gnu/packages/lout.scm (lout)[arguments]: Likewise.
* gnu/packages/lua.scm (luajit)[arguments]: Likewise.
* gnu/packages/machine-learning.scm (shogun)[arguments]: Likewise.
* gnu/packages/mail.scm (exim)[arguments]: Likewise.
* gnu/packages/man.scm (man-pages, txt2man)[arguments]: Likewise.
* gnu/packages/maths.scm (lapack, superlu-dist, openlibm, openspecfun)
[arguments]: Likewise.
* gnu/packages/messaging.scm (bitlbee)[arguments]: Likewise.
* gnu/packages/mp3.scm (libmad, id3lib, mp3info)[arguments]: Likewise.
* gnu/packages/music.scm (solfege)[arguments]: Likewise.
* gnu/packages/noweb.scm (noweb)[arguments]: Likewise.
* gnu/packages/patchutils.scm (patchutils, quilt, colordiff)[arguments]:
Likewise.
* gnu/packages/pdf.scm (xpdf, zathura-cb, zathura-ps, zathura-djvu,
zathura-pdf-poppler, zathura, podofo, fbida)[arguments]: Likewise.
* gnu/packages/perl.scm (perl-file-list, perl-test-harness)[arguments]:
Likewise.
* gnu/packages/photo.scm (gphoto2)[arguments]: Likewise.
* gnu/packages/popt.scm (popt)[arguments]: Likewise.
* gnu/packages/pretty-print.scm (source-highlight, astyle)[arguments]:
Likewise.
* gnu/packages/pumpio.scm (pumpa)[arguments]: Likewise.
* gnu/packages/python.scm (python-passlib, python-pycrypto, python2-empy,
python-sqlalchemy, python-docopt)[arguments]: Likewise.
* gnu/packages/rdf.scm (lrdf)[arguments]: Likewise.
* gnu/packages/regex.scm (tre)[arguments]: Likewise.
* gnu/packages/rrdtool.scm (rrdtool)[arguments]: Likewise.
* gnu/packages/ruby.scm (ruby-2.1, ruby-1.8)[arguments]: Likewise.
* gnu/packages/sawfish.scm (sawfish)[arguments]: Likewise.
* gnu/packages/scheme.scm (racket)[arguments]: Likewise.
* gnu/packages/sdl.scm (guile-sdl)[arguments]: Likewise.
* gnu/packages/serveez.scm (serveez)[arguments]: Likewise.
* gnu/packages/skribilo.scm (skribilo)[arguments]: Likewise.
* gnu/packages/smalltalk.scm (smalltalk)[arguments]: Likewise.
* gnu/packages/suckless.scm (dmenu, slock)[arguments]: Likewise.
* gnu/packages/tcl.scm (expect)[arguments]: Likewise.
* gnu/packages/telephony.scm (commoncpp)[arguments]: Likewise.
* gnu/packages/textutils.scm (recode, libgtextutils)[arguments]:
Likewise.
* gnu/packages/time.scm (time)[arguments]: Likewise.
* gnu/packages/tor.scm (privoxy)[arguments]: Likewise.
* gnu/packages/uucp.scm (uucp)[arguments]: Likewise.
* gnu/packages/video.scm (libdvdnav-4)[arguments]: Likewise.
* gnu/packages/web-browsers.scm (lynx)[arguments]: Likewise.
* gnu/packages/web.scm (tinyproxy)[arguments]: Likewise.
* gnu/packages/wicd.scm (wicd)[arguments]: Likewise.
* gnu/packages/wm.scm (bspwm)[arguments]: Likewise.
* gnu/packages/xdisorg.scm (sxhkd, xcape)[arguments]: Likewise.
* gnu/packages/xfce.scm (xfconf)[arguments]: Likewise.
* gnu/packages/xfig.scm (transfig)[arguments]: Likewise.
* gnu/packages/xorg.scm (imake)[arguments]: Likewise.
2017-09-20 20:58:04 -04:00
Ricardo Wurmus ebfd6a718a
gnu: r-rcas: Add missing inputs.
* gnu/packages/bioinformatics.scm (r-rcas)[propagated-inputs]: Add r-pbapply.
2017-09-18 14:23:03 +02:00
Ricardo Wurmus d82937fbe0
gnu: r-rcas: Update to 1.3.4.
* gnu/packages/bioinformatics.scm (r-rcas): Update to 1.3.4.
2017-09-18 11:33:26 +02:00
Kei Kebreau 4561498e1f
gnu: Fix build failures caused by commit
d10092b849.

* gnu/packages/bioinformatics.scm (seek)[arguments]: Restore previous phase
order.
* gnu/packages/ci.scm (cuirass)[arguments]: Add patch-/bin/sh phase.
2017-09-10 18:21:35 -04:00
Roel Janssen 325c039c1d
gnu: Add r-sparql.
* gnu/packages/bioinformatics.scm (r-sparql): New variable.
2017-09-05 11:02:03 +02:00
Kei Kebreau 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
Ricardo Wurmus 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
Ricardo Wurmus 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
Ricardo Wurmus 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
Ricardo Wurmus 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
Ricardo Wurmus 75690c9f6b
gnu: r-rcas: Correct license.
* gnu/packages/bioinformatics.scm (r-rcas)[license]: Use correct license.
2017-09-01 10:26:31 +02:00
Ricardo Wurmus 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
Ben Woodcroft 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
Ben Woodcroft 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
Ben Woodcroft 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
Ben Woodcroft 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
Ricardo Wurmus 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
Marius Bakke 2718a9cd09
Merge branch 'master' into core-updates 2017-08-21 02:40:37 +02:00
Ricardo Wurmus 17cddc1714
gnu: Add r-annotationfilter.
* gnu/packages/bioinformatics.scm (r-annotationfilter): New variable.
2017-08-20 14:00:04 +02:00
Ricardo Wurmus bf3fa99654
gnu: Add r-methylkit.
* gnu/packages/bioinformatics.scm (r-methylkit): New variable.
2017-08-17 18:00:17 +02:00
Ricardo Wurmus 212f612040
gnu: Add r-qvalue.
* gnu/packages/bioinformatics.scm (r-qvalue): New variable.
2017-08-17 17:26:12 +02:00
Ricardo Wurmus d4a1e918cb
gnu: Add r-fastseg.
* gnu/packages/bioinformatics.scm (r-fastseg): New variable.
2017-08-17 17:26:11 +02:00
Ricardo Wurmus 4a007ffafe
gnu: Add r-annotationhub.
* gnu/packages/bioinformatics.scm (r-annotationhub): New variable.
2017-08-17 17:25:47 +02:00
Ricardo Wurmus 5f96f30f5d
gnu: Add r-interactivedisplaybase.
* gnu/packages/bioinformatics.scm (r-interactivedisplaybase): New variable.
2017-08-17 17:25:46 +02:00
Efraim Flashner 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
Ben Woodcroft 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
Efraim Flashner 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
Mark H Weaver 09ec5a0f0c
Merge branch 'master' into core-updates 2017-08-15 03:10:14 -04:00
Ricardo Wurmus 9634804890
gnu: Add bismark.
* gnu/packages/bioinformatics.scm (bismark): New variable.
2017-08-14 12:00:56 +02:00
Ricardo Wurmus 86763fdd70
gnu: Add r-dexseq.
* gnu/packages/bioinformatics.scm (r-dexseq): New variable.
2017-08-14 12:00:51 +02:00
Mark H Weaver cc294bcee6
Merge branch 'master' into core-updates 2017-08-09 17:25:31 -04:00
Ricardo Wurmus 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
Ricardo Wurmus 18f5d2a70a
gnu: Add reference to (gnu packages graph).
This is a follow-up to 1738138cb3.
2017-08-09 15:43:35 +02:00
Mark H Weaver 2d9495da23
Merge branch 'master' into core-updates 2017-08-07 16:45:16 -04:00
Tobias Geerinckx-Rice 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
Mark H Weaver f167595ba1
Merge branch 'master' into core-updates 2017-08-06 00:23:20 -04:00
Ludovic Courtès 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
Efraim Flashner 7cb6155088
gnu: bioinformatics.scm: Use (gnu packages cran) module.
This is a follow up to a8cba9dd11.

* gnu/packages/bioinformatics.scm: Add (gnu packages cran) to #:use-modules.
2017-08-03 21:39:12 +03:00
Ricardo Wurmus 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
Ricardo Wurmus 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
Ricardo Wurmus 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
Ricardo Wurmus 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
Ricardo Wurmus 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
Ricardo Wurmus 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
Ben Woodcroft 75e6639f36
gnu: htseq: Use PyPI URI.
This is a follow-up to 92971d68ac.

* gnu/packages/bioinformatics.scm (htseq)[source]: Use 'pypi-uri'.
2017-08-03 21:08:13 +10:00
Ben Woodcroft 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
Roel Janssen 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
Roel Janssen 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
Roel Janssen 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
Roel Janssen 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
Roel Janssen 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
Roel Janssen 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
Roel Janssen 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
Roel Janssen 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
Roel Janssen 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
Roel Janssen 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
Roel Janssen 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
Roel Janssen 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
Roel Janssen 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
Roel Janssen 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
Roel Janssen 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
Roel Janssen 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
Roel Janssen 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
Roel Janssen 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
Roel Janssen 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
Roel Janssen 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
Roel Janssen 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
Marius Bakke aa9780daf9
Merge branch 'master' into core-updates 2017-08-01 23:42:28 +02:00
Efraim Flashner 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
Ben Woodcroft 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
Ben Woodcroft 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
Ben Woodcroft 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
Ben Woodcroft 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
Ben Woodcroft 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
Ben Woodcroft 63fa0ffcd4
gnu: samtools: Update to 1.5.
* gnu/packages/bioinformatics.scm (samtools): Update to 1.5.
2017-07-23 10:29:36 +10:00
Ben Woodcroft 4fb6d1280e
gnu: htslib: Update to 1.5.
* gnu/packages/bioinformatics.scm (htslib): Update to 1.5.
2017-07-23 10:29:35 +10:00
Ben Woodcroft 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
Ben Woodcroft 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
Ben Woodcroft 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
Ben Woodcroft 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
Ben Woodcroft 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
Ben Woodcroft c842d42593
gnu: samtools: Use "modify-phases" syntax.
* gnu/packages/bioinformatics.scm (samtools)[arguments]: Use "modify-phases"
syntax.
2017-07-23 10:29:34 +10:00
Ricardo Wurmus 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
Ricardo Wurmus 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
Ricardo Wurmus 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
Efraim Flashner 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
Efraim Flashner 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
Ben Woodcroft 06e372360e
gnu: bowtie: Use 'modify-phases'.
* gnu/packages/bioinformatics.scm (bowtie)[arguments]: Use 'modify-phases'
syntax.
2017-07-14 19:23:37 +10:00
Ben Woodcroft 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
Ricardo Wurmus 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
Ricardo Wurmus eb2200f3bd
gnu: Add python-py2bit.
* gnu/packages/bioinformatics.scm (python-py2bit): New variable.
2017-07-09 17:07:23 +02:00
Ben Woodcroft 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
Leo Famulari 0a66c38764
Revert "gnu: blast+: Update to 2.6.0."
This reverts commit 18dea67dc3.
2017-07-06 19:38:55 -04:00
Efraim Flashner 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
Ben J Woodcroft 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
Ben Woodcroft 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
Ben Woodcroft 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
Ben Woodcroft 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
Ricardo Wurmus 7ceb0a83e3
gnu: Add f-seq.
* gnu/packages/bioinformatics.scm (f-seq): New variable.
2017-06-25 22:26:07 +02:00
Ben Woodcroft 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
Ben Woodcroft 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
Ricardo Wurmus 94820951d6
gnu: Add kentutils.
* gnu/packages/bioinformatics.scm (kentutils): New variable.
2017-06-23 08:09:33 +02:00
Ricardo Wurmus 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
Arun Isaac 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
Ben Woodcroft 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
Tobias Geerinckx-Rice a147fadd3b
gnu: tadbit: Fix typo in description.
* gnu/packages/bioinformatics.scm (tadbit)[description]: Fix typo.
2017-06-16 00:29:21 +02:00
Efraim Flashner 07bf6929b9
gnu: gemma: Fix indentation.
* gnu/packages/bioinformatics.scm (gemma)[arguments]: Fix indentation.
2017-06-15 10:32:03 +03:00
Efraim Flashner 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
Ricardo Wurmus 8befd0940b
gnu: Add tadbit.
* gnu/packages/bioinformatics.scm (tadbit): New variable.
2017-06-09 03:32:23 +02:00
Ricardo Wurmus aa163424b2
gnu: Add imp.
* gnu/packages/bioinformatics.scm (imp): New variable.
2017-06-09 03:31:51 +02:00
Ricardo Wurmus 282b01515b
gnu: Add phylip.
* gnu/packages/bioinformatics.scm (phylip): New variable.
2017-06-09 03:31:50 +02:00
Ricardo Wurmus 3420c905cd
gnu: Add gess.
* gnu/packages/bioinformatics.scm (gess): New variable.
2017-06-09 03:31:50 +02:00
Ricardo Wurmus 44f6c88909
gnu: Add trim-galore.
* gnu/packages/bioinformatics.scm (trim-galore): New variable.
2017-06-09 03:31:50 +02:00
Ricardo Wurmus b8fffd3a53
gnu: Add ritornello.
* gnu/packages/bioinformatics.scm (ritornello): New variable.
2017-06-09 03:31:50 +02:00
Ben Woodcroft 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
Roel Janssen b9a601d9db
gnu: Add kaiju.
* gnu/packages/bioinformatics.scm (kaiju): New variable.
2017-06-02 12:38:23 +02:00
Ben Woodcroft 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
Ben Woodcroft 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
Ben Woodcroft 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
Ricardo Wurmus 296b3c631c
gnu: Add r-edaseq.
* gnu/packages/bioinformatics.scm (r-edaseq): New variable.
2017-05-22 18:54:59 +02:00
Ricardo Wurmus 7b46532779
gnu: Add r-deseq.
* gnu/packages/bioinformatics.scm (r-deseq): New variable.
