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2016-12-29gnu: r-genomicfeatures: Update to 1.26.2.•••* gnu/packages/bioinformatics.scm (r-genomicfeatures): Update to 1.26.2. Ricardo Wurmus
2016-12-29gnu: r-biostrings: Update to 2.42.1.•••* gnu/packages/bioinformatics.scm (r-biostrings): Update to 2.42.1. Ricardo Wurmus
2016-12-29gnu: r-limma: Update to 3.30.7.•••* gnu/packages/bioinformatics.scm (r-limma): Update to 3.30.7. Ricardo Wurmus
2016-12-29gnu: r-variantannotation: Update to 1.20.2.•••* gnu/packages/bioinformatics.scm (r-variantannotation): Update to 1.20.2. Ricardo Wurmus
2016-12-29gnu: r-edger: Update to 3.16.5.•••* gnu/packages/bioinformatics.scm (r-edger): Update to 3.16.5. Ricardo Wurmus
2016-12-29gnu: r-genomeinfodb: Update to 1.10.1.•••* gnu/packages/bioinformatics.scm (r-genomeinfodb): Update to 1.10.1. Ricardo Wurmus
2016-12-29gnu: r-iranges: Update to 2.8.1.•••* gnu/packages/bioinformatics.scm (r-iranges): Update to 2.8.1. Ricardo Wurmus
2016-12-29gnu: r-s4vectors: Update to 0.12.1.•••* gnu/packages/bioinformatics.scm (r-s4vectors): Update to 0.12.1. Ricardo Wurmus
2016-12-29gnu: r-biocstyle: Update to 2.2.1.•••* gnu/packages/bioinformatics.scm (r-biocstyle): Update to 2.2.1. Ricardo Wurmus
2016-12-29gnu: r-deseq2: Update to 1.14.1.•••* gnu/packages/bioinformatics.scm (r-deseq2): Update to 1.14.1. Ricardo Wurmus
2016-12-29gnu: r-annotate: Update to 1.52.1.•••* gnu/packages/bioinformatics.scm (r-annotate): Update to 1.52.1. [propagated-inputs]: Add r-rcurl. Ricardo Wurmus
2016-12-29gnu: r-qtl: Update to 1.40-8.•••* gnu/packages/bioinformatics.scm (r-qtl): Update to 1.40-8. Ricardo Wurmus
2016-12-27gnu: r-rcas: Update to 1.1.1.•••* gnu/packages/bioinformatics.scm (r-rcas): Update to 1.1.1. [propagated-inputs]: Add plotrix. Ricardo Wurmus
2016-12-27gnu: diamond: Update to 0.8.30.•••* gnu/packages/bioinformatics.scm (diamond): Update to 0.8.30. Ben Woodcroft
2016-12-20gnu: cutadapt: Use ‘modify-phases’ syntax.•••* gnu/packages/bioinformatics.scm (cutadapt)[arguments]: Use ‘modify-phases’. Tobias Geerinckx-Rice
2016-12-19gnu: cutadapt: Update to 1.12.•••* gnu/packages/bioinformatics.scm (cutadapt): Update to 1.12. [inputs]: Add python-xopen. Tobias Geerinckx-Rice
2016-12-18gnu: Add attribution line for Raoul Bonnal.•••This is a follow-up commit to c9e9154e993f055a438e2e43518bbd0740aaaf24. * gnu/packages/bioinformatics.scm: Add attribution. Ben Woodcroft
2016-12-17gnu: star: Update to 2.5.2b.•••* gnu/packages/bioinformatics (star): Update to 2.5.2b. [source]: Delete precompiled binary. Co-authored-by: Ben Woodcroft <donttrustben@gmail.com> Raoul Bonnal
2016-12-16gnu: pbtranscript-tofu: Disable tests.•••* gnu/packages/bioinformatics.scm (pbtranscript-tofu)[arguments]: Set #:tests? #f. Marius Bakke
2016-12-16gnu: multiqc: Fix test dependencies.•••* gnu/packages/bioinformatics.scm (multiqc)[native-inputs]: Add python-nose. Marius Bakke
2016-12-16gnu: idr: Remove explicit wrapper. This is now done implicitly.•••* gnu/packages/bioinformatics.scm (idr)[arguments]: Remove #:phases. Marius Bakke
2016-12-16gnu: idr: Correct inputs.•••* gnu/packages/bioinformatics.scm (idr)[inputs]: Move everything from here ... [propagated-inputs]: ... to here. Add python-sympy. Marius Bakke
2016-12-16gnu: idr: Disable tests.•••* gnu/packages/bioinformatics.scm (idr)[arguments]: Set #:tests? #f. Marius Bakke
