Age | Commit message (Expand) | Author |
2016-12-29 | gnu: r-genomicfeatures: Update to 1.26.2.•••* gnu/packages/bioinformatics.scm (r-genomicfeatures): Update to 1.26.2.
| Ricardo Wurmus |
2016-12-29 | gnu: r-biostrings: Update to 2.42.1.•••* gnu/packages/bioinformatics.scm (r-biostrings): Update to 2.42.1.
| Ricardo Wurmus |
2016-12-29 | gnu: r-limma: Update to 3.30.7.•••* gnu/packages/bioinformatics.scm (r-limma): Update to 3.30.7.
| Ricardo Wurmus |
2016-12-29 | gnu: r-variantannotation: Update to 1.20.2.•••* gnu/packages/bioinformatics.scm (r-variantannotation): Update to 1.20.2.
| Ricardo Wurmus |
2016-12-29 | gnu: r-edger: Update to 3.16.5.•••* gnu/packages/bioinformatics.scm (r-edger): Update to 3.16.5.
| Ricardo Wurmus |
2016-12-29 | gnu: r-genomeinfodb: Update to 1.10.1.•••* gnu/packages/bioinformatics.scm (r-genomeinfodb): Update to 1.10.1.
| Ricardo Wurmus |
2016-12-29 | gnu: r-iranges: Update to 2.8.1.•••* gnu/packages/bioinformatics.scm (r-iranges): Update to 2.8.1.
| Ricardo Wurmus |
2016-12-29 | gnu: r-s4vectors: Update to 0.12.1.•••* gnu/packages/bioinformatics.scm (r-s4vectors): Update to 0.12.1.
| Ricardo Wurmus |
2016-12-29 | gnu: r-biocstyle: Update to 2.2.1.•••* gnu/packages/bioinformatics.scm (r-biocstyle): Update to 2.2.1.
| Ricardo Wurmus |
2016-12-29 | gnu: r-deseq2: Update to 1.14.1.•••* gnu/packages/bioinformatics.scm (r-deseq2): Update to 1.14.1.
| Ricardo Wurmus |
2016-12-29 | gnu: 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 |
2016-12-29 | gnu: r-qtl: Update to 1.40-8.•••* gnu/packages/bioinformatics.scm (r-qtl): Update to 1.40-8.
| Ricardo Wurmus |
2016-12-27 | gnu: r-rcas: Update to 1.1.1.•••* gnu/packages/bioinformatics.scm (r-rcas): Update to 1.1.1.
[propagated-inputs]: Add plotrix.
| Ricardo Wurmus |
2016-12-27 | gnu: diamond: Update to 0.8.30.•••* gnu/packages/bioinformatics.scm (diamond): Update to 0.8.30.
| Ben Woodcroft |
2016-12-20 | gnu: cutadapt: Use ‘modify-phases’ syntax.•••* gnu/packages/bioinformatics.scm (cutadapt)[arguments]: Use
‘modify-phases’.
| Tobias Geerinckx-Rice |
2016-12-19 | gnu: cutadapt: Update to 1.12.•••* gnu/packages/bioinformatics.scm (cutadapt): Update to 1.12.
[inputs]: Add python-xopen.
| Tobias Geerinckx-Rice |
2016-12-18 | gnu: Add attribution line for Raoul Bonnal.•••This is a follow-up commit to c9e9154e993f055a438e2e43518bbd0740aaaf24.
* gnu/packages/bioinformatics.scm: Add attribution.
| Ben Woodcroft |
2016-12-17 | gnu: 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 |
2016-12-16 | gnu: pbtranscript-tofu: Disable tests.•••* gnu/packages/bioinformatics.scm (pbtranscript-tofu)[arguments]: Set #:tests? #f.
| Marius Bakke |
2016-12-16 | gnu: multiqc: Fix test dependencies.•••* gnu/packages/bioinformatics.scm (multiqc)[native-inputs]: Add python-nose.
| Marius Bakke |
2016-12-16 | gnu: idr: Remove explicit wrapper. This is now done implicitly.•••* gnu/packages/bioinformatics.scm (idr)[arguments]: Remove #:phases.
| Marius Bakke |
2016-12-16 | gnu: idr: Correct inputs.•••* gnu/packages/bioinformatics.scm (idr)[inputs]: Move everything from here ...