2017-05-22 18:54:59 +02:00
Ricardo Wurmus d4b83651d1
gnu: Add r-aroma-light.
* gnu/packages/bioinformatics.scm (r-aroma-light): New variable.
2017-05-22 18:54:58 +02:00
Ben Woodcroft 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
Ben Woodcroft 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
Ben Woodcroft 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
Roel Janssen 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
Ben Woodcroft 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
Ben Woodcroft 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
Ben Woodcroft 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
Pjotr Prins 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
Ludovic Courtès 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
Ben Woodcroft c033f5d6b5
gnu: Add pplacer.
* gnu/packages/bioinformatics.scm (pplacer, pplacer-scripts): New
variables.
2017-05-10 22:13:55 +02:00
Ben Woodcroft ad0ae297d4
gnu: Add taxtastic.
* gnu/packages/bioinformatics.scm (taxtastic): New variable.
2017-05-10 22:13:55 +02:00
Petter 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
Roel Janssen 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
Efraim Flashner 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
Roel Janssen 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
Roel Janssen 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
Roel Janssen 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
Roel Janssen 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
Roel Janssen 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
Roel Janssen 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
Roel Janssen 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
Roel Janssen 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
Roel Janssen 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
Roel Janssen 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
Roel Janssen 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
Roel Janssen 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
Roel Janssen 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
Roel Janssen 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
Roel Janssen 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
Roel Janssen 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
Roel Janssen 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
Roel Janssen 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
Roel Janssen 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
Roel Janssen 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
Roel Janssen 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
Roel Janssen 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
Roel Janssen 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
Roel Janssen 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
Roel Janssen 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
Roel Janssen 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
Roel Janssen 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
Roel Janssen 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
Roel Janssen 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
Roel Janssen 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
Roel Janssen 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
Roel Janssen 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
Roel Janssen 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
Roel Janssen 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
Roel Janssen 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
Roel Janssen 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
Roel Janssen 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
Roel Janssen 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
Roel Janssen 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
Roel Janssen 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
Roel Janssen 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
Roel Janssen 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
Roel Janssen 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
Roel Janssen 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
Roel Janssen 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
Roel Janssen 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
Roel Janssen 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
Roel Janssen 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
Roel Janssen 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
Roel Janssen 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
Roel Janssen 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
Roel Janssen 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
Roel Janssen 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
Roel Janssen 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
Roel Janssen 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
Roel Janssen 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
Roel Janssen 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
Roel Janssen 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
Roel Janssen 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
Roel Janssen 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
Roel Janssen 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
Roel Janssen 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
Roel Janssen ffef27f3d2
gnu: Add r-genomeinfodbdata.
* gnu/packages/bioinformatics.scm (r-genomeinfodbdata): New variable.
2017-04-28 10:17:06 +02:00
Roel Janssen 71e34e6b5b
gnu: Add r-delayedarray.
* gnu/packages/bioinformatics.scm (r-delayedarray): New variable.
2017-04-28 10:15:12 +02:00
Roel Janssen 2abfc5b827
gnu: Add r-bookdown.
* gnu/packages/bioinformatics.scm (r-bookdown): New variable.
2017-04-28 10:09:31 +02:00
Ricardo Wurmus 31c374e081
gnu: python-pysam: Disable tests.
* gnu/packages/bioinformatics.scm (python-pysam): Disable tests.
2017-04-25 14:05:59 +02:00
Ricardo Wurmus 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
Efraim Flashner 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
Ricardo Wurmus 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
Ben Woodcroft a7d12a9e71
gnu: proteinortho: Update to 5.16.
* gnu/packages/bioinformatics.scm (proteinortho): Update to 5.16.
2017-04-21 23:03:56 +10:00
Ben Woodcroft 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
Tobias Geerinckx-Rice 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
Ben Woodcroft 88eb119f95
gnu: mafft: Update to 7.310.
* gnu/packages/bioinformatics.scm (mafft): Update to 7.310.
2017-04-14 15:19:37 +10:00
Ben Woodcroft 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
Ricardo Wurmus 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
Ricardo Wurmus 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
Ricardo Wurmus 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
Ben Woodcroft 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
Ricardo Wurmus 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
Ricardo Wurmus 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
Ricardo Wurmus 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
Ricardo Wurmus 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
Ricardo Wurmus 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
Ricardo Wurmus 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
Ricardo Wurmus 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
Ricardo Wurmus 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
Ricardo Wurmus 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
Ricardo Wurmus 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
Ricardo Wurmus 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
Ricardo Wurmus 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
Ricardo Wurmus 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
Ricardo Wurmus 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
Ricardo Wurmus 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
Ricardo Wurmus 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
Ricardo Wurmus 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
Ricardo Wurmus 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
Ricardo Wurmus 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
Ricardo Wurmus 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
Ben Woodcroft 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
Leo Famulari 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
Ben Woodcroft 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
Marius Bakke 84157bb8bf
Merge branch 'master' into core-updates
Most conflicts are from 6fd52309b8.
2017-03-30 22:59:53 +02:00
Ricardo Wurmus 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
Ricardo Wurmus 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
Ludovic Courtès 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
Ricardo Wurmus 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
Ricardo Wurmus 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
Ricardo Wurmus 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
Ricardo Wurmus 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
Ludovic Courtès 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
Ricardo Wurmus 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
Ricardo Wurmus 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
Raoul Jean Pierre Bonnal 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
Ricardo Wurmus 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
Ricardo Wurmus 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
Ricardo Wurmus 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
Ricardo Wurmus 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
Ricardo Wurmus 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
Ricardo Wurmus 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
Tobias Geerinckx-Rice 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
Tobias Geerinckx-Rice 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
Ben Woodcroft 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
Raoul Jean Pierre Bonnal 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
Ben J. Woodcroft 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
Ricardo Wurmus 5ded35d89d
gnu: Add sambamba.
* gnu/packages/bioinformatics.scm (htslib-for-sambamba, sambamba): New
variables.
2017-03-10 10:13:59 +01:00
Marius Bakke 3f98071ac5
Merge branch 'python-tests' 2017-03-03 16:55:43 +01:00
Ben Woodcroft 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
Ricardo Wurmus 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
Marius Bakke 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
Ricardo Wurmus 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
Marius Bakke 424b1ae769
Merge branch 'master' into python-tests 2017-02-13 22:35:05 +01:00
Ben Woodcroft 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
Ricardo Wurmus 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
Tobias Geerinckx-Rice 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
Raoul Jean Pierre Bonnal 69f2b3bdf9
gnu: Add r-rhdf5. 2017-01-31 22:35:11 +01:00
Raoul Jean Pierre Bonnal d4af25b51b
gnu: Add r-tximport. 2017-01-31 22:35:08 +01:00
Roel Janssen 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
Ben Woodcroft 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
Ben Woodcroft 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
Ricardo Wurmus 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
Ricardo Wurmus 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
Ricardo Wurmus 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
Ricardo Wurmus 66da3a9f31
gnu: Add r-msnid.
* gnu/packages/bioinformatics.scm (r-msnid): New variable.
2017-01-17 21:46:50 +01:00
Ricardo Wurmus 11879284cb
gnu: Add r-msnbase.
* gnu/packages/bioinformatics.scm (r-msnbase): New variable.
2017-01-17 21:46:50 +01:00
Ricardo Wurmus 6a67e181ac
gnu: Add r-pcamethods.
* gnu/packages/bioinformatics.scm (r-pcamethods): New variable.
2017-01-17 21:46:50 +01:00
Ricardo Wurmus 4aa7d592f1
gnu: Add r-mzid.
* gnu/packages/bioinformatics.scm (r-mzid): New variable.
2017-01-17 21:46:50 +01:00
Ricardo Wurmus 7c08afaf7b
gnu: Add r-vsn.
* gnu/packages/bioinformatics.scm (r-vsn): New variable.
2017-01-17 21:46:50 +01:00
Ricardo Wurmus 05c7e5fb76
gnu: Add r-affy.
* gnu/packages/bioinformatics.scm (r-affy): New variable.
2017-01-17 21:46:49 +01:00
Ricardo Wurmus 5c9d15055f
gnu: Add r-affyio.
* gnu/packages/bioinformatics.scm (r-affyio): New variable.
2017-01-17 21:46:49 +01:00
Ricardo Wurmus 71676a1f4c
gnu: Add r-mzr.
* gnu/packages/bioinformatics.scm (r-mzr): New variable.
2017-01-17 21:46:49 +01:00
Ricardo Wurmus ae26217430
gnu: Add r-protgenerics.
* gnu/packages/bioinformatics.scm (r-protgenerics): New variable.
2017-01-17 21:46:49 +01:00
Ricardo Wurmus 0e7d058e44
gnu: Add r-maldiquant.
* gnu/packages/bioinformatics.scm (r-maldiquant): New variable.
2017-01-17 21:46:49 +01:00
Ricardo Wurmus 1f40e73cb5
gnu: Add r-raremetals2.
* gnu/packages/bioinformatics.scm (r-raremetals2): New variable.
2017-01-17 21:46:48 +01:00
Ricardo Wurmus fb1e528ef1
gnu: Add r-seqminer.
* gnu/packages/bioinformatics.scm (r-seqminer): New variable.
2017-01-17 21:46:48 +01:00
Ricardo Wurmus 769fc6bb18
gnu: Add ribodiff.
* gnu/packages/bioinformatics.scm (ribodiff): New variable.
2017-01-17 21:46:48 +01:00
Ricardo Wurmus e84efc50d7
gnu: Add hisat2.
* gnu/packages/bioinformatics.scm (hisat2): New variable.
2017-01-17 21:46:48 +01:00
Ricardo Wurmus b91cfa22e1
gnu: Add r-centipede.
* gnu/packages/bioinformatics.scm (r-centipede): New variable.
2017-01-16 23:18:27 +01:00
Raoul Jean Pierre Bonnal dd42a330d1
gnu: Add r-sva.
* gnu/packages/bioinformatics.scm (r-sva): New variable.
2017-01-14 11:15:18 +01:00
Leo Famulari cc0725914e
Merge branch 'master' into python-tests 2017-01-13 10:21:17 -05:00
Roel Janssen 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
Ricardo Wurmus 3a3bf2f819
gnu: Add r-copywriter.
* gnu/packages/bioinformatics.scm (r-copywriter): New variable.
2017-01-06 16:31:19 +01:00
Ricardo Wurmus d407bdb931
gnu: Add r-copyhelper.
* gnu/packages/bioinformatics.scm (r-copyhelper): New variable.
2017-01-06 16:31:14 +01:00
Ricardo Wurmus 6193563a36
gnu: Add r-chipseq.
* gnu/packages/bioinformatics.scm (r-chipseq): New variable.
2017-01-06 16:31:02 +01:00
Ben J Woodcroft 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
Ben J Woodcroft 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
Tobias Geerinckx-Rice 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
Roel Janssen 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
Roel Janssen 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
Ben Woodcroft 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
Ben Woodcroft 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
Ben Woodcroft 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
Ricardo Wurmus 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
Ricardo Wurmus 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
Ricardo Wurmus 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
Ricardo Wurmus 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
Ricardo Wurmus 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
Ricardo Wurmus 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
Ricardo Wurmus 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
Ricardo Wurmus 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
Ricardo Wurmus 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
Ricardo Wurmus 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
Ricardo Wurmus 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
Ricardo Wurmus 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
Ricardo Wurmus 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
Ben Woodcroft 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
Tobias Geerinckx-Rice 33d5b2464d
gnu: cutadapt: Use ‘modify-phases’ syntax.
* gnu/packages/bioinformatics.scm (cutadapt)[arguments]: Use
‘modify-phases’.
2016-12-20 05:36:55 +01:00
Tobias Geerinckx-Rice 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
Ben Woodcroft 3fffabce2a
gnu: Add attribution line for Raoul Bonnal.
This is a follow-up commit to c9e9154e99.

* gnu/packages/bioinformatics.scm: Add attribution.
2016-12-18 10:01:04 +10:00
Raoul Bonnal 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
Marius Bakke cdc2bb50b2
gnu: pbtranscript-tofu: Disable tests.
* gnu/packages/bioinformatics.scm (pbtranscript-tofu)[arguments]: Set #:tests? #f.
2016-12-16 18:15:47 +01:00
Marius Bakke 0d90875974
gnu: multiqc: Fix test dependencies.
* gnu/packages/bioinformatics.scm (multiqc)[native-inputs]: Add python-nose.
2016-12-16 13:28:49 +01:00
Marius Bakke 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
Marius Bakke 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
Marius Bakke 1c10a1d75c
gnu: idr: Disable tests.
* gnu/packages/bioinformatics.scm (idr)[arguments]: Set #:tests? #f.
2016-12-16 13:08:57 +01:00
Marius Bakke aaffb9c97b
gnu: deeptools: Fix test dependency.
* gnu/packages/bioinformatics.scm (deeptools)[native-inputs]: Add python-nose.
2016-12-16 04:27:35 +01:00
Marius Bakke d281be18bc
gnu: clipper: Fix test dependency.
* gnu/packages/bioinformatics.scm (clipper)[native-inputs]: Add python2-nose.
2016-12-16 04:26:32 +01:00
Tobias Geerinckx-Rice 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
Marius Bakke 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
Ben Woodcroft 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
Ben Woodcroft 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
Ben Woodcroft 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
Ben Woodcroft 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
Ben Woodcroft 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
Ben Woodcroft 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
Ben Woodcroft 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
Hartmut Goebel 3bf4280659
Merge branch 'master' into python-build-system 2016-11-29 18:47:16 +01:00
Ricardo Wurmus bd3be46e7f
gnu: Add r-gkmsvm.
* gnu/packages/bioinformatics.scm (r-gkmsvm): New variable.
2016-11-28 22:43:18 +01:00
Ricardo Wurmus 2d9fb1702f
gnu: Add r-seqgl.
* gnu/packages/bioinformatics.scm (r-seqgl): New variable.
2016-11-28 22:43:17 +01:00
Ricardo Wurmus c827f20286
gnu: Add r-chipkernels.
* gnu/packages/bioinformatics.scm (r-chipkernels): New variable.
