| Age | Commit message (Expand) | Author |
|---|
| 2017-12-09 | 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>.
| Ricardo Wurmus |
| 2017-12-06 | gnu: bedtools: Update to 2.27.0....* gnu/packages/bioinformatics.scm (bedtools): Update to 2.27.0.
[arguments]: Remove custom "install" phase; specify prefix.
| Ricardo Wurmus |
| 2017-12-03 | gnu: Add kallisto....* gnu/packages/bioinformatics.scm (kallisto): New variable.
| Ricardo Wurmus |
| 2017-11-30 | 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.
| Ricardo Wurmus |
| 2017-11-30 | gnu: r-annotationhub: Update to 2.10.1....* gnu/packages/bioinformatics.scm (r-annotationhub): Update to 2.10.1.
| Ricardo Wurmus |
| 2017-11-30 | gnu: r-msnid: Update to 1.12.1....* gnu/packages/bioinformatics.scm (r-msnid): Update to 1.12.1.
| Ricardo Wurmus |
| 2017-11-30 | gnu: r-maldiquant: Update to 1.17....* gnu/packages/bioinformatics.scm (r-maldiquant): Update to 1.17.
| Ricardo Wurmus |
| 2017-11-30 | gnu: r-genomicalignments: Update to 1.14.1....* gnu/packages/bioinformatics.scm (r-genomicalignments): Update to 1.14.1.
| Ricardo Wurmus |
| 2017-11-30 | gnu: r-limma: Update to 3.34.2....* gnu/packages/bioinformatics.scm (r-limma): Update to 3.34.2.
| Ricardo Wurmus |
| 2017-11-30 | gnu: r-variantannotation: Update to 1.24.2....* gnu/packages/bioinformatics.scm (r-variantannotation): Update to 1.24.2.
| Ricardo Wurmus |
| 2017-11-30 | gnu: r-getopt: Update to 1.20.1....* gnu/packages/bioinformatics.scm (r-getopt): Update to 1.20.1.
| Ricardo Wurmus |
| 2017-11-30 | gnu: r-gseabase: Update to 1.40.1....* gnu/packages/bioinformatics.scm (r-gseabase): Update to 1.40.1.
| Ricardo Wurmus |
| 2017-11-30 | gnu: r-dexseq: Update to 1.24.1....* gnu/packages/bioinformatics.scm (r-dexseq): Update to 1.24.1.
| Ricardo Wurmus |
| 2017-11-30 | gnu: r-deseq2: Update to 1.18.1....* gnu/packages/bioinformatics.scm (r-deseq2): Update to 1.18.1.
| Ricardo Wurmus |
| 2017-11-30 | gnu: r-annotate: Update to 1.56.1....* gnu/packages/bioinformatics.scm (r-annotate): Update to 1.56.1.
| Ricardo Wurmus |
| 2017-11-30 | gnu: metabat: Use scons-build-system....* gnu/packages/bioinformatics.scm (metabat): Switch to scons-build-system.
| Arun Isaac |
| 2017-11-29 | gnu: Update r-mutationalpatterns to 1.4.1....* gnu/packages/bioinformatics.scm (r-mutationalpatterns): Update to 1.4.1.
| Roel Janssen |
| 2017-11-29 | gnu: Add r-copynumber....* gnu/packages/bioinformatics.scm (r-copynumber): New variable.
| Roel Janssen |
| 2017-11-27 | gnu: Add java-picard-1.113....* gnu/packages/bioinformatics.scm (java-picard-1.113): New variable.
| Ricardo Wurmus |
| 2017-11-27 | gnu: Add java-picard....* gnu/packages/bioinformatics.scm (java-picard): New variable.
| Ricardo Wurmus |
| 2017-11-27 | 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.
| Ricardo Wurmus |
| 2017-11-27 | gnu: r-rhdf5: Fix build phase....* gnu/packages/bioinformatics.scm (r-rhdf5)[arguments]: Fix "unpack-smallhdf5"
phase.
| Ricardo Wurmus |
| 2017-11-23 | gnu: subread: Update to 1.6.0....* gnu/packages/bioinformatics.scm (subread): Update to 1.6.0.
| Ricardo Wurmus |
| 2017-11-21 | gnu: idr: Update to 2.0.3....* gnu/packages/bioinformatics.scm (idr): Update to 2.0.3.
