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* gnu: Use INSTALL-FILE where appropriate.Tobias Geerinckx-Rice2017-03-15
| | | | | | | | | | | | * 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.
* gnu: samtools: End installation phases with truth.Tobias Geerinckx-Rice2017-03-15
| | | | | * gnu/packages/bioinformatics.scm (samtools, samtools-0.1)[arguments]: Return #T instead of the undefined results of COPY-FILE or INSTALL-FILE.
* gnu: vsearch: Update to 2.4.2.Ben Woodcroft2017-03-11
| | | | * gnu/packages/bioinformatics.scm (vsearch): Update to 2.4.2.
* gnu: Add r-ape.Raoul Jean Pierre Bonnal2017-03-11
| | | | | | * gnu/packages/bioinformatics.scm (r-ape): New variable. Co-authored-by: Ben Woodcroft <donttrustben@gmail.com>
* gnu: hmmer: Build reproducibly.Ben J. Woodcroft2017-03-10
| | | | | * gnu/packages/patches/hmmer-remove-cpu-specificity.patch: New file. * gnu/packages/bioinformatics.scm (hmmer): Use it.
* gnu: Add sambamba.Ricardo Wurmus2017-03-10
| | | | | * gnu/packages/bioinformatics.scm (htslib-for-sambamba, sambamba): New variables.
* Merge branch 'python-tests'Marius Bakke2017-03-03
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| * gnu: ribodiff: Fix test failure.Marius Bakke2017-02-27
| | | | | | | | | | * gnu/packages/bioinformatics.scm (ribodiff)[native-inputs]: Add PYTHON2-MOCK and PYTHON2-NOSE.
| * gnu: python-dendropy: Fix failing tests.Ricardo Wurmus2017-02-24
| | | | | | | | | | | | * 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.
| * Merge branch 'master' into python-testsMarius Bakke2017-02-13
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| * \ Merge branch 'master' into python-testsLeo Famulari2017-01-13
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| * | | gnu: pbtranscript-tofu: Disable tests.Marius Bakke2016-12-16
| | | | | | | | | | | | | | | | * gnu/packages/bioinformatics.scm (pbtranscript-tofu)[arguments]: Set #:tests? #f.
| * | | gnu: multiqc: Fix test dependencies.Marius Bakke2016-12-16
| | | | | | | | | | | | | | | | * gnu/packages/bioinformatics.scm (multiqc)[native-inputs]: Add python-nose.
| * | | gnu: idr: Remove explicit wrapper. This is now done implicitly.Marius Bakke2016-12-16
| | | | | | | | | | | | | | | | * gnu/packages/bioinformatics.scm (idr)[arguments]: Remove #:phases.
| * | | gnu: idr: Correct inputs.Marius Bakke2016-12-16
| | | | | | | | | | | | | | | | | | | | * gnu/packages/bioinformatics.scm (idr)[inputs]: Move everything from here ... [propagated-inputs]: ... to here. Add python-sympy.
| * | | gnu: idr: Disable tests.Marius Bakke2016-12-16
| | | | | | | | | | | | | | | | * gnu/packages/bioinformatics.scm (idr)[arguments]: Set #:tests? #f.
| * | | gnu: deeptools: Fix test dependency.Marius Bakke2016-12-16
| | | | | | | | | | | | | | | | * gnu/packages/bioinformatics.scm (deeptools)[native-inputs]: Add python-nose.
| * | | gnu: clipper: Fix test dependency.Marius Bakke2016-12-16
| | | | | | | | | | | | | | | | * gnu/packages/bioinformatics.scm (clipper)[native-inputs]: Add python2-nose.
| * | | gnu: python-biom-format: Fix tests.Marius Bakke2016-12-14
| | | | | | | | | | | | | | | | | | | | * gnu/packages/bioinformatics.scm (python-biom-format, python2-biom-format)[native-inputs]: Add python-nose.
* | | | gnu: diamond: Update to 0.8.36.Ben Woodcroft2017-03-02
| | | | | | | | | | | | | | | | * gnu/packages/bioinformatics.scm (diamond): Update to 0.8.36.
* | | | gnu: bamtools: Update to 2.4.1.Ricardo Wurmus2017-02-28
| |_|/ |/| | | | | | | | * gnu/packages/bioinformatics.scm (bamtools): Update to 2.4.1.
* | | gnu: vsearch: Update to 2.4.0.Ben Woodcroft2017-02-09
| | | | | | | | | | | | | | | | | | | | | | | | * 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.
* | | gnu: r-edger: Add r-statmod to inputs.Ricardo Wurmus2017-02-01
| | | | | | | | | | | | * gnu/packages/bioinformatics.scm (r-edger)[propagated-inputs]: Add r-statmod.
* | | download: url-fetch/tarball: Make ‘name’ truly optional.Tobias Geerinckx-Rice2017-02-01
| | | | | | | | | | | | | | | | | | | | | | | | * 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.