2016-11-28 22:43:17 +01:00
Ricardo Wurmus d71605294f
gnu: Add r-wgcna.
* gnu/packages/bioinformatics.scm (r-wgcna): New variable.
2016-11-28 22:43:17 +01:00
Ricardo Wurmus e619a5c245
gnu: Add r-r4rna.
* gnu/packages/bioinformatics.scm (r-r4rna): New variable.
2016-11-28 22:43:16 +01:00
Ben Woodcroft 9926875572
gnu: Add newick-utils.
* gnu/packages/bioinformatics.scm (newick-utils): New variable.
2016-11-28 09:00:41 +10:00
Ben Woodcroft 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
Ben Woodcroft 31a9d653ad
gnu: Add proteinortho.
* gnu/packages/bioinformatics.scm (proteinortho): New variable.
2016-11-26 20:15:37 +10:00
Leo Famulari de32aa74b4
Merge branch 'master' into python-build-system 2016-11-25 11:20:21 -05:00
Ben Woodcroft 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
Petter 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
Hartmut Goebel 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
Hartmut Goebel 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
Hartmut Goebel 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
Hartmut Goebel 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
Hartmut Goebel 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
Hartmut Goebel 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
Hartmut Goebel 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
Hartmut Goebel 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
Hartmut Goebel 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
Ricardo Wurmus 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
Ricardo Wurmus 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
Ricardo Wurmus 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
Ricardo Wurmus 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
Ricardo Wurmus 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
Ben Woodcroft 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
Ricardo Wurmus 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
Ricardo Wurmus 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
Ricardo Wurmus 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
Ricardo Wurmus 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
Ricardo Wurmus 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
Leo Famulari 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
Leo Famulari 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
Roel Janssen 7500e42b3e
gnu: Add r-mutationalpatterns.
* gnu/packages/bioinformatics.scm (r-mutationalpatterns): New variable.
2016-10-27 20:07:05 +02:00
Ricardo Wurmus 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
Ricardo Wurmus 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
Ricardo Wurmus 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
Ricardo Wurmus 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
Ricardo Wurmus 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
Ricardo Wurmus 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
Ricardo Wurmus 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
Ricardo Wurmus 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
Ricardo Wurmus 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
Ricardo Wurmus 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
Ricardo Wurmus 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
Ricardo Wurmus 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
Ricardo Wurmus 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
Ricardo Wurmus 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
Ricardo Wurmus 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
Ricardo Wurmus 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
Ricardo Wurmus 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
Ricardo Wurmus 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
Ricardo Wurmus 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
Ricardo Wurmus 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
Ricardo Wurmus 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
Ricardo Wurmus 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
Ricardo Wurmus 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
Ricardo Wurmus 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
Ricardo Wurmus 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
Ricardo Wurmus 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
Ricardo Wurmus 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
Ricardo Wurmus 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
Ricardo Wurmus 37d96f1dde
gnu: r-variantannotation: Update to 1.20.0.
* gnu/packages/bioinformatics.scm (r-variantannotation): Update to
1.20.0.
[propagated-inputs]: Add r-biobase, r-biostrings, r-iranges,
r-rtracklayer, r-s4vectors, r-xvector.
2016-10-26 09:28:14 +02:00
Ricardo Wurmus 5e48005fa9
gnu: r-edger: Update to 3.16.0.
* gnu/packages/bioinformatics.scm (r-edger): Update to 3.16.0.
[propagated-inputs]: Add r-locfit.
2016-10-26 09:28:14 +02:00
Ricardo Wurmus dece310a25
gnu: r-genomeinfodb: Update to 1.10.0.
* gnu/packages/bioinformatics.scm (r-genomeinfodb): Update to 1.10.0.
2016-10-26 09:28:13 +02:00
Ricardo Wurmus 7f354dafb1
gnu: r-iranges: Update to 2.8.0.
* gnu/packages/bioinformatics.scm (r-iranges): Update to 2.8.0.
2016-10-26 09:28:13 +02:00
Ricardo Wurmus b120c5f3a2
gnu: r-s4vectors: Update to 0.12.0.
* gnu/packages/bioinformatics.scm (r-s4vectors): Update to 0.12.0.
2016-10-26 09:28:13 +02:00
Ricardo Wurmus 22c5d736af
gnu: r-dnacopy: Update to 1.48.0.
* gnu/packages/bioinformatics.scm (r-dnacopy): Update to 1.48.0.
2016-10-26 09:28:12 +02:00
Ricardo Wurmus 5c7b04e0c3
gnu: r-biocinstaller: Update to 1.24.0.
* gnu/packages/bioinformatics.scm (r-biocinstaller): Update to 1.24.0.
2016-10-26 09:28:12 +02:00
Ricardo Wurmus f0b297e17b
gnu: r-biocgenerics: Update to 0.20.0.
* gnu/packages/bioinformatics.scm (r-biocgenerics): Update to 0.20.0.
2016-10-26 09:28:11 +02:00
Ricardo Wurmus c9b5046a18
gnu: r-grohmm: Update to 1.8.0.
* gnu/packages/bioinformatics.scm (r-grohmm): Update to 1.8.0.
2016-10-26 09:28:11 +02:00
Ricardo Wurmus 1265d3877b
gnu: r-systempiper: Update to 1.8.1.
* gnu/packages/bioinformatics.scm (r-systempiper): Update to 1.8.1.
2016-10-26 09:28:11 +02:00
Ricardo Wurmus b87b41a74d
gnu: r-shortread: Update to 1.32.0.
* gnu/packages/bioinformatics.scm (r-shortread): Update to 1.32.0.
2016-10-26 09:28:10 +02:00
Ricardo Wurmus ae6899b683
gnu: r-gostats: Update to 2.40.0.
* gnu/packages/bioinformatics.scm (r-gostats): Update to 2.40.0.
2016-10-26 09:28:10 +02:00
Ricardo Wurmus 816599c1e7
gnu: r-category: Update to 2.40.0.
* gnu/packages/bioinformatics.scm (r-category): Update to 2.40.0.
2016-10-26 09:28:10 +02:00
Ricardo Wurmus 558d02c361
gnu: r-gseabase: Update to 1.36.0.
* gnu/packages/bioinformatics.scm (r-gseabase): Update to 1.36.0.
2016-10-26 09:28:09 +02:00
Ricardo Wurmus 700c780dcf
gnu: r-rbgl: Update to 1.50.0.
* gnu/packages/bioinformatics.scm (r-rbgl): Update to 1.50.0.
2016-10-26 09:28:09 +02:00
Ricardo Wurmus 55cd914c3d
gnu: r-annotationforge: Update to 1.16.0.
* gnu/packages/bioinformatics.scm (r-annotationforge): Update to 1.16.0.
[propagated-inputs]: Add r-rcurl.
2016-10-26 09:28:09 +02:00
Ricardo Wurmus e1db8dd813
gnu: r-deseq2: Update to 1.14.0.
* gnu/packages/bioinformatics.scm (r-deseq2): Update to 1.14.0.
2016-10-26 09:28:08 +02:00
Ricardo Wurmus 1e66e71921
gnu: r-genefilter: Update to 1.56.0.
* gnu/packages/bioinformatics.scm (r-genefilter): Update to 1.56.0.
2016-10-26 09:28:08 +02:00
Ricardo Wurmus 6faa2a48f0
gnu: r-geneplotter: Update to 1.52.0.
* gnu/packages/bioinformatics.scm (r-geneplotter): Update to 1.52.0.
2016-10-26 09:28:08 +02:00
Ricardo Wurmus 9beba74f66
gnu: r-annotate: Update to 1.52.0.
* gnu/packages/bioinformatics.scm (r-annotate): Update to 1.52.0.
2016-10-26 09:28:07 +02:00
Roel Janssen 4644644ace
gnu: Add r-bioccheck.
* gnu/packages/bioinformatics.scm (r-bioccheck): New variable.
2016-10-20 09:53:02 +02:00
Roel Janssen 99df12cd19
gnu: Add r-biocstyle.
* gnu/packages/bioinformatics.scm (r-biocstyle): New variable.
2016-10-19 15:22:06 +02:00
Roel Janssen 207ce8fbe5
gnu: Add r-biocviews.
* gnu/packages/bioinformatics.scm (r-biocviews): New variable.
2016-10-19 15:09:55 +02:00
Roel Janssen c79ad57a8d
gnu: Add r-optparse.
* gnu/packages/bioinformatics.scm (r-optparse): New variable.
2016-10-19 10:48:56 +02:00
Roel Janssen 2acaaee550
gnu: Add r-getopt.
* gnu/packages/bioinformatics.scm (r-getopt): New variable.
2016-10-19 09:55:45 +02:00
Ricardo Wurmus 5093729704
gnu: Add rcas-web.
* gnu/packages/bioinformatics.scm (rcas-web): New variable.
2016-10-17 18:09:20 +02:00
Ricardo Wurmus 89984be46e
gnu: Add r-rcas.
* gnu/packages/bioinformatics.scm (r-rcas): New variable.
2016-10-17 18:09:16 +02:00
Ben Woodcroft 3dd50d974b
gnu: vsearch: Update to 2.3.0.
* gnu/packages/bioinformatics.scm (vsearch): Update to 2.3.0.
2016-10-11 22:29:48 +10:00
Ben Woodcroft 99c9056141
gnu: diamond: Update to 0.8.23.
* gnu/packages/bioinformatics.scm (diamond): Update to 0.8.23.
2016-10-11 19:51:49 +10:00
Ben Woodcroft 9602e3cce9
gnu: python2-dendropy: Fix tests.
* gnu/packages/bioinformatics.scm (python2-dendropy)[source]: Use unpatched
source.
[arguments]: Use nose to run tests.
[native-inputs]: Add python2-nose.
2016-10-08 21:38:17 +10:00
Ricardo Wurmus fc47c7d635
gnu: Add r-bsgenome-celegans-ucsc-ce10.
* gnu/packages/bioinformatics.scm (r-bsgenome-celegans-ucsc-ce10): New
variable.
2016-10-06 10:33:43 +02:00
Ben Woodcroft 2c3eb4b85b
gnu: metabat: Update to 0.32.4-1.cbdca756.
* gnu/packages/bioinformatics.scm (metabat): Update to 0.32.4-1.cbdca756.
* gnu/packages/patches/metabat-remove-compilation-date.patch: New file.
* gnu/local.mk (dist_patch_DATA): Add it.
2016-10-04 22:02:52 +10:00
Ben Woodcroft 4bdc3df92d
gnu: vsearch: Update to 2.1.2.
* gnu/packages/bioinformatics.scm (vsearch): Update to 2.1.2.
2016-10-02 22:25:39 +10:00
Ricardo Wurmus 2320e76b82
gnu: sra-tools: Fix build on i686.
* gnu/packages/bioinformatics.scm (sra-tools)[arguments]: Pass
"VDB_LIBDIR" in make-flags; dynamically link libmagic.
2016-09-28 22:30:41 +02:00
Ben J Woodcroft 99caa6f75f
gnu: python-plastid: Update to 1.4.6.
* gnu/packages/bioinformatics.scm (python-plastid, python2-plastid): Update to
1.4.6.
[propagated-inputs]: Add python-termcolor.
2016-09-27 20:07:12 +10:00
Marius Bakke f536dce522
gnu: python-pysam: Enable tests.
* gnu/packages/bioinformatics.scm (python-pysam)[source]: Change from
PyPi to source archive due to missing test data.
[arguments]: Add check phase after install.
[native-inputs]: Add python-nose, samtools and bcftools.
2016-09-27 20:06:00 +10:00
Marius Bakke dff26b2363
gnu: python-pysam: Delete bundled htslib.
* gnu/packages/bioinformatics.scm (python-pysam)[source]: Add snippet
to delete htslib.
[arguments]: Add htslib flags in 'set-flags phase.
[propagated-inputs]: New field. Add htslib.
2016-09-27 20:06:00 +10:00
Marius Bakke 397d463a12
gnu: python-pysam: Use 'modify-phases'.
* gnu/packages/bioinformatics.scm (python-pysam)[arguments]: Use
'modify-phases'.
2016-09-27 20:06:00 +10:00
Marius Bakke bdc7be59eb
gnu: Add bcftools.
* gnu/packages/bioinformatics.scm (bcftools): New variable.
2016-09-27 20:06:00 +10:00
Marius Bakke e301bfc886
gnu: python2-pbcore: Update to 1.2.10.
* gnu/packages/bioinformatics.scm (python2-pbcore): Update to 1.2.10.
[propagated-inputs]: New field. Add python2-pyxb.
2016-09-27 20:06:00 +10:00
Marius Bakke fd49eb213f
gnu: python-pysam: Update to 0.9.1.4.
* gnu/packages/bioinformatics.scm (python-pysam, python2-pysam): Update
to 0.9.1.4.
2016-09-27 20:05:57 +10:00
Ricardo Wurmus 675d7ae26f
gnu: ncbi-vdb: Only build on i686 and x86_64.
* gnu/packages/bioinformatics.scm (ncbi-vdb)[supported-systems]: Only
build on i686 and x86_64.
[arguments]: Add mandatory "-msse2" flag to CFLAGS.
2016-09-26 14:30:59 +02:00
Ben Woodcroft af8de20386
gnu: vsearch: Update to 2.1.1.
* gnu/packages/bioinformatics.scm (vsearch): Update to 2.1.1.
2016-09-26 20:35:32 +10:00
Ricardo Wurmus f3cfe4515a
gnu: Add r-txdb-hsapiens-ucsc-hg19-knowngene.
* gnu/packages/bioinformatics.scm (r-txdb-hsapiens-ucsc-hg19-knowngene):
  New variable.
2016-09-26 07:47:55 +02:00
Ricardo Wurmus 684f29bd2e
gnu: Add r-grohmm.
* gnu/packages/bioinformatics.scm (r-grohmm): New variable.
2016-09-26 07:47:55 +02:00
Ricardo Wurmus 7f903d7300
gnu: Add r-systempiper.
* gnu/packages/bioinformatics.scm (r-systempiper): New variable.
2016-09-26 07:47:55 +02:00
Ricardo Wurmus cb99d457f0
gnu: Add r-shortread.
