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 |