* | | gnu: Add r-rhdf5.Raoul Jean Pierre Bonnal2017-01-31
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* | | gnu: Add r-tximport.Raoul Jean Pierre Bonnal2017-01-31
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* | | gnu: Add r-bsgenome-hsapiens-1000genomes-hs37d5.Roel Janssen2017-01-30
| | | | | | | | | | | | | | | * gnu/packages/bioinformatics.scm (r-bsgenome-hsapiens-1000genomes-hs37d5): New variable.
* | | gnu: r-vegan: Update to 2.4-2.Ben Woodcroft2017-01-21
| | | | | | | | | | | | * gnu/packages/bioinformatics.scm (r-vegan): Update to 2.4-2.
* | | gnu: diamond: Update to 0.8.34.Ben Woodcroft2017-01-21
| | | | | | | | | | | | * gnu/packages/bioinformatics.scm (diamond): Update to 0.8.34.
* | | gnu: r-msnid: Expand abbreviation in description.Ricardo Wurmus2017-01-20
| | | | | | | | | | | | | | | * gnu/packages/bioinformatics.scm (r-msnid)[description]: Expand "MS/MS" to "tandem mass spectrometry".
* | | gnu: r-msnbase: Expand abbreviation in description.Ricardo Wurmus2017-01-20
| | | | | | | | | | | | | | | * gnu/packages/bioinformatics.scm (r-msnbase)[description]: Expand "MS" to "mass spectrometry".
* | | gnu: multiqc: Add python-nose to inputs.Ricardo Wurmus2017-01-18
| | | | | | | | | | | | | | | * gnu/packages/bioinformatics.scm (multiqc)[propagated-inputs]: Add python-nose.
* | | gnu: Add r-msnid.Ricardo Wurmus2017-01-17
| | | | | | | | | | | | * gnu/packages/bioinformatics.scm (r-msnid): New variable.
* | | gnu: Add r-msnbase.Ricardo Wurmus2017-01-17
| | | | | | | | | | | | * gnu/packages/bioinformatics.scm (r-msnbase): New variable.
* | | gnu: Add r-pcamethods.Ricardo Wurmus2017-01-17
| | | | | | | | | | | | * gnu/packages/bioinformatics.scm (r-pcamethods): New variable.
* | | gnu: Add r-mzid.Ricardo Wurmus2017-01-17
| | | | | | | | | | | | * gnu/packages/bioinformatics.scm (r-mzid): New variable.
* | | gnu: Add r-vsn.Ricardo Wurmus2017-01-17
| | | | | | | | | | | | * gnu/packages/bioinformatics.scm (r-vsn): New variable.
* | | gnu: Add r-affy.Ricardo Wurmus2017-01-17
| | | | | | | | | | | | * gnu/packages/bioinformatics.scm (r-affy): New variable.
* | | gnu: Add r-affyio.Ricardo Wurmus2017-01-17
| | | | | | | | | | | | * gnu/packages/bioinformatics.scm (r-affyio): New variable.
* | | gnu: Add r-mzr.Ricardo Wurmus2017-01-17
| | | | | | | | | | | | * gnu/packages/bioinformatics.scm (r-mzr): New variable.
* | | gnu: Add r-protgenerics.Ricardo Wurmus2017-01-17
| | | | | | | | | | | | * gnu/packages/bioinformatics.scm (r-protgenerics): New variable.
* | | gnu: Add r-maldiquant.Ricardo Wurmus2017-01-17
| | | | | | | | | | | | * gnu/packages/bioinformatics.scm (r-maldiquant): New variable.
* | | gnu: Add r-raremetals2.Ricardo Wurmus2017-01-17
| | | | | | | | | | | | * gnu/packages/bioinformatics.scm (r-raremetals2): New variable.
* | | gnu: Add r-seqminer.Ricardo Wurmus2017-01-17
| | | | | | | | | | | | * gnu/packages/bioinformatics.scm (r-seqminer): New variable.
* | | gnu: Add ribodiff.Ricardo Wurmus2017-01-17
| | | | | | | | | | | | * gnu/packages/bioinformatics.scm (ribodiff): New variable.
* | | gnu: Add hisat2.Ricardo Wurmus2017-01-17
| | | | | | | | | | | | * gnu/packages/bioinformatics.scm (hisat2): New variable.
* | | gnu: Add r-centipede.Ricardo Wurmus2017-01-16
| | | | | | | | | | | | * gnu/packages/bioinformatics.scm (r-centipede): New variable.
* | | gnu: Add r-sva.Raoul Jean Pierre Bonnal2017-01-14
| |/ |/| | | | | * gnu/packages/bioinformatics.scm (r-sva): New variable.
* | gnu: Add r-txdb-mmusculus-ucsc-mm10-knowngene.Roel Janssen2017-01-12
| | | | | | | | * gnu/packages/bioinformatics.scm (r-txdb-mmusculus-ucsc-mm10-knowngene): New variable.
* | gnu: Add r-copywriter.Ricardo Wurmus2017-01-06
| | | | | | | | * gnu/packages/bioinformatics.scm (r-copywriter): New variable.
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