* gnu/packages/bioinformatics.scm (r-shortread): New variable.
2016-09-26 07:47:54 +02:00
Ricardo Wurmus 89f40c5e4e
gnu: Add r-gostats.
* gnu/packages/bioinformatics.scm (r-gostats): New variable.
2016-09-26 07:47:54 +02:00
Ricardo Wurmus 1a1931f7e0
gnu: Add r-category.
* gnu/packages/bioinformatics.scm (r-category): New variable.
2016-09-26 07:47:54 +02:00
Ricardo Wurmus ad740ff818
gnu: Add r-gseabase.
* gnu/packages/bioinformatics.scm (r-gseabase): New variable.
2016-09-26 07:47:53 +02:00
Ricardo Wurmus cd9e7dc7ff
gnu: Add r-rbgl.
* gnu/packages/bioinformatics.scm (r-rbgl): New variable.
2016-09-26 03:25:23 +02:00
Ricardo Wurmus e816377374
gnu: Add r-annotationforge.
* gnu/packages/bioinformatics.scm (r-annotationforge): New variable.
2016-09-26 03:25:17 +02:00
Ricardo Wurmus ad34f0ac96
gnu: Add r-deseq2.
* gnu/packages/bioinformatics.scm (r-deseq2): New variable.
2016-09-26 03:21:27 +02:00
Ricardo Wurmus 2301fd3e4d
gnu: Add r-genefilter.
* gnu/packages/bioinformatics.scm (r-genefilter): New variable.
2016-09-26 03:21:19 +02:00
Ricardo Wurmus 07a664cde0
gnu: Add r-geneplotter.
* gnu/packages/bioinformatics.scm (r-geneplotter): New variable.
2016-09-26 03:21:07 +02:00
Ricardo Wurmus 8c6de58849
gnu: Add r-annotate.
* gnu/packages/bioinformatics.scm (r-annotate): New variable.
2016-09-26 03:20:59 +02:00
Ricardo Wurmus 646a84338d
gnu: sra-tools: Update to 2.7.0.
* gnu/packages/bioinformatics.scm (sra-tools): Update to 2.7.0.
2016-09-23 11:46:53 +02:00
Ricardo Wurmus 40974c933e
gnu: ncbi-vdb: Update to 2.7.0.
* gnu/packages/bioinformatics.scm (ncbi-vdb): Update to 2.7.0.
2016-09-23 11:46:26 +02:00
Ricardo Wurmus 48b419ebd6
gnu: ngs-sdk: Update to 1.2.5.
* gnu/packages/bioinformatics.scm (ngs-sdk): Update to 1.2.5.
2016-09-23 11:45:24 +02:00
Efraim Flashner 0dbb7ac2df
gnu: plink: Set endian-ness on more architectures.
* gnu/packages/patches/plink-endian-detection.patch: New file.
* gnu/packages/bioinformatics.scm (plink)[source]: Use it.
* gnu/local.mk (dist_patch_DATA): Register it.
2016-09-22 22:42:37 +03:00
Efraim Flashner 62d00095c2
gnu: prank: Allow building on 32-bit machines.
* gnu/packages/bioinformatics.scm (prank)[arguments]: Add a phase
removing the '-m64' compiler flag.
2016-09-22 19:21:16 +03:00
Ben Woodcroft 951da521a9
gnu: diamond: Update to 0.8.22.
* gnu/packages/bioinformatics.scm (diamond): Update to 0.8.22.
2016-09-22 16:36:00 +10:00
Efraim Flashner 6e8faf7794
gnu: jellyfish: Limit to x86_64.
* gnu/packages/bioinformatics.scm (jellyfish)[supported-systems}: New
field, limit support to x86_64.
2016-09-21 22:36:52 +03:00
Ben Woodcroft 79558df220
gnu: vsearch: Update to 2.1.0.
* gnu/packages/bioinformatics.scm (vsearch): Update to 2.1.0.
2016-09-21 18:44:22 +10:00
Roel Janssen eb24341ffb
gnu: Add r-biocinstaller.
* gnu/packages/bioinformatics.scm (r-biocinstaller): New variable.
2016-09-19 11:56:44 +02:00
Ben Woodcroft de96ea286d
gnu: python-biom-format: Move inputs to propagated-inputs.
* gnu/packages/bioinformatics.scm (python-biom-format, python2-biom-format)
[inputs]: Move all from here ...
[propagated-inputs]: ... to here.
2016-09-19 15:44:20 +10:00
Ben Woodcroft 7bba95b769
gnu: seqmagick: Use BioPython 1.66.
* gnu/packages/bioinformatics.scm (seqmagick)[inputs]: Use
python2-biopython-1.66 instead of python2-biopython.
2016-09-19 15:44:20 +10:00
Ben Woodcroft 4b1a152826
gnu: Add python2-biopython-1.66.
* gnu/packages/bioinformatics.scm (python2-biopython-1.66): New variable.
2016-09-19 15:44:20 +10:00
Ben Woodcroft 8c8da1389e
gnu: python-biopython: Use 'python2-variant'.
* gnu/packages/bioinformatics.scm (python-biopython)[properties]: New field.
[native-inputs]: Remove field.
(python-biopython): Use 'strip-python-variant'.
2016-09-19 15:44:20 +10:00
Ben Woodcroft 4ce6030588
gnu: python-biopython: Update to 1.68.
* gnu/packages/bioinformatics.scm (python-biopython): Update to 1.68.
[arguments]: New field.
2016-09-19 15:44:18 +10:00
Ben J Woodcroft 66daf78c0a
gnu: Add seqtk.
* gnu/packages/bioinformatics.scm (seqtk): New variable.
2016-09-13 20:27:29 +10:00
Leo Famulari 2642231b39
gnu: bowtie: Update to 2.2.9.
* gnu/packages/bioinformatics.scm (bowtie): Update to 2.2.9.
2016-09-12 14:19:37 -04:00
Ricardo Wurmus d108c21228
gnu: r-org-mm-eg-db: Update to 3.3.0.
* gnu/packages/bioinformatics.scm (r-org-mm-eg-db): Update to 3.3.0.
2016-09-12 17:44:49 +02:00
Ricardo Wurmus 6ab7ca24f2
gnu: r-org-dm-eg-db: Update to 3.3.0.
* gnu/packages/bioinformatics.scm (r-org-dm-eg-db): Update to 3.3.0.
2016-09-12 17:44:48 +02:00
Ricardo Wurmus 019be09060
gnu: r-org-ce-eg-db: Update to 3.3.0.
* gnu/packages/bioinformatics.scm (r-org-ce-eg-db): Update to 3.3.0.
2016-09-12 17:44:48 +02:00
Ricardo Wurmus 5cc7cff6ef
gnu: r-org-hs-eg-db: Update to 3.3.0.
* gnu/packages/bioinformatics.scm (r-org-hs-eg-db): Update to 3.3.0.
2016-09-12 17:44:48 +02:00
Ricardo Wurmus 401528b2b5
gnu: r-go-db: Update to 3.3.0.
* gnu/packages/bioinformatics.scm (r-go-db): Update to 3.3.0.
2016-09-12 17:44:48 +02:00
Ricardo Wurmus 44f711dbe6
gnu: r-biocparallel: Update to 1.6.6.
* gnu/packages/bioinformatics.scm (r-biocparallel): Update to 1.6.6.
2016-09-12 17:44:42 +02:00
Ricardo Wurmus 10e479a7c0
gnu: r-genomicranges: Update to 1.24.3.
* gnu/packages/bioinformatics.scm (r-genomicranges): Update to 1.24.3.
2016-09-12 17:44:42 +02:00
Ricardo Wurmus 01ebbb1b76
gnu: r-limma: Update to 3.28.21.
* gnu/packages/bioinformatics.scm (r-limma): Update to 3.28.21.
2016-09-12 17:44:42 +02:00
Ricardo Wurmus bbf53cb527
gnu: r-variantannotation: Update to 1.18.7.
* gnu/packages/bioinformatics.scm (r-variantannotation): Update to 1.18.7.
2016-09-12 17:44:42 +02:00
Ricardo Wurmus 4fa7091d54
gnu: r-genomeinfodb: Update to 1.8.7.
* gnu/packages/bioinformatics.scm (r-genomeinfodb): Update to 1.8.7.
2016-09-12 17:44:41 +02:00
Ricardo Wurmus 3b851cd4ac
gnu: r-seqinr: Update to 3.3-1.
* gnu/packages/bioinformatics.scm (r-seqinr): Update to 3.3-1.
[propagated-inputs]: Add "r-segmented".
2016-09-12 17:44:41 +02:00
Ricardo Wurmus 2b1cc79d98
gnu: r-s4vectors: Update to 0.10.3.
* gnu/packages/bioinformatics.scm (r-s4vectors): Update to 0.10.3.
2016-09-12 17:44:41 +02:00
Ricardo Wurmus 0b54b4c986
gnu: r-acsnminer: Update to 0.16.8.25.
* gnu/packages/bioinformatics.scm (r-acsnminer): Update to 0.16.8.25.
2016-09-12 17:44:41 +02:00
Ricardo Wurmus 2c575bb9a2
gnu: r-vegan: Update to 2.4-1.
* gnu/packages/bioinformatics.scm (r-vegan): Update to 2.4-1.
2016-09-12 17:44:40 +02:00
Marius Bakke 84be3b9920
gnu: Add mash.
* gnu/packages/bioinformatics.scm (mash): New variable.

Signed-off-by: Leo Famulari <leo@famulari.name>
2016-09-10 17:41:38 -04:00
Ben Woodcroft 4b6da268ff
gnu: bamm: Update to 1.7.3.
* gnu/packages/bioinformatics.scm (bamm): Update to 1.7.3.
2016-09-10 09:47:42 +10:00
Efraim Flashner 48409ef269
gnu: infernal: Limit to i686 and x86_64 systems.
* gnu/packages/bioinformatics.scm (infernal)[supported-systems]: The
package requires VMX or SSE capability for parallel instructions, so
limit it to those supported systems.
2016-09-04 12:43:10 +03:00
Ricardo Wurmus 35aa90a1fd
gnu: Add Infernal.
* gnu/packages/bioinformatics.scm (infernal): New variable.
2016-09-02 16:46:37 +02:00
Ricardo Wurmus c180533bb5
gnu: subread: Update to 1.5.1.
* gnu/packages/bioinformatics.scm (subread): Update to 1.5.1.
2016-08-31 15:23:03 +02:00
Ben Woodcroft 7d57ebaa7c
gnu: aragorn: Update to 1.2.37.
* gnu/packages/bioinformatics.scm (aragorn): Update to 1.2.37.
2016-08-31 15:52:49 +10:00
Ben Woodcroft caa9bc7dc5
gnu: diamond: Update to 0.8.20.
* gnu/packages/bioinformatics.scm (diamond): Update to 0.8.20.
2016-08-30 10:46:30 +10:00
Ricardo Wurmus fe02c4c98a
gnu: Add r-bamsignals.
* gnu/packages/bioinformatics.scm (r-bamsignals): New variable.
2016-08-22 16:52:40 +02:00
Ricardo Wurmus 52765a63ca
gnu: Add r-rhtslib.
* gnu/packages/bioinformatics.scm (r-rhtslib): New variable.
2016-08-22 16:52:22 +02:00
Ricardo Wurmus 433530a5fc
gnu: clipper: Update to 1.1.
* gnu/packages/bioinformatics.scm (clipper): Update to 1.1.
[source]: Delete pre-built libraries.
[inputs]: Add python2-pandas.
2016-08-17 19:35:05 +02:00
Marius Bakke 318c0aee1e
gnu: Add minced.
* gnu/packages/bioinformatics.scm (minced): New variable.

Signed-off-by: Ben Woodcroft <donttrustben@gmail.com>
2016-08-17 20:56:21 +10:00
Ben Woodcroft 71461f88ee
gnu: mafft: Update to 7.305.
* gnu/packages/bioinformatics.scm (mafft): Update to 7.305.
[inputs]: Add ruby.
2016-08-16 19:49:15 +10:00
Ben Woodcroft 0ed8f0cd4c
gnu: mafft: Update to 7.304.
* gnu/packages/bioinformatics.scm (mafft): Update to 7.304.
2016-08-15 20:59:41 +10:00
Ben Woodcroft 101e8f7171
gnu: mafft: Wrap programs.
* gnu/packages/bioinformatics.scm (mafft)[arguments]: Add 'wrap-programs'
phase.
[propagated-inputs]: Move coreutils from here ...
[inputs]: ... to here.
2016-08-15 20:51:00 +10:00
Ben Woodcroft 93b8316e08
gnu: mafft: Update to 7.300.
* gnu/packages/bioinformatics.scm (mafft): Update to 7.300.
2016-08-15 20:51:00 +10:00
Ben Woodcroft a12ba6e878
gnu: Add bamm.
* gnu/packages/bioinformatics.scm (bamm): New variable.
2016-08-14 14:55:23 +10:00
Efraim Flashner 3e6fdd5f8a
gnu: snap-aligner: Limit to x86_64.
* gnu/packages/bioinformatics.scm (snap-aligner)[supported-systems]: Add
note explaining why we build for x86_64 only.
2016-08-11 22:44:07 +03:00
Ben Woodcroft 7024aeaaaa
gnu: diamond: Update to 0.8.18.
* gnu/packages/bioinformatics.scm (diamond): Update to 0.8.18.
2016-08-11 20:39:54 +10:00
Ben Woodcroft ceb62d5436
gnu: Add roary.
* gnu/packages/bioinformatics.scm (roary): New variable.
2016-08-08 22:08:17 +10:00
Ben Woodcroft 608dd93267
gnu: Add raxml.
* gnu/packages/bioinformatics.scm (raxml): New variable.
2016-08-08 22:08:17 +10:00
Ben Woodcroft 024130d258
gnu: Add prank.
* gnu/packages/bioinformatics.scm (prank): New variable.
2016-08-08 22:08:17 +10:00
Ben Woodcroft b16728b068
gnu: Add exonerate.
* gnu/packages/bioinformatics.scm (exonerate): New variable.