2016-12-16gnu: deeptools: Fix test dependency.•••* gnu/packages/bioinformatics.scm (deeptools)[native-inputs]: Add python-nose. Marius Bakke
2016-12-16gnu: clipper: Fix test dependency.•••* gnu/packages/bioinformatics.scm (clipper)[native-inputs]: Add python2-nose. Marius Bakke
2016-12-14gnu: Update more dead Google Code home pages.•••* gnu/packages/bioinformatics.scm (cutadapt, mosaik, pepr)[home-page]: Update to their respective replacements. Tobias Geerinckx-Rice
2016-12-14gnu: python-biom-format: Fix tests.•••* gnu/packages/bioinformatics.scm (python-biom-format, python2-biom-format)[native-inputs]: Add python-nose. Marius Bakke
2016-12-13gnu: diamond: Update to 0.8.29.•••* gnu/packages/bioinformatics.scm (diamond): Update to 0.8.29. Ben Woodcroft
2016-12-13gnu: orfm: Update to 0.6.1.•••* gnu/packages/bioinformatics.scm (orfm): Update to 0.6.1. Ben Woodcroft
2016-12-12gnu: orfm: Update to 0.6.0.•••* gnu/packages/bioinformatics.scm (orfm): Update to 0.6.0. Ben Woodcroft
2016-12-10gnu: vsearch: Update to 2.3.4.•••* gnu/packages/bioinformatics.scm (vsearch): Update to 2.3.4. Ben Woodcroft
2016-12-10gnu: pardre: Update to 1.1.5-1.•••* gnu/packages/bioinformatics.scm (pardre): update to 1.1.5-1. [source]: Update source hash. Ben Woodcroft
2016-12-08gnu: vsearch: Update to 2.3.3.•••* gnu/packages/bioinformatics.scm (vsearch): Update to 2.3.3. Ben Woodcroft
2016-12-04gnu: aragorn: Update to 1.2.38.•••* gnu/packages/bioinformatics.scm (aragorn): Update to 1.2.38. Ben Woodcroft
2016-11-29Merge branch 'master' into python-build-systemHartmut Goebel
2016-11-28gnu: Add r-gkmsvm.•••* gnu/packages/bioinformatics.scm (r-gkmsvm): New variable. Ricardo Wurmus
2016-11-28gnu: Add r-seqgl.•••* gnu/packages/bioinformatics.scm (r-seqgl): New variable. Ricardo Wurmus
2016-11-28gnu: Add r-chipkernels.•••* gnu/packages/bioinformatics.scm (r-chipkernels): New variable. Ricardo Wurmus
2016-11-28gnu: Add r-wgcna.•••* gnu/packages/bioinformatics.scm (r-wgcna): New variable. Ricardo Wurmus
2016-11-28gnu: Add r-r4rna.•••* gnu/packages/bioinformatics.scm (r-r4rna): New variable. Ricardo Wurmus
2016-11-28gnu: Add newick-utils.•••* gnu/packages/bioinformatics.scm (newick-utils): New variable. Ben Woodcroft
2016-11-26gnu: roary: Update to 3.7.0.•••* gnu/packages/bioinformatics.scm (roary): Update to 3.7.0. Ben Woodcroft
2016-11-26gnu: Add proteinortho.•••* gnu/packages/bioinformatics.scm (proteinortho): New variable. Ben Woodcroft
2016-11-25Merge branch 'master' into python-build-systemLeo Famulari
2016-11-22gnu: diamond: Update to 0.8.27.•••* gnu/packages/bioinformatics.scm (diamond): Update to 0.8.27. Ben Woodcroft
2016-11-21gnu: Remove redundancy where mkdir-p <dir> is followed by install-file <file>...•••* 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> Petter
2016-11-15gnu: python2-pbcore: Fix inputs:•••* 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]. Hartmut Goebel
2016-11-15gnu: python2-warpedlmm: Remove phase remove-bin-directory.•••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. Hartmut Goebel
2016-11-15gnu: Fix python inputs, part 7: Ensure python-cython is a native-input.•••* 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. Hartmut Goebel
2016-11-15gnu: Fix python inputs, part 1: all inputs become propagated-inputs.•••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 Hartmut Goebel