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1179 Commits

Author SHA1 Message Date
Ricardo Wurmus 7665fb39f5
gnu: r-biocstyle: Update to 2.6.1. 
* gnu/packages/bioinformatics.scm (r-biocstyle): Update to 2.6.1.
 2017-12-19 20:35:03 +01:00
Ricardo Wurmus 756ac7254c
gnu: r-dexseq: Update to 1.24.2. 
* gnu/packages/bioinformatics.scm (r-dexseq): Update to 1.24.2.
 2017-12-19 20:35:03 +01:00
Ricardo Wurmus 8d11ef4470
gnu: r-vegan: Update to 2.4-5. 
* gnu/packages/bioinformatics.scm (r-vegan): Update to 2.4-5.
 2017-12-19 20:35:02 +01:00
Efraim Flashner 677bc34d5b
gnu: Remove redundant cmake libdir configure flags. 
* gnu/packages/bioinformatics.scm (imp)[arguments]: Remove
CMAKE_INSTALL_LIBDIR flag.
* gnu/packages/calendar.scm (libical): Same.
* gnu/packages/engineering.scm (kicad): Same.
* gnu/packages/games.scm (openrct2, mgba): Same.
* gnu/packages/gl.scm (virtualgl): Same.
* gnu/packages/image-processing.scm (mia): Same.
* gnu/packages/linux.scm (rdma-core): Same.
* gnu/packages/machine-learning.scm (dlib): Same.
* gnu/packages/maths.scm (lapack, superlu, z3): Same.
* gnu/packages/password-utils.scm (keepassxc): Same.
* gnu/packages/photo.scm (darktable): Same.
* gnu/packages/rdesktop.scm (freerdp): Same.
 2017-12-19 19:52:01 +02:00
Ricardo Wurmus f1a2b1cb20
gnu: r-seurat: Update to 2.1.0. 
* gnu/packages/bioinformatics.scm (r-seurat): Update to 2.1.0.
[propagated-inputs]: Add r-diffusionmap, r-dtw, r-ggjoy, r-hmisc, r-ica,
r-mass, r-matrix, r-nmf, r-plotly, r-sdmtools, r-tidyr; remove r-plyr,
r-rcppeigen, r-fastica.
 2017-12-18 12:01:35 +01:00
Ricardo Wurmus 8271b8d22a
gnu: r-seurat: Fix ModularityOptimizer.jar. 
* gnu/packages/bioinformatics.scm (r-seurat)[arguments]: Include Main-Class
attribute in manifest.
 2017-12-18 12:01:34 +01:00
Ben Woodcroft 6098a386a9
gnu: bedtools: Update to 2.27.1. 
* gnu/packages/ruby.scm (bedtools): Update to 2.27.1.
 2017-12-15 13:56:51 +10:00
Ben Woodcroft 4e0b3583ea
gnu: diamond: Update to 0.9.14. 
* gnu/packages/bioinformatics.scm (diamond): Update to 0.9.14.
 2017-12-14 22:50:10 +10:00
Christopher Baines 9cf5f134d5
gnu: Switch to using the version-major procedure. 
* gnu/packages/audio.scm (ardour)[arguments]: Switch to using version-major.
  (hmmer)[source]: Switch to using version-major.
  (pidgin)[native-search-paths]: Switch to using version-major.
  (r-minimal)[source]: Switch to using version-major.
 2017-12-11 19:12:33 +00:00
Ricardo Wurmus 83b9d121a7
gnu: bedtools-2.18: Fix build. 
* gnu/packages/bioinformatics.scm (bedtools-2.18)[arguments]: Restore custom
install phase.

Reported by Mark H Weaver <mhw@netris.org>.
 2017-12-09 13:01:15 +01:00
Ricardo Wurmus 0d9824cc12
gnu: bedtools: Update to 2.27.0. 
* gnu/packages/bioinformatics.scm (bedtools): Update to 2.27.0.
[arguments]: Remove custom "install" phase; specify prefix.
 2017-12-06 19:13:35 +01:00
Ricardo Wurmus d112e5a8c2
gnu: Add kallisto. 
* gnu/packages/bioinformatics.scm (kallisto): New variable.
 2017-12-03 18:38:58 +01:00
Ricardo Wurmus 117d8cc40e
gnu: jellyfish: Update to 2.2.7. 
* gnu/packages/bioinformatics.scm (jellyfish): Update to 2.2.7.
[native-inputs]: Add pkg-config.
[inputs]: Add htslib.
 2017-11-30 17:38:36 +01:00
Ricardo Wurmus 9b8d02011f
gnu: r-annotationhub: Update to 2.10.1. 
* gnu/packages/bioinformatics.scm (r-annotationhub): Update to 2.10.1.
 2017-11-30 17:28:24 +01:00
Ricardo Wurmus 87e91a9fff
gnu: r-msnid: Update to 1.12.1. 
* gnu/packages/bioinformatics.scm (r-msnid): Update to 1.12.1.
 2017-11-30 17:28:23 +01:00
Ricardo Wurmus 439492654b
gnu: r-maldiquant: Update to 1.17. 
* gnu/packages/bioinformatics.scm (r-maldiquant): Update to 1.17.
 2017-11-30 17:28:23 +01:00
Ricardo Wurmus 06e8e0fc6c
gnu: r-genomicalignments: Update to 1.14.1. 
* gnu/packages/bioinformatics.scm (r-genomicalignments): Update to 1.14.1.
 2017-11-30 17:28:22 +01:00
Ricardo Wurmus 1ce5d32b49
gnu: r-limma: Update to 3.34.2. 
* gnu/packages/bioinformatics.scm (r-limma): Update to 3.34.2.
 2017-11-30 17:28:22 +01:00
Ricardo Wurmus 8131cf4162
gnu: r-variantannotation: Update to 1.24.2. 
* gnu/packages/bioinformatics.scm (r-variantannotation): Update to 1.24.2.
 2017-11-30 17:28:21 +01:00
Ricardo Wurmus d2081a17ed
gnu: r-getopt: Update to 1.20.1. 
* gnu/packages/bioinformatics.scm (r-getopt): Update to 1.20.1.
 2017-11-30 17:28:20 +01:00
Ricardo Wurmus 4220ab0c81
gnu: r-gseabase: Update to 1.40.1. 
* gnu/packages/bioinformatics.scm (r-gseabase): Update to 1.40.1.
 2017-11-30 17:28:20 +01:00
Ricardo Wurmus d259932ca8
gnu: r-dexseq: Update to 1.24.1. 
* gnu/packages/bioinformatics.scm (r-dexseq): Update to 1.24.1.
 2017-11-30 17:28:19 +01:00
Ricardo Wurmus 058644c0f2
gnu: r-deseq2: Update to 1.18.1. 
* gnu/packages/bioinformatics.scm (r-deseq2): Update to 1.18.1.
 2017-11-30 17:28:18 +01:00
Ricardo Wurmus 654c29aceb
gnu: r-annotate: Update to 1.56.1. 
* gnu/packages/bioinformatics.scm (r-annotate): Update to 1.56.1.
 2017-11-30 17:28:18 +01:00
Arun Isaac 9364a520ce
gnu: metabat: Use scons-build-system. 
* gnu/packages/bioinformatics.scm (metabat): Switch to scons-build-system.
 2017-11-30 18:19:32 +05:30
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