2016-08-08 22:08:17 +10:00
Ben Woodcroft db7a344427
gnu: Add bppsuite.
* gnu/packages/bioinformatics.scm (bppsuite): New variable.
2016-08-08 22:08:17 +10:00
Ben Woodcroft 159a701678
gnu: Add bpp-popgen.
* gnu/packages/bioinformatics.scm (bpp-popgen): New variable.
2016-08-08 22:08:17 +10:00
Ben Woodcroft 8b5f4d5700
gnu: Add bpp-phyl.
* gnu/packages/bioinformatics.scm (bpp-phyl): New variable.
2016-08-08 22:08:17 +10:00
Ben Woodcroft 70f1bc051a
gnu: Add bpp-seq.
* gnu/packages/bioinformatics.scm (bpp-seq): New variable.
2016-08-08 22:08:17 +10:00
Ben Woodcroft 985d841144
gnu: Add bpp-core.
* gnu/packages/bioinformatics.scm (bpp-core): New variable.
2016-08-08 22:08:17 +10:00
Ben Woodcroft 9e12eba866
gnu: Add python-biom-format.
* gnu/packages/bioinformatics.scm (python-biom-format,
python2-biom-format): New variables.
2016-08-06 09:44:28 +10:00
Ricardo Wurmus 97b9da6897
gnu: Add discrover.
* gnu/packages/bioinformatics.scm (discrover): New variable.
2016-08-03 17:20:26 +02:00
Ben Woodcroft afde1a264b
gnu: fxtract: Restrict to x86_64-linux.
* gnu/packages/bioinformatics.scm (fxtract)[supported-systems]: Restrict to
  x86_64-linux.
2016-08-03 21:22:02 +10:00
Ricardo Wurmus dda3627141
gnu: r-variantannotation: Update to 1.18.6.
* gnu/packages/bioinformatics.scm (r-variantannotation): Update to 1.18.6.
2016-08-02 14:47:46 +02:00
Ricardo Wurmus 005ca42396
gnu: r-genomationdata: Update to 1.4.2.
* gnu/packages/bioinformatics.scm (r-genomationdata): Update to 1.4.2.
2016-08-02 14:47:46 +02:00
Ben Woodcroft c4382cd18f
gnu: diamond: Update to 0.8.17.
* gnu/packages/bioinformatics.scm (diamond): Update to 0.8.17.
2016-07-30 23:02:57 +10:00
Ben Woodcroft 6547708f71
gnu: r-genomicfeatures: Update to 1.24.5.
* gnu/packages/bioinformatics.scm (r-genomicfeatures): Update to 1.24.5.
2016-07-28 21:54:44 +10:00
Ben Woodcroft 2c9f6251fc
gnu: r-bsgenome: Update to 1.40.1.
* gnu/packages/bioinformatics.scm (r-bsgenome): Update to 1.40.1.
2016-07-28 21:45:17 +10:00
Ben Woodcroft b0f0778a7c
gnu: r-iranges: Update to 2.6.1.
* gnu/packages/bioinformatics.scm (r-iranges): Update to 2.6.1.
2016-07-28 21:45:17 +10:00
Ben Woodcroft f403941f81
gnu: r-limma: Update to 3.28.17.
* gnu/packages/bioinformatics.scm (r-limma): Update to 3.28.17.
2016-07-28 21:45:16 +10:00
Ben Woodcroft 2b2ff0bd91
gnu: r-xvector: Update to 0.12.1.
* gnu/packages/bioinformatics.scm (r-xvector): Update to 0.12.1.
2016-07-28 21:45:16 +10:00
Ben Woodcroft a463055862
gnu: r-genomicranges: Update to 1.24.2.
* gnu/packages/bioinformatics.scm (r-genomicranges): Update to 1.24.2.
2016-07-28 21:45:16 +10:00
Ben Woodcroft bab15ccec4
gnu: r-annotationdbi: Update to 1.34.4.
* gnu/packages/bioinformatics.scm (r-annotationdbi): Update to 1.34.4.
2016-07-28 21:45:15 +10:00
Ben Woodcroft a22999f245
gnu: r-biocparallel: Update to 1.6.3.
* gnu/packages/bioinformatics.scm (r-biocparallel): Update to 1.6.3.
2016-07-28 21:45:15 +10:00
Ben Woodcroft d104fc607d
gnu: r-biostrings: Update to 2.40.2.
* gnu/packages/bioinformatics.scm (r-biostrings): Update to 2.40.2.
2016-07-28 21:45:15 +10:00
Ben Woodcroft 1864e051c9
gnu: r-summarizedexperiment: Update to 1.2.3.
* gnu/packages/bioinformatics.scm (r-summarizedexperiment): Update to 1.2.3.
2016-07-28 21:45:15 +10:00
Ben Woodcroft 29b0cc8ad5
gnu: r-genomicalignments: Update to 1.8.4.
* gnu/packages/bioinformatics.scm (r-genomicalignments): Update to 1.8.4.
2016-07-28 21:45:14 +10:00
Ben Woodcroft 5131e21064
gnu: r-rtracklayer: Update to 1.32.2.
* gnu/packages/bioinformatics.scm (r-rtracklayer): Update to 1.32.2.
2016-07-28 21:45:14 +10:00
Ben Woodcroft 2a3e325f5e
gnu: r-genomeinfodb: Update to 1.8.3.
* gnu/packages/bioinformatics.scm (r-genomeinfodb): Update to 1.8.3.
2016-07-28 21:45:14 +10:00
Ben Woodcroft f2e791750b
gnu: r-s4vectors: Update to 0.10.2.
* gnu/packages/bioinformatics.scm (r-s4vectors): Update to 0.10.2.
2016-07-28 20:13:42 +10:00
Ben Woodcroft 12c8f210ee
gnu: diamond: Update to 0.8.16.
* gnu/packages/bioinformatics.scm (diamond): Update to 0.8.16.
2016-07-27 23:17:57 +10:00
Ben Woodcroft e03a515304
gnu: fasttree: Update to 2.1.9.
* gnu/packages/bioinformatics.scm (fasttree): Update to 2.1.9.
2016-07-23 15:15:12 +10:00
Leo Famulari de67e92288
gnu: Update URLs for sourceforge.net.
* gnu/packages/admin.scm: Update URLs pointing to sourceforge.net.
* gnu/packages/audacity.scm: Likewise.
* gnu/packages/audio.scm: Likewise.
* gnu/packages/bioinformatics.scm: Likewise.
* gnu/packages/boost.scm: Likewise.
* gnu/packages/cdrom.scm: Likewise.
* gnu/packages/code.scm: Likewise.
* gnu/packages/compression.scm: Likewise.
* gnu/packages/cups.scm: Likewise.
* gnu/packages/djvu.scm: Likewise.
* gnu/packages/docbook.scm: Likewise.
* gnu/packages/documentation.scm: Likewise.
* gnu/packages/flashing-tools.scm: Likewise.
* gnu/packages/fonts.scm: Likewise.
* gnu/packages/fontutils.scm: Likewise.
* gnu/packages/games.scm: Likewise.
* gnu/packages/ghostscript.scm: Likewise.
* gnu/packages/gl.scm: Likewise.
* gnu/packages/gnucash.scm: Likewise.
* gnu/packages/graphviz.scm: Likewise.
* gnu/packages/image.scm: Likewise.
* gnu/packages/libreoffice.scm: Likewise.
* gnu/packages/libusb.scm: Likewise.
* gnu/packages/linux.scm: Likewise.
* gnu/packages/lirc.scm: Likewise.
* gnu/packages/maths.scm: Likewise.
* gnu/packages/mcrypt.scm: Likewise.
* gnu/packages/mp3.scm: Likewise.
* gnu/packages/music.scm: Likewise.
* gnu/packages/networking.scm: Likewise.
* gnu/packages/onc-rpc.scm: Likewise.
* gnu/packages/password-utils.scm: Likewise.
* gnu/packages/pdf.scm: Likewise.
* gnu/packages/perl.scm: Likewise.
* gnu/packages/photo.scm: Likewise.
* gnu/packages/popt.scm: Likewise.
* gnu/packages/python.scm: Likewise.
* gnu/packages/rdesktop.scm: Likewise.
* gnu/packages/screen.scm: Likewise.
* gnu/packages/swig.scm: Likewise.
* gnu/packages/tcl.scm: Likewise.
* gnu/packages/version-control.scm: Likewise.
* gnu/packages/video.scm: Likewise.
* gnu/packages/w3m.scm: Likewise.
* gnu/packages/web.scm: Likewise.
* gnu/packages/wm.scm: Likewise.
* gnu/packages/xdisorg.scm: Likewise.
* gnu/packages/xml.scm: Likewise.
2016-07-21 18:09:40 -04:00
Ben Woodcroft 7593e50b26
gnu: diamond: Update to 0.8.15.
* gnu/packages/bioinformatics.scm (diamond): Update to 0.8.15.
2016-07-18 00:06:21 +10:00
Ricardo Wurmus 2c0d8e0d09
gnu: eigensoft: Do not refer to "lapacke" output.
* gnu/packages/bioinformatics.scm (eigensoft)[inputs]: Remove reference
  to non-existing "lapacke" output.
2016-07-17 12:04:04 +02:00
Ricardo Wurmus 6619f9c769
gnu: Add eigensoft.
* gnu/packages/bioinformatics.scm (eigensoft): New variable.
2016-07-14 08:58:35 +02:00
Ricardo Wurmus 17dc32a400
gnu: Add Ribotaper.
* gnu/packages/bioinformatics.scm (ribotaper): New variable.
2016-07-12 12:19:39 +02:00
Ricardo Wurmus 9a8f309cf1
gnu: Add bedtools-2.18.
* gnu/packages/bioinformatics.scm (bedtools-2.18): New variable.
2016-07-12 12:19:15 +02:00
Ben Woodcroft 7f575d3e56
gnu: diamond: Update to 0.8.12.
* gnu/packages/bioinformatics.scm (diamond): Update to 0.8.12.
2016-07-10 22:32:57 +10:00
Ben Woodcroft ec2a67de88
gnu: Add python-dendropy.
* gnu/packages/bioinformatics.scm (python-dendropy, python2-dendropy): New
variables.
* gnu/packages/patches/python-dendropy-exclude-failing-tests.patch: New
file.
* gnu/local.mk (dist_patch_DATA): Add it.
2016-07-09 08:00:34 +10:00
Ben Woodcroft c11f79a49e
gnu: star: Restrict supported systems to 64-bit systems.
* gnu/packages/bioinformatics.scm (star)[supported-systems]: Restrict to
x86_64-linux and mips64el-linux.
2016-07-08 22:10:05 +10:00
Ben Woodcroft d285657eae
gnu: bedtools: Update to 2.26.0.
* gnu/packages/bioinformatics.scm (bedtools): Update to 2.26.0.
2016-07-07 23:27:19 +10:00
Ben Woodcroft 7c7643a7f0
gnu: diamond: Update to 0.8.11.
* gnu/packages/bioinformatics.scm (diamond): Update to 0.8.11.
2016-07-07 18:21:10 +08:00
Ricardo Wurmus 274da826f9
gnu: Add r-seqinr.
* gnu/packages/bioinformatics.scm (r-seqinr): New variable.
2016-07-07 10:46:17 +02:00
Efraim Flashner 8157af2e09
gnu: khmer: Limit to x86_64 systems only.
* gnu/packages/bioinformatics.scm (khmer)[supported-systems]: New field.
2016-07-07 06:33:28 +03:00
Ricardo Wurmus 5fb5dffbd4
gnu: Add multiqc.
* gnu/packages/bioinformatics.scm (multiqc): New variable.
2016-07-05 16:32:37 +02:00
Ricardo Wurmus 1f1b20b8be
gnu: Add bits.
* gnu/packages/bioinformatics.scm (bits): New variable.
2016-07-05 15:43:36 +02:00
Ricardo Wurmus 66e40e0065
gnu: Add EMBOSS.
* gnu/packages/bioinformatics.scm (emboss): New variable.
2016-07-05 12:32:12 +02:00
Roel Janssen 744004a31f
gnu: Add r-edger.
* gnu/packages/bioinformatics.scm (r-edger): New variable.
2016-07-04 14:49:07 +02:00
Roel Janssen 7d4224d794
gnu: Add r-limma.
* gnu/packages/bioinformatics.scm (r-limma):  New variable.
2016-07-04 14:39:16 +02:00
Ben Woodcroft 71830f0e49
gnu: vsearch: Update to 2.0.1.
*  gnu/packages/bioinformatics.scm (vsearch): Update to 2.0.1.
2016-07-01 09:01:28 +10:00
Ben Woodcroft 8dec2229a2
gnu: blast+: Update to 2.4.0.
* gnu/packages/bioinformatics.scm (blast+): Update to 2.4.0.
2016-06-29 22:42:47 +10:00
Ben Woodcroft 3bce0f14b2
gnu: star: Update to 2.5.2a.
* gnu/packages/bioinformatics.scm (star): Update to 2.5.2a.
2016-06-29 10:14:22 +10:00
Ben Woodcroft 6c737963f6
gnu: htslib: Update to 1.3.1.
* gnu/packages/bioinformatics.scm (htslib): Update to 1.3.1.
2016-06-29 10:14:22 +10:00
Ricardo Wurmus ec9466388e
gnu: Add SEEK.
* gnu/packages/bioinformatics.scm (seek): New variable.
2016-06-28 22:49:05 +02:00
Ben Woodcroft d6e374a0d9
gnu: mafft: Update to 7.299.
* gnu/packages/bioinformatics.scm (mafft): Update to 7.299.
2016-06-28 21:42:15 +10:00
Ben Woodcroft 45469ebe52
gnu: metabat: Update to 0.26.3.
* gnu/packages/bioinformatics.scm (metabat): Update to 0.26.3.
[arguments]: Update include and linking paths accordingly.
2016-06-28 21:28:06 +10:00
Ben Woodcroft af45244e36
gnu: diamond: Update to 0.8.9.
* gnu/packages/bioinformatics.scm (diamond): Update to 0.8.9.
2016-06-28 19:31:25 +10:00
Ben Woodcroft 94ff31572d
gnu: Add khmer.