[source]: Add snippet to remove generated code.
| Ricardo Wurmus |
| 2017-11-21 | gnu: idr: Correct license....* gnu/packages/bioinformatics.scm (idr)[license]: Change to GPLv2+.
| Ricardo Wurmus |
| 2017-11-18 | gnu: r-genomeinfodbdata: Update to 0.99.1....* gnu/packages/bioinformatics.scm (r-genomeinfodbdata): Update to 0.99.1.
| Ricardo Wurmus |
| 2017-11-18 | gnu: r-go-db: Update to 3.5.0....* gnu/packages/bioinformatics.scm (r-go-db): Update to 3.5.0.
| Ricardo Wurmus |
| 2017-11-18 | 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.
| Ricardo Wurmus |
| 2017-11-18 | 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.
| Ricardo Wurmus |
| 2017-11-18 | 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.
| Ricardo Wurmus |
| 2017-11-18 | gnu: r-genomationdata: Update to 1.10.0....* gnu/packages/bioinformatics.scm (r-genomationdata): Update to 1.10.0.
| Ricardo Wurmus |
| 2017-11-18 | gnu: Remove duplicate from (gnu packages bioinformatics)....* gnu/packages/bioinformatics.scm (r-annotationfilter): Remove duplicate.
| Ricardo Wurmus |
| 2017-11-18 | gnu: r-org-hs-eg-db: Clarify description....* gnu/packages/bioinformatics.scm (r-org-hs-eg-db)[description]: Clarify.
| Ricardo Wurmus |
| 2017-11-18 | 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.
| Ricardo Wurmus |
| 2017-11-18 | gnu: r-org-hs-eg-db: Remove duplicate package definition....* gnu/packages/bioinformatics.scm (r-org-hs-eg-db): Remove duplicate variable.
| Ricardo Wurmus |
| 2017-11-17 | 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.
| Ricardo Wurmus |
| 2017-11-16 | 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.
| Ludovic Courtès |
| 2017-11-14 | gnu: diamond: Update to 0.9.13....* gnu/packages/bioinformatics.scm (diamond): Update to 0.9.13.
| Ben Woodcroft |
| 2017-11-13 | 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.
| Ricardo Wurmus |
| 2017-11-13 | gnu: cd-hit: Update source tarball hash....* gnu/packages/bioinformatics.scm (cd-hit)[source]: Update hash.
| Ricardo Wurmus |
| 2017-11-11 | gnu: methylkit: Use new home page....* gnu/packages/bioinformatics.scm (methylkit)[home-page]: Update.
| Tobias Geerinckx-Rice |
| 2017-11-11 | gnu: vsearch: Update to 2.6.0....* gnu/packages/bioinformatics.scm (vsearch): Update to 2.6.0.
| Ben Woodcroft |
| 2017-11-10 | gnu: cutadapt: Update to 1.14....* gnu/packages/bioinformatics.scm (cutadapt): Update to 1.14.
| Ricardo Wurmus |
| 2017-11-09 | gnu: roary: Update to 3.11.0....* gnu/packages/bioinformatics.scm (roary): Update to 3.11.0.
[inputs]: Add perl-digest-md5-file.
| Ben Woodcroft |
| 2017-11-08 | gnu: miso: Use pypi-uri....* gnu/packages/bioinformatics.scm (miso)[source]: Use pypi-uri.
| Ricardo Wurmus |
| 2017-11-07 | gnu: Add r-hitc....* gnu/packages/bioinformatics.scm (r-hitc): New variable.
| Ricardo Wurmus |
| 2017-11-07 | gnu: Add r-fithic....* gnu/packages/bioinformatics.scm (r-fithic): New variable.
| Ricardo Wurmus |
| 2017-11-07 | gnu: Add r-sushi....* gnu/packages/bioinformatics.scm (r-sushi): New variable.
| Ricardo Wurmus |
| 2017-11-07 | gnu: Add r-gwascat....* gnu/packages/bioinformatics.scm (r-gwascat): New variable.
| Ricardo Wurmus |
| 2017-11-07 | gnu: Add r-gviz....* gnu/packages/bioinformatics.scm (r-gviz): New variable.
| Ricardo Wurmus |