[propagated-inputs]: ... to here. Add python-sympy.
| Marius Bakke |
2016-12-16 | gnu: idr: Disable tests.•••* gnu/packages/bioinformatics.scm (idr)[arguments]: Set #:tests? #f.
| Marius Bakke |
2016-12-16 | gnu: deeptools: Fix test dependency.•••* gnu/packages/bioinformatics.scm (deeptools)[native-inputs]: Add python-nose.
| Marius Bakke |
2016-12-16 | gnu: clipper: Fix test dependency.•••* gnu/packages/bioinformatics.scm (clipper)[native-inputs]: Add python2-nose.
| Marius Bakke |
2016-12-14 | gnu: Update more dead Google Code home pages.•••* gnu/packages/bioinformatics.scm (cutadapt, mosaik, pepr)[home-page]:
Update to their respective replacements.
| Tobias Geerinckx-Rice |
2016-12-14 | gnu: python-biom-format: Fix tests.•••* gnu/packages/bioinformatics.scm (python-biom-format,
python2-biom-format)[native-inputs]: Add python-nose.
| Marius Bakke |
2016-12-13 | gnu: diamond: Update to 0.8.29.•••* gnu/packages/bioinformatics.scm (diamond): Update to 0.8.29.
| Ben Woodcroft |
2016-12-13 | gnu: orfm: Update to 0.6.1.•••* gnu/packages/bioinformatics.scm (orfm): Update to 0.6.1.
| Ben Woodcroft |
2016-12-12 | gnu: orfm: Update to 0.6.0.•••* gnu/packages/bioinformatics.scm (orfm): Update to 0.6.0.
| Ben Woodcroft |
2016-12-10 | gnu: vsearch: Update to 2.3.4.•••* gnu/packages/bioinformatics.scm (vsearch): Update to 2.3.4.
| Ben Woodcroft |
2016-12-10 | gnu: pardre: Update to 1.1.5-1.•••* gnu/packages/bioinformatics.scm (pardre): update to 1.1.5-1.
[source]: Update source hash.
| Ben Woodcroft |
2016-12-08 | gnu: vsearch: Update to 2.3.3.•••* gnu/packages/bioinformatics.scm (vsearch): Update to 2.3.3.
| Ben Woodcroft |
2016-12-04 | gnu: aragorn: Update to 1.2.38.•••* gnu/packages/bioinformatics.scm (aragorn): Update to 1.2.38.
| Ben Woodcroft |
2016-11-29 | Merge branch 'master' into python-build-system | Hartmut Goebel |
2016-11-28 | gnu: Add r-gkmsvm.•••* gnu/packages/bioinformatics.scm (r-gkmsvm): New variable.
| Ricardo Wurmus |
2016-11-28 | gnu: Add r-seqgl.•••* gnu/packages/bioinformatics.scm (r-seqgl): New variable.
| Ricardo Wurmus |
2016-11-28 | gnu: Add r-chipkernels.•••* gnu/packages/bioinformatics.scm (r-chipkernels): New variable.
| Ricardo Wurmus |
2016-11-28 | gnu: Add r-wgcna.•••* gnu/packages/bioinformatics.scm (r-wgcna): New variable.
| Ricardo Wurmus |
2016-11-28 | gnu: Add r-r4rna.•••* gnu/packages/bioinformatics.scm (r-r4rna): New variable.
| Ricardo Wurmus |
2016-11-28 | gnu: Add newick-utils.•••* gnu/packages/bioinformatics.scm (newick-utils): New variable.
| Ben Woodcroft |
2016-11-26 | gnu: roary: Update to 3.7.0.•••* gnu/packages/bioinformatics.scm (roary): Update to 3.7.0.
| Ben Woodcroft |
2016-11-26 | gnu: Add proteinortho.•••* gnu/packages/bioinformatics.scm (proteinortho): New variable.
| Ben Woodcroft |
2016-11-25 | Merge branch 'master' into python-build-system | Leo Famulari |
2016-11-22 | gnu: diamond: Update to 0.8.27.•••* gnu/packages/bioinformatics.scm (diamond): Update to 0.8.27.
| Ben Woodcroft |
2016-11-21 | gnu: 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 |
2016-11-15 | gnu: 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 |
2016-11-15 | gnu: 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 |
2016-11-15 | gnu: 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 |
2016-11-15 | gnu: 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 |