* gnu/packages/bioinformatics.scm (khmer): New variable.
* gnu/packages/patches/khmer-use-libraries.patch: New file.
* gnu/local.mk (dist_patch_DATA): Add it.
2016-06-27 21:35:16 +10:00
Ben Woodcroft 9ded145717
gnu: Add python-screed.
* gnu/packages/bioinformatics.scm (python-screed, python2-screed):
New variables.
2016-06-27 21:16:39 +10:00
Ben Woodcroft c2e575185b
gnu: vsearch: Update to 2.0.0.
* gnu/packages/bioinformatics.scm (vsearch): Update to 2.0.0.
2016-06-26 12:43:39 +10:00
Ben Woodcroft 69af462496
gnu: vsearch: Update to 0.11.2.
* gnu/packages/bioinformatics.scm (vsearch): Update to 0.11.2.
2016-06-22 07:51:12 +10:00
Ben Woodcroft 7b3df1e56e
gnu: Add r-vegan.
* gnu/packages/bioinformatics.scm (r-vegan): New variable.
2016-06-21 21:29:17 +10:00
Ben Woodcroft cec2653bb4
gnu: diamond: Update to 0.8.7.
* gnu/packages/bioinformatics.scm (diamond): Update to 0.8.7.
2016-06-21 20:00:38 +10:00
Ricardo Wurmus 4714d521e3
gnu: Add r-bsgenome-mmusculus-ucsc-mm10.
* gnu/packages/bioinformatics.scm (r-bsgenome-mmusculus-ucsc-mm10): New
  variable.
2016-06-15 17:08:08 +02:00
Ben Woodcroft e4a44a6aa5
gnu: Add ruby-bio-kseq.
* gnu/packages/bioinformatics.scm (ruby-bio-kseq): New variable.
2016-06-14 07:57:09 +10:00
Ricardo Wurmus 883302daf2
gnu: piranha: Update to 1.2.1.
* gnu/packages/bioinformatics.scm (piranha): Update to 1.2.1.
2016-06-13 11:53:38 +02:00
Hartmut Goebel 698bd29799
gnu: Use full SHA1 commit ids.
* gnu/packages/bioinformatics.scm (pbtranscript-tofu, mosaik,
  smithlab-cpp, piranha): Use full SHA1 commit ids.
* gnu/packages/ci.scm (hydra): Likewise.
* gnu/packages/compression.scm (sfarkxtc): Likewise.
* gnu/packages/emacs.scm (emacs-ob-ipython): Likewise.
* gnu/packages/games.scm (mars, emulation-station): Likewise.
* gnu/packages/gnunet.scm (guile-gnunet): Likewise.
* gnu/packages/music.scm (non-sequencer): Likewise.
* gnu/packages/version-control.scm (git-flow, git-test-sequence): Likewise.
* gnu/packages/xorg.scm (xf86-video-intel): Likewise.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2016-06-05 00:05:38 +02:00
Ben Woodcroft 6ac0a0fbe7
gnu: diamond: Update to 0.8.5.
* gnu/packages/bioinformatics.scm (diamond): Update to 0.8.5.
2016-06-04 09:28:54 +10:00
Ricardo Wurmus 64efa3078a
gnu: Add r-genomationdata.
* gnu/packages/bioinformatics.scm (r-genomationdata): New variable.
2016-05-31 16:29:37 +02:00
Ben Woodcroft 9fcc3509a7 gnu: Update diamond to 0.8.3.
* gnu/packages/bioinformatics.scm (diamond): Update to 0.8.3.
2016-05-28 23:44:16 +10:00
Ricardo Wurmus 0783787436 gnu: Add ParDRe.
* gnu/packages/bioinformatics.scm (pardre): New variable.
2016-05-23 12:55:09 +02:00
Ricardo Wurmus 7740f58128
gnu: r-genomation: Update to 1.4.2.
* gnu/packages/bioinformatics.scm (r-genomation): Update to 1.4.2.
2016-05-20 15:18:23 +02:00
Ricardo Wurmus 8ede249e0a
gnu: r-genomicfeatures: Update to 1.24.2.
* gnu/packages/bioinformatics.scm (r-genomicfeatures): Update to 1.24.2.
2016-05-20 15:18:23 +02:00
Ricardo Wurmus 192e1ea8d1
gnu: r-summarizedexperiment: Update to 1.2.2.
* gnu/packages/bioinformatics.scm (r-summarizedexperiment): Update to 1.2.2.
2016-05-20 15:18:23 +02:00
Ricardo Wurmus d7420566a9
gnu: r-biocparallel: Update to 1.6.2.
* gnu/packages/bioinformatics.scm (r-biocparallel): Update to 1.6.2.
2016-05-20 15:18:23 +02:00
Ricardo Wurmus 73af676feb
gnu: r-annotationdbi: Update to 1.34.2.
* gnu/packages/bioinformatics.scm (r-annotationdbi): Update to 1.34.2.
2016-05-20 15:18:23 +02:00
Ricardo Wurmus 679e670b36
gnu: r-variantannotation: Update to 1.18.1.
* gnu/packages/bioinformatics.scm (r-variantannotation): Update to 1.18.1.
2016-05-20 15:18:23 +02:00
Ricardo Wurmus 186ed87337
gnu: r-genomeinfodb: Update to 1.8.1.
* gnu/packages/bioinformatics.scm (r-genomeinfodb): Update to 1.8.1.
2016-05-20 15:18:23 +02:00
Ben Woodcroft 7c544991dc gnu: diamond: Do not specify target architecture.
* gnu/packages/bioinformatics.scm (diamond)[arguments]: Do not
specify target architecture.
2016-05-18 21:25:06 +10:00
Ricardo Wurmus e62ffce538 gnu: Add Piranha.
* gnu/packages/bioinformatics.scm (piranha): New variable.
2016-05-18 11:59:34 +02:00
Ben Woodcroft 849485f5a0 gnu: sortmerna: Update to 2.1b.
* gnu/packages/bioinformatics.scm (sortmerna): Update to 2.1b.
[inputs]: New field.
2016-05-17 21:45:49 +10:00
Ben Woodcroft daaeed765a gnu: vsearch: Update to 1.11.1.
* gnu/packages/bioinformatics.scm (vsearch): Update to 1.11.1.
2016-05-17 21:36:46 +10:00
Ben Woodcroft 122395f9fc gnu: diamond: Update to 0.8.1.
* gnu/packages/bioinformatics.scm (diamond): Update to 0.8.1.
[source]: Remove 'snippet'.
[build-system]: Use cmake-build-system.
[arguments]: Remove modifications to phases.
[native-inputs]: Remove field.
[inputs]: Remove 'boost'.
2016-05-17 21:07:00 +10:00
Ricardo Wurmus 96101b6718
gnu: r-zlibbioc: Update to 1.18.0.
* gnu/packages/bioinformatics.scm (r-zlibbioc): Update to 1.18.0.
2016-05-16 20:59:50 +02:00
Ricardo Wurmus a0fe3aeecf
gnu: r-motifrg: Update to 1.16.0.
* gnu/packages/bioinformatics.scm (r-motifrg): Update to 1.16.0.
2016-05-16 20:59:38 +02:00
Ricardo Wurmus 1f5786a918
gnu: r-seqlogo: Update to 1.38.0.
* gnu/packages/bioinformatics.scm (r-seqlogo): Update to 1.38.0.
2016-05-16 20:59:27 +02:00
Ricardo Wurmus 8adc3b628d
gnu: r-genomation: Update to 1.4.0.
* gnu/packages/bioinformatics.scm (r-genomation): Update to 1.4.0.
2016-05-16 20:59:14 +02:00
Ricardo Wurmus 7555817c2b
gnu: r-seqpattern: Update to 1.4.0.
* gnu/packages/bioinformatics.scm (r-seqpattern): Update to 1.4.0.
2016-05-16 20:59:04 +02:00
Ricardo Wurmus d1bff89d26
gnu: r-impute: Update to 1.46.0.
* gnu/packages/bioinformatics.scm (r-impute): Update to 1.46.0.
2016-05-16 20:58:49 +02:00
Ricardo Wurmus 5190ed1751
gnu: r-bsgenome: Update to 1.40.0.
* gnu/packages/bioinformatics.scm (r-bsgenome): Update to 1.40.0.
2016-05-16 20:58:35 +02:00
Ricardo Wurmus e48e88c217
gnu: r-topgo: Update to 2.24.0.
* gnu/packages/bioinformatics.scm (r-topgo): Update to 2.24.0.
[propagated-inputs]: Add r-matrixstats.
2016-05-16 20:58:24 +02:00
Ricardo Wurmus 0c56023557
gnu: r-graph: Update to 1.50.0.
* gnu/packages/bioinformatics.scm (r-graph): Update to 1.50.0.
2016-05-16 20:58:08 +02:00
Ricardo Wurmus c12b0a5a30
gnu: r-genomicfeatures: Update to 1.24.0.
* gnu/packages/bioinformatics.scm (r-genomicfeatures): Update to 1.24.0.
2016-05-16 20:57:55 +02:00
Ricardo Wurmus d23fbf1eb9
gnu: r-rtracklayer: Update to 1.32.0.
* gnu/packages/bioinformatics.scm (r-rtracklayer): Update to 1.32.0.
2016-05-16 20:57:43 +02:00
Ricardo Wurmus 3cd551ea7b
gnu: r-genomicalignments: Update to 1.8.0.
* gnu/packages/bioinformatics.scm (r-genomicalignments): Update to 1.8.0.
2016-05-16 20:57:30 +02:00
Ricardo Wurmus d848ed7cf2
gnu: r-summarizedexperiment: Update to 1.2.0.
* gnu/packages/bioinformatics.scm (r-summarizedexperiment): Update to 1.2.0.
2016-05-16 20:57:21 +02:00
Ricardo Wurmus b4c5a0db22
gnu: r-rsamtools: Update to 1.24.0.
* gnu/packages/bioinformatics.scm (r-rsamtools): Update to 1.24.0.
2016-05-16 20:57:10 +02:00
Ricardo Wurmus 2477d9773a
gnu: r-biostrings: Update to 2.40.0.
* gnu/packages/bioinformatics.scm (r-biostrings): Update to 2.40.0.
2016-05-16 20:56:58 +02:00
Ricardo Wurmus 6a2a0de1ab
gnu: r-biocparallel: Update to 1.6.0.
* gnu/packages/bioinformatics.scm (r-biocparallel): Update to 1.6.0.
2016-05-16 20:56:39 +02:00
Ricardo Wurmus 63cea37234
gnu: r-biomart: Update to 2.28.0.
* gnu/packages/bioinformatics.scm (r-biomart): Update to 2.28.0.
2016-05-16 20:56:29 +02:00
Ricardo Wurmus c4a4e17938
gnu: r-annotationdbi: Update to 1.34.0.
* gnu/packages/bioinformatics.scm (r-annotationdbi): Update to 1.34.0.
2016-05-16 20:56:19 +02:00
Ricardo Wurmus 4466a02c9f
gnu: r-biobase: Update to 2.32.0.
* gnu/packages/bioinformatics.scm (r-biobase): Update to 2.32.0.
2016-05-16 20:56:09 +02:00
Ricardo Wurmus 828980cad6
gnu: r-genomicranges: Update to 1.24.0.
* gnu/packages/bioinformatics.scm (r-genomicranges): Update to 1.24.0.
2016-05-16 20:55:58 +02:00
Ricardo Wurmus e782ca3e97
gnu: r-xvector: Update to 0.12.0.
* gnu/packages/bioinformatics.scm (r-xvector): Update to 0.12.0.
2016-05-16 20:55:46 +02:00
Ricardo Wurmus 052ee32b24
gnu: r-variantannotation: Update to 1.18.0.
* gnu/packages/bioinformatics.scm (r-variantannotation): Update to
  1.18.0.
2016-05-16 20:55:32 +02:00
Ricardo Wurmus d1ab3d8fa5
gnu: r-genomeinfodb: Update to 1.8.0.
* gnu/packages/bioinformatics.scm (r-genomeinfodb): Update to 1.8.0.
2016-05-16 20:55:20 +02:00
Ricardo Wurmus 952ff8c862
gnu: r-iranges: Update to 2.6.0.
* gnu/packages/bioinformatics (r-iranges): Update to 2.6.0.
2016-05-16 20:55:11 +02:00
Ricardo Wurmus 3654a61146
gnu: r-s4vectors: Update to 0.10.0.
* gnu/packages/bioinformatics.scm (r-s4vectors): Update to 0.10.0.
2016-05-16 20:54:59 +02:00
Ricardo Wurmus a936bf59ea
gnu: r-dnacopy: Update to 1.46.0.
* gnu/packages/bioinformatics.scm (r-dnacopy): Update to 1.46.0.
2016-05-16 20:54:37 +02:00
Ricardo Wurmus dbfeba5209
gnu: r-biocgenerics: Update to 0.18.0.
* gnu/packages/bioinformatics.scm (r-biocgenerics): Update to 0.18.0.
2016-05-16 20:53:48 +02:00
Efraim Flashner a83e604662
gnu: hmmer: Update urls.
* gnu/packages/bioinformatics.scm (hmmer)[source]: Project has moved to
eddylab, with their downloads.
[home-page]: Update to new homepage.
2016-05-16 14:28:53 +03:00
Mark H Weaver 99828fa788
gnu: Update module imports for asciidoc and doxygen.
This is a followup to commit 0573a923de.

* gnu/packages/algebra.scm, gnu/packages/bioinformatics.scm,
gnu/packages/fcitx.scm, gnu/packages/fish.scm,
gnu/packages/freedesktop.scm, gnu/packages/game-development.scm,
gnu/packages/gcc.scm, gnu/packages/graphics.scm, gnu/packages/image.scm,
gnu/packages/kodi.scm, gnu/packages/libreoffice.scm,
gnu/packages/linux.scm, gnu/packages/messaging.scm,
gnu/packages/mpd.scm, gnu/packages/music.scm, gnu/packages/rdf.scm,
gnu/packages/serialization.scm, gnu/packages/version-control.scm,
gnu/packages/web.scm, gnu/packages/wm.scm, gnu/packages/xdisorg.scm,
gnu/packages/xiph.scm: Change imports of (gnu packages asciidoc) or
(gnu packages doxygen) to (gnu packages documentation).
