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* gnu: Use HTTPS for all sourceforge.net home pages.Tobias Geerinckx-Rice2017-01-04
| | | | | | | | | | | | | | | | | | | | | | * 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.
* gnu: r-genomicranges: Update to 1.26.2.Roel Janssen2017-01-03
| | | | * gnu/packages/bioinformatics.scm (r-genomicranges): Update to 1.26.2.
* gnu: r-genomeinfodb: Update to 1.10.2.Roel Janssen2017-01-03
| | | | * gnu/packages/bioinformatics.scm (r-genomeinfodb): Update to 1.10.2.
* gnu: python-dendropy: Update to 4.2.0.Ben Woodcroft2017-01-01
| | | | | | | | | * 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.
* gnu: diamond: Update to 0.8.31.Ben Woodcroft2017-01-01
| | | | * gnu/packages/bioinformatics.scm (diamond): Update to 0.8.31.
* gnu: multiqc: Update to 0.9.Ben Woodcroft2016-12-30
| | | | | | | | | Suggested by Raoul Bonnal <ilpuccio.febo@gmail.com>. * gnu/packages/bioinformatics.scm (multiqc): Update to 0.9. [origin]: Add patch. * gnu/packages/patches/multiqc-fix-git-subprocess-error.patch: New file. * gnu/local.mk (dist_patch_DATA): Add it.
* gnu: r-genomicfeatures: Update to 1.26.2.Ricardo Wurmus2016-12-29
| | | | * gnu/packages/bioinformatics.scm (r-genomicfeatures): Update to 1.26.2.
* gnu: r-biostrings: Update to 2.42.1.Ricardo Wurmus2016-12-29
| | | | * gnu/packages/bioinformatics.scm (r-biostrings): Update to 2.42.1.
* gnu: r-limma: Update to 3.30.7.Ricardo Wurmus2016-12-29
| | | | * gnu/packages/bioinformatics.scm (r-limma): Update to 3.30.7.
* gnu: r-variantannotation: Update to 1.20.2.Ricardo Wurmus2016-12-29
| | | | * gnu/packages/bioinformatics.scm (r-variantannotation): Update to 1.20.2.
* gnu: r-edger: Update to 3.16.5.Ricardo Wurmus2016-12-29
| | | | * gnu/packages/bioinformatics.scm (r-edger): Update to 3.16.5.
* gnu: r-genomeinfodb: Update to 1.10.1.Ricardo Wurmus2016-12-29
| | | | * gnu/packages/bioinformatics.scm (r-genomeinfodb): Update to 1.10.1.
* gnu: r-iranges: Update to 2.8.1.Ricardo Wurmus2016-12-29
| | | | * gnu/packages/bioinformatics.scm (r-iranges): Update to 2.8.1.
* gnu: r-s4vectors: Update to 0.12.1.Ricardo Wurmus2016-12-29
| | | | * gnu/packages/bioinformatics.scm (r-s4vectors): Update to 0.12.1.
* gnu: r-biocstyle: Update to 2.2.1.Ricardo Wurmus2016-12-29
| | | | * gnu/packages/bioinformatics.scm (r-biocstyle): Update to 2.2.1.
* gnu: r-deseq2: Update to 1.14.1.Ricardo Wurmus2016-12-29
| | | | * gnu/packages/bioinformatics.scm (r-deseq2): Update to 1.14.1.
* gnu: r-annotate: Update to 1.52.1.Ricardo Wurmus2016-12-29
| | | | | * gnu/packages/bioinformatics.scm (r-annotate): Update to 1.52.1. [propagated-inputs]: Add r-rcurl.
* gnu: r-qtl: Update to 1.40-8.Ricardo Wurmus2016-12-29
| | | | * gnu/packages/bioinformatics.scm (r-qtl): Update to 1.40-8.
* gnu: r-rcas: Update to 1.1.1.Ricardo Wurmus2016-12-27
| | | | | * gnu/packages/bioinformatics.scm (r-rcas): Update to 1.1.1. [propagated-inputs]: Add plotrix.
* gnu: diamond: Update to 0.8.30.Ben Woodcroft2016-12-27
| | | | * gnu/packages/bioinformatics.scm (diamond): Update to 0.8.30.
* gnu: cutadapt: Use ‘modify-phases’ syntax.Tobias Geerinckx-Rice2016-12-20
| | | | | * gnu/packages/bioinformatics.scm (cutadapt)[arguments]: Use ‘modify-phases’.
* gnu: cutadapt: Update to 1.12.Tobias Geerinckx-Rice2016-12-19
| | | | | * gnu/packages/bioinformatics.scm (cutadapt): Update to 1.12. [inputs]: Add python-xopen.
