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2017-03-15gnu: Use INSTALL-FILE where appropriate.Tobias Geerinckx-Rice
* 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.
2017-03-15gnu: samtools: End installation phases with truth.Tobias Geerinckx-Rice
* gnu/packages/bioinformatics.scm (samtools, samtools-0.1)[arguments]: Return #T instead of the undefined results of COPY-FILE or INSTALL-FILE.
2017-03-11gnu: vsearch: Update to 2.4.2.Ben Woodcroft
* gnu/packages/bioinformatics.scm (vsearch): Update to 2.4.2.
2017-03-11gnu: Add r-ape.Raoul Jean Pierre Bonnal
* gnu/packages/bioinformatics.scm (r-ape): New variable. Co-authored-by: Ben Woodcroft <donttrustben@gmail.com>
2017-03-10gnu: hmmer: Build reproducibly.Ben J. Woodcroft
* gnu/packages/patches/hmmer-remove-cpu-specificity.patch: New file. * gnu/packages/bioinformatics.scm (hmmer): Use it.
2017-03-10gnu: Add sambamba.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (htslib-for-sambamba, sambamba): New variables.
2017-03-03Merge branch 'python-tests'Marius Bakke
2017-03-02gnu: diamond: Update to 0.8.36.Ben Woodcroft
* gnu/packages/bioinformatics.scm (diamond): Update to 0.8.36.
2017-02-28gnu: bamtools: Update to 2.4.1.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (bamtools): Update to 2.4.1.
2017-02-27gnu: ribodiff: Fix test failure.Marius Bakke
* gnu/packages/bioinformatics.scm (ribodiff)[native-inputs]: Add PYTHON2-MOCK and PYTHON2-NOSE.
2017-02-24gnu: python-dendropy: Fix failing tests.Ricardo Wurmus
* 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.
2017-02-13Merge branch 'master' into python-testsMarius Bakke
2017-02-09gnu: vsearch: Update to 2.4.0.Ben Woodcroft
* 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.
2017-02-01gnu: r-edger: Add r-statmod to inputs.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-edger)[propagated-inputs]: Add r-statmod.
2017-02-01download: url-fetch/tarball: Make ‘name’ truly optional.Tobias Geerinckx-Rice
* 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.
2017-01-31gnu: Add r-rhdf5.Raoul Jean Pierre Bonnal
2017-01-31gnu: Add r-tximport.Raoul Jean Pierre Bonnal
2017-01-30gnu: Add r-bsgenome-hsapiens-1000genomes-hs37d5.Roel Janssen
* gnu/packages/bioinformatics.scm (r-bsgenome-hsapiens-1000genomes-hs37d5): New variable.
2017-01-21gnu: r-vegan: Update to 2.4-2.Ben Woodcroft
* gnu/packages/bioinformatics.scm (r-vegan): Update to 2.4-2.
2017-01-21gnu: diamond: Update to 0.8.34.Ben Woodcroft
* gnu/packages/bioinformatics.scm (diamond): Update to 0.8.34.
2017-01-20gnu: r-msnid: Expand abbreviation in description.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-msnid)[description]: Expand "MS/MS" to "tandem mass spectrometry".
2017-01-20gnu: r-msnbase: Expand abbreviation in description.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-msnbase)[description]: Expand "MS" to "mass spectrometry".
2017-01-18gnu: multiqc: Add python-nose to inputs.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (multiqc)[propagated-inputs]: Add python-nose.
2017-01-17gnu: Add r-msnid.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-msnid): New variable.
2017-01-17gnu: Add r-msnbase.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-msnbase): New variable.
2017-01-17gnu: Add r-pcamethods.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-pcamethods): New variable.
2017-01-17gnu: Add r-mzid.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-mzid): New variable.
2017-01-17gnu: Add r-vsn.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-vsn): New variable.
2017-01-17gnu: Add r-affy.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-affy): New variable.
2017-01-17gnu: Add r-affyio.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-affyio): New variable.
2017-01-17gnu: Add r-mzr.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-mzr): New variable.
2017-01-17gnu: Add r-protgenerics.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-protgenerics): New variable.
2017-01-17gnu: Add r-maldiquant.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-maldiquant): New variable.
2017-01-17gnu: Add r-raremetals2.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-raremetals2): New variable.
2017-01-17gnu: Add r-seqminer.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-seqminer): New variable.
2017-01-17gnu: Add ribodiff.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (ribodiff): New variable.
2017-01-17gnu: Add hisat2.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (hisat2): New variable.
2017-01-16gnu: Add r-centipede.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-centipede): New variable.
2017-01-14gnu: Add r-sva.Raoul Jean Pierre Bonnal
* gnu/packages/bioinformatics.scm (r-sva): New variable.
2017-01-13Merge branch 'master' into python-testsLeo Famulari
2017-01-12gnu: Add r-txdb-mmusculus-ucsc-mm10-knowngene.Roel Janssen
* gnu/packages/bioinformatics.scm (r-txdb-mmusculus-ucsc-mm10-knowngene): New variable.
2017-01-06gnu: Add r-copywriter.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-copywriter): New variable.
2017-01-06gnu: Add r-copyhelper.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-copyhelper): New variable.
2017-01-06gnu: Add r-chipseq.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-chipseq): New variable.
2017-01-06gnu: bioruby: Update to 1.5.1.Ben J Woodcroft
* gnu/packages/bioinformatics.scm (bioruby): Update to 1.5.1.
2017-01-06gnu: cd-hit: Update to 4.6.6.Ben J Woodcroft
* gnu/packages/bioinformatics.scm (cd-hit): Update to 4.6.6.
2017-01-04gnu: Use HTTPS for all sourceforge.net home pages.Tobias Geerinckx-Rice
* 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.
2017-01-03gnu: r-genomicranges: Update to 1.26.2.Roel Janssen
* gnu/packages/bioinformatics.scm (r-genomicranges): Update to 1.26.2.
2017-01-03gnu: r-genomeinfodb: Update to 1.10.2.Roel Janssen
* gnu/packages/bioinformatics.scm (r-genomeinfodb): Update to 1.10.2.
2017-01-01gnu: python-dendropy: Update to 4.2.0.Ben Woodcroft
* 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.
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