2016-05-12 20:18:15 -04:00
Ricardo Wurmus 83b84fa812 gnu: edirect: Update to 4.10.
* gnu/packages/bioinformatics.scm (edirect): Update to 4.10.
2016-05-04 16:45:43 +02:00
Ben Woodcroft 324efb8888 gnu: Add muscle.
* gnu/packages/bioinformatics.scm (muscle): New variable.
2016-04-30 15:46:24 +10:00
Ricardo Wurmus fb868e3395 gnu: r-acsnminer: Update to 0.16.01.29.
* gnu/packages/bioinformatics.scm (r-acsnminer): Update to 0.16.01.29.
2016-04-26 17:06:17 +02:00
Ricardo Wurmus e1c2ad6777 gnu: r-qtl: Update to 1.39-5.
* gnu/packages/bioinformatics.scm (r-qtl): Update to 1.39-5.
2016-04-26 17:06:17 +02:00
Roel Janssen 6b49a37e6b gnu: Add filevercmp.
* gnu/packages/bioinformatics.scm (filevercmp): New variable.
2016-04-26 16:41:15 +02:00
Ben Woodcroft 79b555edeb gnu: samtools: Update to 1.3.1.
* gnu/packages/bioinformatics.scm (samtools): Update to 1.3.1.
2016-04-24 09:45:07 +10:00
Hartmut Goebel 1ad15c1669 gnu: Rename Java packages to match new naming specification.
* gnu/packages/bioinformatics.scm (htsjdk): Rename to...
(java-htsjdk): ...this.
(ngs-java): Rename to...
(java-ngs): ...this.
(ncbi-vdb)[arguments,inputs]: Use new name.
* gnu/packages/java.scm (swt): Rename to...
(java-swt): ...this.
* gnu/packages/music.scm (tuxguitar)[make-flags,inputs,arguments]: Use
new name of package "swt".
2016-04-19 16:55:03 +02:00
Ricardo Wurmus 4d16cc5133 gnu: python2-plastid: Propagate setuptools.
* gnu/packages/bioinformatics.scm (python2-plastid)[native-inputs]: Move
python2-setuptools from here...
[propagated-inputs]: ...to here.
2016-04-19 16:12:51 +02:00
Ricardo Wurmus f94bf1983b gnu: Add python-plastid.
* gnu/packages/bioinformatics.scm (python-plastid, python2-plastid): New
  variables.
2016-04-19 12:16:01 +02:00
Ricardo Wurmus 4db9433aa0 gnu: Add python-twobitreader.
* gnu/packages/bioinformatics.scm (python-twobitreader,
  python2-twobitreader): New variables.
2016-04-19 12:16:01 +02:00
Alex Kost fc1adab148 gnu: packages: Use 'search-patches' everywhere.
* gnu/packages/abiword.scm: Use 'search-patches' for 'patches' field.
* gnu/packages/acl.scm: Likewise.
* gnu/packages/admin.scm: Likewise.
* gnu/packages/algebra.scm: Likewise.
* gnu/packages/animation.scm: Likewise.
* gnu/packages/apr.scm: Likewise.
* gnu/packages/audacity.scm: Likewise.
* gnu/packages/audio.scm: Likewise.
* gnu/packages/autotools.scm: Likewise.
* gnu/packages/avahi.scm: Likewise.
* gnu/packages/backup.scm: Likewise.
* gnu/packages/base.scm: Likewise.
* gnu/packages/bash.scm: Likewise.
* gnu/packages/bioinformatics.scm: Likewise.
* gnu/packages/cdrom.scm: Likewise.
* gnu/packages/ci.scm: Likewise.
* gnu/packages/cmake.scm: Likewise.
* gnu/packages/cpio.scm: Likewise.
* gnu/packages/cross-base.scm: Likewise.
* gnu/packages/dico.scm: Likewise.
* gnu/packages/doxygen.scm: Likewise.
* gnu/packages/ebook.scm: Likewise.
* gnu/packages/elf.scm: Likewise.
* gnu/packages/emacs.scm: Likewise.
* gnu/packages/engineering.scm: Likewise.
* gnu/packages/firmware.scm: Likewise.
* gnu/packages/flashing-tools.scm: Likewise.
* gnu/packages/fltk.scm: Likewise.
* gnu/packages/ftp.scm: Likewise.
* gnu/packages/games.scm: Likewise.
* gnu/packages/gawk.scm: Likewise.
* gnu/packages/gcc.scm: Likewise.
* gnu/packages/gd.scm: Likewise.
* gnu/packages/ghostscript.scm: Likewise.
* gnu/packages/glib.scm: Likewise.
* gnu/packages/gnome.scm: Likewise.
* gnu/packages/gnucash.scm: Likewise.
* gnu/packages/gnunet.scm: Likewise.
* gnu/packages/gnupg.scm: Likewise.
* gnu/packages/gnuzilla.scm: Likewise.
* gnu/packages/graphics.scm: Likewise.
* gnu/packages/grub.scm: Likewise.
* gnu/packages/gtk.scm: Likewise.
* gnu/packages/guile.scm: Likewise.
* gnu/packages/icu4c.scm: Likewise.
* gnu/packages/idutils.scm: Likewise.
* gnu/packages/image.scm: Likewise.
* gnu/packages/imagemagick.scm: Likewise.
* gnu/packages/irc.scm: Likewise.
* gnu/packages/ldc.scm: Likewise.
* gnu/packages/libcanberra.scm: Likewise.
* gnu/packages/libevent.scm: Likewise.
* gnu/packages/libreoffice.scm: Likewise.
* gnu/packages/libunwind.scm: Likewise.
* gnu/packages/libusb.scm: Likewise.
* gnu/packages/linux.scm: Likewise.
* gnu/packages/lirc.scm: Likewise.
* gnu/packages/llvm.scm: Likewise.
* gnu/packages/lsh.scm: Likewise.
* gnu/packages/lua.scm: Likewise.
* gnu/packages/lxqt.scm: Likewise.
* gnu/packages/mail.scm: Likewise.
* gnu/packages/maths.scm: Likewise.
* gnu/packages/mcrypt.scm: Likewise.
* gnu/packages/messaging.scm: Likewise.
* gnu/packages/mit-krb5.scm: Likewise.
* gnu/packages/mp3.scm: Likewise.
* gnu/packages/multiprecision.scm: Likewise.
* gnu/packages/music.scm: Likewise.
* gnu/packages/ninja.scm: Likewise.
* gnu/packages/nvi.scm: Likewise.
* gnu/packages/ocaml.scm: Likewise.
* gnu/packages/orpheus.scm: Likewise.
* gnu/packages/ots.scm: Likewise.
* gnu/packages/parallel.scm: Likewise.
* gnu/packages/patchutils.scm: Likewise.
* gnu/packages/pcre.scm: Likewise.
* gnu/packages/pdf.scm: Likewise.
* gnu/packages/perl.scm: Likewise.
* gnu/packages/plotutils.scm: Likewise.
* gnu/packages/polkit.scm: Likewise.
* gnu/packages/pulseaudio.scm: Likewise.
* gnu/packages/python.scm: Likewise.
* gnu/packages/qemu.scm: Likewise.
* gnu/packages/qt.scm: Likewise.
* gnu/packages/ratpoison.scm: Likewise.
* gnu/packages/rdf.scm: Likewise.
* gnu/packages/readline.scm: Likewise.
* gnu/packages/rush.scm: Likewise.
* gnu/packages/scheme.scm: Likewise.
* gnu/packages/screen.scm: Likewise.
* gnu/packages/sdl.scm: Likewise.
* gnu/packages/slim.scm: Likewise.
* gnu/packages/ssh.scm: Likewise.
* gnu/packages/tcl.scm: Likewise.
* gnu/packages/tcsh.scm: Likewise.
* gnu/packages/texinfo.scm: Likewise.
* gnu/packages/tls.scm: Likewise.
* gnu/packages/tor.scm: Likewise.
* gnu/packages/tv.scm: Likewise.
* gnu/packages/valgrind.scm: Likewise.
* gnu/packages/version-control.scm: Likewise.
* gnu/packages/video.scm: Likewise.
* gnu/packages/vpn.scm: Likewise.
* gnu/packages/vtk.scm: Likewise.
* gnu/packages/w3m.scm: Likewise.
* gnu/packages/web.scm: Likewise.
* gnu/packages/wicd.scm: Likewise.
* gnu/packages/wm.scm: Likewise.
* gnu/packages/xdisorg.scm: Likewise.
* gnu/packages/xfce.scm: Likewise.
* gnu/packages/xiph.scm: Likewise.
* gnu/packages/xml.scm: Likewise.
* gnu/packages/xorg.scm: Likewise.
* gnu/packages/zip.scm: Likewise.
2016-04-14 10:38:21 +03:00
Ricardo Wurmus 6dc6099853 gnu: Add r-bsgenome-dmelanogaster-ucsc-dm3.
* gnu/packages/bioinformatics.scm (r-bsgenome-dmelanogaster-ucsc-dm3):
  New variable.
2016-04-11 15:11:16 +02:00
Ricardo Wurmus 943bd6279f gnu: Add r-bsgenome-celegans-ucsc-ce6.
* gnu/packages/bioinformatics.scm (r-bsgenome-celegans-ucsc-ce6): New
  variable.
2016-04-11 15:11:16 +02:00
Ricardo Wurmus a3e9028770 gnu: Add r-bsgenome-mmusculus-ucsc-mm9.
* gnu/packages/bioinformatics.scm (r-bsgenome-mmusculus-ucsc-mm9): New
  variable.
2016-04-11 15:11:15 +02:00
Ricardo Wurmus ae2462f7dd gnu: Add r-motifrg.
* gnu/packages/bioinformatics.scm (r-motifrg): New variable.
2016-04-11 11:03:27 +02:00
Ricardo Wurmus c90a4baff6 gnu: Add r-bsgenome-hsapiens-ucsc-hg19.
* gnu/packages/bioinformatics.scm (r-bsgenome-hsapiens-ucsc-hg19): New
  variable.
2016-04-11 11:03:27 +02:00
Ricardo Wurmus 936e7d6774 gnu: Add r-seqlogo.
* gnu/packages/bioinformatics.scm (r-seqlogo): New variable.
2016-04-11 11:03:27 +02:00
Roel Janssen 9e3ba31c53 gnu: Add r-zlibbioc.
* gnu/packages/bioinformatics.scm (r-zlibbioc): New variable.

Signed-off-by: Leo Famulari <leo@famulari.name>
2016-04-06 17:38:42 -04:00
Roel Janssen b669d9c4c8 gnu: Add r-variantannotation.
* gnu/packages/bioinformatics.scm (r-variantannotation): New variable.

Signed-off-by: Leo Famulari <leo@famulari.name>
2016-04-06 17:38:42 -04:00
Roel Janssen 9b36e25607 gnu: vcftools: Update to 0.1.14.
* gnu/packages/bioinformatics.scm (vcftools): Update to 0.1.14.
[arguments]: Do not modify phases as it is not needed anymore.
[native-inputs]: Add 'pkg-config'.
[home-page]: Update to new location.

Signed-off-by: Alex Kost <alezost@gmail.com>
2016-04-05 11:29:32 +03:00
Efraim Flashner ddb8312911 gnu: python2-pbcore: Update to 1.2.8.
* gnu/packages/bioinformatics.scm (python2-pbcore): Update to 1.2.8.
[native-inputs]: Add python2-docutils, python2-nose, python2-sphinx.
2016-03-30 22:45:35 +03:00
Ricardo Wurmus f315f4fcab gnu: r-genomation: Update to 1.2.2.
* gnu/packages/bioinformatics.scm (r-genomation): Update to 1.2.2.
2016-03-30 11:59:16 +02:00
Ricardo Wurmus 571f0b63d5 gnu: r-genomicfeatures: Update to 1.22.13.
* gnu/packages/bioinformatics.scm (r-genomicfeatures): Update to
  1.22.13.
2016-03-30 11:59:16 +02:00
Ricardo Wurmus ffaf72ad96 gnu: r-rtracklayer: Update to 1.30.4.
* gnu/packages/bioinformatics.scm (r-rtracklayer): Update to 1.30.4.
2016-03-30 11:59:15 +02:00
Ricardo Wurmus ac2d8b0fb8 gnu: r-genomicalignments: Update to 1.6.3.
* gnu/packages/bioinformatics.scm (r-genomicalignments): Update to
  1.6.3.
2016-03-30 11:59:15 +02:00
Ricardo Wurmus 7eade1c5f9 gnu: r-summarizedexperiment: Update to 1.0.2.
* gnu/packages/bioinformatics.scm (r-summarizedexperiment): Update to
  1.0.2.
2016-03-30 11:59:15 +02:00
Ricardo Wurmus 53fd0f5e1d gnu: r-biostrings: Update to 2.38.4.
* gnu/packages/bioinformatics.scm (r-biostrings): Update to 2.38.4.
2016-03-30 11:59:15 +02:00
Ricardo Wurmus 5fe3115415 gnu: r-genomicranges: Update to 1.22.4.
* gnu/packages/bioinformatics.scm (r-genomicranges): Update to 1.22.4.
2016-03-30 11:59:15 +02:00
Ricardo Wurmus 9cc22d28d8 gnu: r-genomeinfodb: Update to 1.6.3.
* gnu/packages/bioinformatics.scm (r-genomeinfodb): Update to 1.6.3.
2016-03-30 11:59:15 +02:00
Ricardo Wurmus 1d216b6ec9 gnu: Remove "r-repository" property.
* gnu/packages/bioinformatics.scm (r-biocgenerics, r-s4vectors,
r-iranges, r-genomeinfodb, r-xvector, r-genomicranges)[properties]:
Remove "r-repository" property.
2016-03-24 16:18:01 +01:00
Ludovic Courtès 5697fdc366 gnu: r-dnacopy: Fix home page URL.