* gnu: Add attribution line for Raoul Bonnal.Ben Woodcroft2016-12-18
| | | | | | This is a follow-up commit to c9e9154e993f055a438e2e43518bbd0740aaaf24. * gnu/packages/bioinformatics.scm: Add attribution.
* gnu: star: Update to 2.5.2b.Raoul Bonnal2016-12-17
| | | | | | | * gnu/packages/bioinformatics (star): Update to 2.5.2b. [source]: Delete precompiled binary. Co-authored-by: Ben Woodcroft <donttrustben@gmail.com>
* gnu: Update more dead Google Code home pages.Tobias Geerinckx-Rice2016-12-14
| | | | | * gnu/packages/bioinformatics.scm (cutadapt, mosaik, pepr)[home-page]: Update to their respective replacements.
* gnu: diamond: Update to 0.8.29.Ben Woodcroft2016-12-13
| | | | * gnu/packages/bioinformatics.scm (diamond): Update to 0.8.29.
* gnu: orfm: Update to 0.6.1.Ben Woodcroft2016-12-13
| | | | * gnu/packages/bioinformatics.scm (orfm): Update to 0.6.1.
* gnu: orfm: Update to 0.6.0.Ben Woodcroft2016-12-12
| | | | * gnu/packages/bioinformatics.scm (orfm): Update to 0.6.0.
* gnu: vsearch: Update to 2.3.4.Ben Woodcroft2016-12-10
| | | | * gnu/packages/bioinformatics.scm (vsearch): Update to 2.3.4.
* gnu: pardre: Update to 1.1.5-1.Ben Woodcroft2016-12-10
| | | | | * gnu/packages/bioinformatics.scm (pardre): update to 1.1.5-1. [source]: Update source hash.
* gnu: vsearch: Update to 2.3.3.Ben Woodcroft2016-12-08
| | | | * gnu/packages/bioinformatics.scm (vsearch): Update to 2.3.3.
* gnu: aragorn: Update to 1.2.38.Ben Woodcroft2016-12-04
| | | | * gnu/packages/bioinformatics.scm (aragorn): Update to 1.2.38.
* Merge branch 'master' into python-build-systemHartmut Goebel2016-11-29
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| * gnu: Add r-gkmsvm.Ricardo Wurmus2016-11-28
| | | | | | | | * gnu/packages/bioinformatics.scm (r-gkmsvm): New variable.
| * gnu: Add r-seqgl.Ricardo Wurmus2016-11-28
| | | | | | | | * gnu/packages/bioinformatics.scm (r-seqgl): New variable.
| * gnu: Add r-chipkernels.Ricardo Wurmus2016-11-28
| | | | | | | | * gnu/packages/bioinformatics.scm (r-chipkernels): New variable.
| * gnu: Add r-wgcna.Ricardo Wurmus2016-11-28
| | | | | | | | * gnu/packages/bioinformatics.scm (r-wgcna): New variable.
| * gnu: Add r-r4rna.Ricardo Wurmus2016-11-28
| | | | | | | | * gnu/packages/bioinformatics.scm (r-r4rna): New variable.
| * gnu: Add newick-utils.Ben Woodcroft2016-11-28
| | | | | | | | * gnu/packages/bioinformatics.scm (newick-utils): New variable.
| * gnu: roary: Update to 3.7.0.Ben Woodcroft2016-11-26
| | | | | | | | * gnu/packages/bioinformatics.scm (roary): Update to 3.7.0.
| * gnu: Add proteinortho.Ben Woodcroft2016-11-26
| | | | | | | | * gnu/packages/bioinformatics.scm (proteinortho): New variable.
* | Merge branch 'master' into python-build-systemLeo Famulari2016-11-25
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| * gnu: diamond: Update to 0.8.27.Ben Woodcroft2016-11-22
| | | | | | | | * gnu/packages/bioinformatics.scm (diamond): Update to 0.8.27.
| * gnu: Remove redundancy where mkdir-p <dir> is followed by install-file ↵Petter2016-11-21
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | <file> <dir>. * gnu/packages/bioinformatics.scm (bwa)[arguments]: Remove redundant mkdir-p. (eigensoft)[arguments]: Likewise. (snap-aligner)[arguments]: Likewise. (pardre)[arguments]: Likewise. (piranha)[arguments]: Likewise. * gnu/packages/maths.scm (hypre)[arguments]: Likewise. * gnu/packages/mp3.scm (mpc123)[arguments]: Likewise. * gnu/packages/music.scm (tuxguitar)[arguments]: Likewise. * gnu/packages/pdf.scm (impressive)[arguments]: Likewise. * gnu/packages/qemu.scm (qemu)[arguments]: Likewise. Signed-off-by: Leo Famulari <leo@famulari.name>
| * gnu: hisat: Fix typo.Ricardo Wurmus2016-11-15
| | | | | | | | | | * gnu/packages/bioinformatics.scm (hisat)[arguments]: Fix directory name in install phase.
* | gnu: python2-pbcore: Fix inputs:Hartmut Goebel2016-11-15
| | | | | | | | | | | | | | * gnu/packages/bioinformatics.scm (python2-pbcore) [inputs] change to [propagated-inputs]. [native-inputs]: Remove python-docutils, which comes with sphinx. [former propagated-inputs]: move all (which is only pyxb) to [inputs].
* | gnu: python2-warpedlmm: Remove phase remove-bin-directory.Hartmut Goebel2016-11-15
| | | | | | | | | | | | | | | | | | | | | | | | This directory did contain contain wrappers for `nose`, which should not be there anyway (since nose already was a native-input). The new python build system no longer creates this directory, while the old one did. (This difference is due to the bloody details of how packages are installed.) * gnu/packages/bioinformatics.scm (python2-warpedlmm) [modify-phases] Remove, since remove-bin-directory was the only modification here.
* | gnu: Fix python inputs, part 7: Ensure python-cython is a native-input.Hartmut Goebel2016-11-15
| | | | | | | | | | | | | | | | * gnu/packages/audio.scm (python-pyliblo): [inputs] Move python-cyton to [native-inputs]. * gnu/packages/bioinformatics.scm (python2-pybedtools): dito. * gnu/packages/music.scm (beast, python-pyportmidi): dito. * gnu/packages/python.scm (python2-fastlmm, python-kivy): dito.
* | gnu: Fix python inputs, part 1: all inputs become propagated-inputs.Hartmut Goebel2016-11-15
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | This patch contains the changes where all [inputs] are changed to [propagated-inputs] * gnu/packages/python.scm (python-passlib, python-paramiko, python-ccm, python-babel, python-keyring python-pandas, python-tzlocal, python-parse-type, python-nose2, python-pytest, python-pytest-mock, python-pytest-xdist, python-scripttest, python-testtools, python-pytest-cov, python-testscenarios, python-pbr-0.11, python-oauthlib, python-jinja2, python-sphinx, python-tzlocal, python-bugz, python2-pytest-mock, behave, pelican, sqlalchemy-utils, python-pygridtools, python-urwidtrees, python-tornado, python2-tornado, python-debian, python-execnet, python-pytest-cache, pytest-localserver, python-clint, python-rply, python-hy, python-rauth, python-rsa, python-celery, python-vobject, s3cmd, python-prompt-toolkit, ptpython, python-requests-oauthlib, python-stem, python-binaryornot, python2-binaryornot, python-nltk, python-pymongo, python-schematics, python-url, python2-url, python-freezegun, python-glances, python-graphql-core, python-graphql-relay, python-graphene, python-nautilus, python-s3transfer): All [inputs] become [propagated-inputs]. * gnu/packages/bioinformatics.scm (python-biopython): Likewise. * gnu/packages/django.scm (pytest-django): Likewise. * gnu/packages/mail.scm (python-mailmanclient): Likewise. * gnu/packages/password-utils.scm (python-bcrypt): Likewise. * gnu/packages/propbuf.scm (python-protobuf): Likewise. * gnu/packages/rdf.scm (python-rdflib): Likewise. SQACH all become propagated
* | gnu: Remove work-arounds for bug 20765 (ensure uncompressed eggs).Hartmut Goebel2016-11-15
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | Bug 20765 is solved since we build all Python packages using option "--single-version-externally-managed". * gnu/packages/bioinformatics.scm (pbtranscript-tofu): Remove configure-flags. (pepr): remove phase "disable-egg-generation". * gnu/packages/pdf.scm (reportlab): Remove configure-flags. * gnu/packages/python.scm (python-sphinx-rtd-theme, python2-elib.intl, python-pkgconfig, python-pytest-pep8, python-pytest-flakes): Remove configure-flags. (python-pillow) remove phase "disable-egg-generation". (python-libarchive-c) Remove patching setup.cfg. * gnu/packages/statistics.scm (python-patsy): remove phase "prevent-generation-of-egg-archive". * gnu/packages/tls.scm (python-acme): remove phase "disable-egg-compression". * gnu/packages/tor.scm (onionshare): Remove configure-flags.
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