* gnu/packages/bioinformatics.scm (r-dnacopy)[home-page]: Add missing
URI scheme.
2016-03-18 23:00:04 +01:00
Ricardo Wurmus 953c12232f gnu: bless: Remove bundled sources for sparsehash.
* gnu/packages/bioinformatics.scm (bless)[source]: Delete
"google-sparsehash" sources.
[inputs]: Add "sparsehash".
2016-03-17 13:01:31 +01:00
Ricardo Wurmus 6c1305f9ec gnu: Add CD-HIT.
* gnu/packages/bioinformatics.scm (cd-hit): New variable.
2016-03-17 13:01:31 +01:00
Roel Janssen 247d498aaa gnu: Add r-dnacopy.
* gnu/packages/bioinformatics.scm (r-dnacopy): New variable.
2016-03-16 11:23:27 +01:00
Rob Syme 6a35566df7 gnu: Add codingquarry.
* gnu/packages/bioinformatics.scm (codingquarry): New variable.

Signed-off-by: Leo Famulari <leo@famulari.name>
2016-03-16 04:49:27 -04:00
Ricardo Wurmus 10b4a969be gnu: htsjdk: Use ant-build-system.
* gnu/packages/bioinformatics.scm (htsjdk)[build-system]: Use
ant-build-system.
[arguments]: Adapt for ant-build-system.
2016-03-14 14:30:03 +01:00
Ricardo Wurmus 846e340954 gnu: Add pyicoteo.
* gnu/packages/bioinformatics.scm (pyicoteo): New variable.
2016-03-14 12:36:49 +01:00
Roel Janssen a0a71439fa gnu: Add bioawk.
* gnu/packages/bioinformatics.scm (bioawk): New variable.

Signed-off-by: Leo Famulari <leo@famulari.name>
2016-03-10 18:37:25 -05:00
Ricardo Wurmus 649e9b3b47 gnu: python-pysam: Move cython and setuptools to native inputs.
* gnu/packages/bioinformatics.scm (python-pysam)[inputs]: Move
"python-cython" and "python-setuptools" from here...
[native-inputs]: ... to here.
2016-03-03 13:47:19 +01:00
Ricardo Wurmus 3acb8c857c gnu: deeptools: Update to 2.1.1.
* gnu/packages/bioinformatics.scm (deeptools): Update to 2.1.1.
[inputs]: Add "python2-numpydoc" and "python2-pybigwig".
2016-03-03 13:47:12 +01:00
Ricardo Wurmus 14bda1ff49 gnu: deeptools: Change "propagated-inputs" to "inputs".
* gnu/packages/bioinformatics.scm (deeptools)[propagated-inputs]: Move
all inputs from here...
[inputs]: ...to here.
2016-03-03 13:47:02 +01:00
Ricardo Wurmus 69e0e03c36 gnu: Add python-pybigwig.
* gnu/packages/bioinformatics.scm (python-pybigwig, python2-pybigwig):
  New variables.
2016-03-03 13:46:52 +01:00
Ricardo Wurmus d454640c38 gnu: python-pysam: Update to 0.8.4.
* gnu/packages/bioinformatics.scm (python-pysam): Update to 0.8.4.
2016-03-03 13:46:39 +01:00
Ricardo Wurmus 55a9a8c2b9 gnu: python-pysam, python2-pysam: Move to bioinformatics.scm.
* gnu/packages/python.scm (python-pysam, python2-pysam): Move to...
* gnu/packages/bioinformatics.scm (python-pysam, python2-pysam):
  ...here.
2016-03-03 13:46:26 +01:00
Pjotr Prins f82c8c3cba gnu: r-go-db: Bioconductor changed URL for data downloads.
* gnu/packages/bioinformatics.scm (r-go-db)[source]: Update data URL.
2016-03-01 19:47:26 +02:00
Pjotr Prins 27acfaea4c gnu: r-iranges: Update to 2.4.8.
* gnu/packages/bioinformatics.scm (r-iranges): Update to 2.4.8.
2016-03-01 19:47:26 +02:00
Pjotr Prins 8921841da8 gnu: r-s4vectors: Update to 0.8.11.
* gnu/packages/bioinformatics.scm (r-s4vectors): Update to 0.8.11.
2016-03-01 19:47:25 +02:00
Ricardo Wurmus d1e32822b4 gnu: Add PePr.
* gnu/packages/bioinformatics.scm (pepr): New variable.
2016-03-01 11:51:24 +01:00
Ricardo Wurmus d29150b55d gnu: Add bwa-pssm.
* gnu/packages/bioinformatics.scm (bwa-pssm): New variable.
2016-03-01 10:31:04 +01:00
Mark H Weaver b35461748b gnu: Fix misplaced commas (unquote).
Fix many occurrences of comma (unquote) being placed immediately after the
previous list item, e.g. ("ncurses", ncurses) in the inputs.

* gnu/packages/base.scm (patch, gnu-make),
  gnu/packages/bioinformatics.scm (hmmer),
  gnu/packages/bittorrent.scm (aria2),
  gnu/packages/compression.scm (pbzip2),
  gnu/packages/databases.scm (recutils),
  gnu/packages/fonts.scm (font-terminus),
  gnu/packages/freedesktop.scm (xdg-utils, elogind),
  gnu/packages/games.scm (gnujump),
  gnu/packages/gnome.scm (libidl, gnumeric, eog, gedit),
  gnu/packages/gnunet.scm (gnunet),
  gnu/packages/gnuzilla.scm (mozjs, nspr),
  gnu/packages/gtk.scm (gtksourceview, gdk-pixbuf),
  gnu/packages/lua.scm (lua),
  gnu/packages/openstack.scm (python-swiftclient),
  gnu/packages/perl.scm (perl-json-any),
  gnu/packages/polkit.scm (polkit-qt),
  gnu/packages/python.scm (wrap-python3, python-oauthlib)
  (python-mccabe-0.2.1, python-contextlib2, python2-rauth),
  gnu/packages/qt.scm (qtkeychain),
  gnu/packages/ruby.scm (ruby-nokogiri),
  gnu/packages/screen.scm (screen),
  gnu/packages/ssh.scm (libssh),
  gnu/packages/video.scm (ffmpeg, mplayer),
  gnu/packages/vim.scm (vim),
  gnu/packages/xdisorg.scm (redshift),
  gnu/packages/xfce.scm (xfce4-panel, xfce4-settings),
  gnu/packages/xnee.scm (xnee),
  gnu/packages/xorg.scm (font-adobe100dpi, font-adobe75dpi),
  gnu/packages/zsh.scm (zsh): Fix misplaced commas (unquote).
2016-02-27 08:49:26 -05:00
Ludovic Courtès 736f9ffce2 gnu: Add missing import in bioinformatics.scm.
This is a followup to 1baee94.

* gnu/packages/bioinformatics.scm: Add missing import.
2016-02-25 12:48:08 +01:00
Ricardo Wurmus 1baee943ca gnu: Add libBigWig.
* gnu/packages/bioinformatics.scm (libbigwig): New variable.
2016-02-25 11:43:44 +01:00
Ricardo Wurmus 6d415db23d gnu: r-topgo: Add missing input.
* gnu/packages/bioinformatics.scm (r-topgo)[propagated-inputs]: Add
  "r-graph".
2016-02-24 17:36:55 +01:00
Ricardo Wurmus d1dbde6ac1 gnu: Add r-graph.
* gnu/packages/bioinformatics.scm (r-graph): New variable.
2016-02-24 17:36:55 +01:00
Ricardo Wurmus e761beb9a9 gnu: Add r-org-mm-eg-db.
* gnu/packages/bioinformatics.scm (r-org-mm-eg-db): New variable.
2016-02-24 17:26:39 +01:00
Ricardo Wurmus 16c53a1e26 gnu: Add r-org-dm-eg-db.
* gnu/packages/bioinformatics.scm (r-org-dm-eg-db): New variable.
2016-02-24 17:26:39 +01:00
Ricardo Wurmus fefedf98cb gnu: Add r-org-ce-eg-db.
* gnu/packages/bioinformatics.scm (r-org-ce-eg-db): New variable.
2016-02-24 17:26:39 +01:00
Ricardo Wurmus 486da49143 gnu: Add r-org-hs-eg-db.
* gnu/packages/bioinformatics.scm (r-org-hs-eg-db): New variable.
2016-02-24 17:26:39 +01:00
Ricardo Wurmus 578b05d99e gnu: htseq: Add PySam to inputs.
* gnu/packages/bioinformatics.scm (htseq)[inputs]: Add "python2-pysam".
2016-02-16 15:32:15 +01:00
Ricardo Wurmus d15d981ea2 gnu: Add StringTie.
* gnu/packages/bioinformatics.scm (stringtie): New variable.
2016-02-16 14:51:10 +01:00
Ben Woodcroft e70f7a2306 gnu: prodigal: Update to 2.6.3.
* gnu/packages/bioinformatics.scm (prodigal): Update to 2.6.3.
2016-02-16 07:18:59 +10:00
Ricardo Wurmus 258c0a365e gnu: r-annotationdbi: Update to 1.32.3.
* gnu/packages/bioinformatics.scm (r-annotationdbi): Update to 1.32.3.
2016-02-15 16:11:22 +01:00
Ben Woodcroft cf6edaba74 gnu: vsearch: Update to 1.10.0.
* gnu/packages/bioinformatics.scm (vsearch): Update to 1.10.0.
[origin]: Adapt to changes in bundling of cityhash.
2016-02-15 22:54:25 +10:00
Ricardo Wurmus 0d0bcaa08e gnu: macs: Update to 2.1.0.20151222.
* gnu/packages/bioinformatics.scm (macs): Update to 2.1.0.20151222.
2016-02-12 18:16:16 +01:00
Ricardo Wurmus 43ec07f17c gnu: macs: Use "pypi-uri".
* gnu/packages/bioinformatics.scm (macs)[source]: Use "pypi-uri" to
  build source URI.
2016-02-12 18:16:16 +01:00
Ben J. Woodcroft ce294c0445 gnu: Update sortmerna to 2.1.
* gnu/packages/bioinformatics.scm (sortmerna): Update to 2.1.
2016-02-02 22:42:38 +10:00
Ben Woodcroft a78d62f432 gnu: sra-tools: Update to 2.5.7.
* gnu/packages/bioinformatics.scm (sra-tools): Update to 2.5.7.
2016-01-26 10:59:13 +10:00
Ben Woodcroft fe91666b79 gnu: ncbi-vdb: Update to 2.5.7.
gnu/packages/bioinformatics.scm (ncbi-vdb): Update to 2.5.7.
2016-01-26 10:59:13 +10:00
Ben Woodcroft d3b39bc231 gnu: ngs-sdk: Update to 1.2.3.
gnu/packages/bioinformatics.scm (ngs-sdk): Update to 1.2.3.
2016-01-26 10:59:13 +10:00
Ben Woodcroft bcadaf0050 gnu: Add sortmerna.
* gnu/packages/bioinformatics.scm (sortmerna): New variable.
2016-01-25 08:35:11 +10:00
Ricardo Wurmus 3a40a92c73 gnu: Add cufflinks.
* gnu/packages/bioinformatics.scm (cufflinks): New variable.
2016-01-23 09:15:11 +01:00
Ricardo Wurmus 94ce537eac gnu: Add TopHat.
* gnu/packages/bioinformatics.scm (tophat): New variable.
* gnu/packages/patches/tophat-build-with-later-seqan.patch: New file.
* gnu-system.am (dist_patch_DATA): Add it.
2016-01-23 08:53:10 +01:00
Ricardo Wurmus 3062d750b4 gnu: star: Update to 2.5.1b.
* gnu/packages/bioinformatics.scm (star): Update to 2.5.1b.
[source]: Remove bundled htslib sources and pre-built binaries.
[arguments]: Add phase "do-not-use-bundled-htslib".
[inputs]: Add "htslib".
2016-01-23 08:40:14 +01:00
Ricardo Wurmus c0266e8d03 gnu: star: Use "modify-phases" syntax.
* gnu/packages/bioinformatics.scm (star)[arguments]: Use "modify-phases"
  syntax.
2016-01-23 08:40:14 +01:00
Pjotr Prins 897092875e gnu: r-qtl: Update to 1.38-4.
* gnu/packages/bioinformatics.scm (r-qtl): Update to 1.38-4.
2016-01-21 11:16:12 +01:00
Ricardo Wurmus 2309ed6862 gnu: samtools-0.1: Adapt to changes in "samtools" variable.
* gnu/packages/bioinformatics.scm (samtools-0.1)[arguments]: Add
  "LIBCURSES" make flag; delete "configure" phase; disable tests outside
  of "substitute-keyword-arguments".
2016-01-16 15:50:51 +01:00
Ricardo Wurmus 3141b83d4d gnu: r-go-db: Add missing input.
* gnu/packages/bioinformatics.scm (r-go-db)[propagated-inputs]: Add
  "r-annotationdbi".
2016-01-14 14:43:59 +01:00
Ricardo Wurmus 0047d26a22 gnu: bowtie: Update to 2.2.6.
* gnu/packages/bioinformatics.scm (bowtie): Update to 2.2.6.
[source]: Remove patch; do not set CC and CPP variables.
[inputs]: Add "tbb".
[arguments]: Pass "prefix" and "WITH_TBB" make flags; remove custom
"install" phase.
* gnu/packages/patches/bowtie-fix-makefile.patch: Remove file.
* gnu-system.am (dist_patch_DATA): Remove patch file.
2016-01-14 14:43:25 +01:00
Ben Woodcroft 6b6f7d6a0e gnu: orfm: Update to 0.5.3.
* gnu/packages/bioinformatics.scm (orfm): Update to 0.5.3.
[native-inputs]: Add inputs required for tests.
[description]: Add commas.
2016-01-14 08:00:10 +10:00
Ricardo Wurmus c44734115a gnu: samtools: Update to 1.3.
* gnu/packages/bioinformatics.scm (samtools): Update to 1.3.
[arguments]: Enable tests for all architectures; set ncurses in
configure-flags instead of make-flags; simplify "patch-tests" phase;
restore "configure" phase.
2016-01-13 15:12:22 +01:00