| Age | Commit message (Expand) | Author |
|---|
| 2020-05-05 | Merge branch 'master' into core-updates | Marius Bakke |
| 2020-05-05 | gnu: Add grocsvs....* gnu/packages/bioinformatics.scm (grocsvs): New variable.
* gnu/packages/patches/grocsvs-dont-use-admiral.patch: New file.
* gnu/local.mk (dist_patch_DATA): Register it.
| Efraim Flashner |
| 2020-04-30 | Merge branch 'master' into core-updates... Conflicts:
gnu/local.mk
gnu/packages/backup.scm
gnu/packages/emacs-xyz.scm
gnu/packages/guile.scm
gnu/packages/lisp.scm
gnu/packages/openldap.scm
gnu/packages/package-management.scm
gnu/packages/web.scm
gnu/packages/xorg.scm
| Marius Bakke |
| 2020-04-30 | gnu: Add miniasm....* gnu/packages/bioinformatics.scm (miniasm): New variable.
| Roel Janssen |
| 2020-04-30 | gnu: python2-warpedlmm: Fix build....* gnu/packages/bioinformatics.scm (python2-warpedlmm)[propagated-inputs]: Add
python2-weave.
[arguments]: Disable tests and add "use-weave" phase.
| Ricardo Wurmus |
| 2020-04-28 | gnu: Add variant-tools....* gnu/packages/bioinformatics.scm (variant-tools): New variable.
| Ricardo Wurmus |
| 2020-04-28 | gnu: r-hdf5array: Update to 1.14.4....* gnu/packages/bioinformatics.scm (r-hdf5array): Update to 1.14.4.
| Ricardo Wurmus |
| 2020-04-28 | gnu: r-seurat: Update to 3.1.5....* gnu/packages/bioinformatics.scm (r-seurat): Update to 3.1.5.
[propagated-inputs]: Remove r-metap.
| Ricardo Wurmus |
| 2020-04-27 | gnu: Update minimap2 to 2.17....* gnu/packages/bioinformatics.scm (minimap2): Update to 2.17.
| Roel Janssen |
| 2020-04-27 | gnu: Add python-deeptools....* gnu/packages/bioinformatics.scm (python-deeptools): New variable.
| Roel Janssen |
| 2020-04-27 | gnu: Add python-deeptoolsintervals....* gnu/packages/bioinformatics.scm (python-deeptoolsintervals): New variable.
| Roel Janssen |
| 2020-04-26 | gnu: python-scanpy: Update to 1.4.6....* gnu/packages/bioinformatics.scm (python-scanpy): Update to 1.4.6.
[arguments]: Add another network based test to skip.
[propagated-inputs]: Add python-tqdm.
| Efraim Flashner |
| 2020-04-19 | Merge branch 'master' into core-updates | Marius Bakke |
| 2020-04-17 | gnu: python-pygenometracks: Update to 3.3....* gnu/packages/bioinformatics.scm (python-pygenometracks): Update to 3.3.
[arguments]: Add phase "relax-requirements"; disable tests.
[propagated-inputs]: Remove python-configparser and python-hicexplorer; add
python-gffutils, python-pysam, and python-tqdm.
| Ricardo Wurmus |
| 2020-04-17 | gnu: Add python-hicmatrix....* gnu/packages/bioinformatics.scm (python-hicmatrix): New variable.
| Ricardo Wurmus |
| 2020-04-17 | gnu: python-cooler: Update to 0.8.7....* gnu/packages/bioinformatics.scm (python-cooler): Update to 0.8.7.
[propagated-inputs]: Add python-asciitree, python-numpy, python-pyyaml, and
python-simplejson.
[native-inputs]: Remove python-nose, python-numpydoc, and python-sphinx; add
python-pytest.
| Ricardo Wurmus |
| 2020-04-17 | gnu: python-pybigwig: Update to 0.3.17....* gnu/packages/bioinformatics.scm (python-pybigwig): Update to 0.3.17.
| Ricardo Wurmus |
| 2020-04-15 | Merge branch 'master' into core-updates | Marius Bakke |
| 2020-04-14 | gnu: r-delayedarray: Update to 0.12.3....* gnu/packages/bioinformatics.scm (r-delayedarray): Update to 0.12.3.
[native-inputs]: Add r-knitr.
| Ricardo Wurmus |
| 2020-04-14 | gnu: r-s4vectors: Update to 0.24.4....* gnu/packages/bioinformatics.scm (r-s4vectors): Update to 0.24.4.
| Ricardo Wurmus |
| 2020-04-14 | gnu: pigx-chipseq: Update to 0.0.42....* gnu/packages/bioinformatics.scm (pigx-chipseq): Update to 0.0.42.
| Ricardo Wurmus |
| 2020-04-13 | Merge branch 'master' into core-updates | Marius Bakke |
| 2020-04-12 | gnu: r-bamsignals: Fix grammar of "allows to efficiently obtain" to..."efficiently obtains".
* gnu/packages/bioinformatics (r-bamsignals): Fix grammar.
| Vagrant Cascadian |
| 2020-04-12 | gnu: r-qtl: Fix grammar "allows to estimate" to "estimates"....* gnu/packages/bioinformatics (r-qtl): Fix grammar.
| Vagrant Cascadian |
| 2020-04-11 | Merge branch 'master' into core-updates | Marius Bakke |
| 2020-04-09 | gnu: minimap2: Fix cond expression for Guile 3 compatibility....* gnu/packages/bioinformatics.scm (minimap2)[arguments]: Make the last COND
test the symbol else instead of _.
| Marius Bakke |
| 2020-04-08 | Merge branch 'master' into core-updates... Conflicts:
etc/news.scm
gnu/local.mk
gnu/packages/check.scm
gnu/packages/cross-base.scm
gnu/packages/gimp.scm
gnu/packages/java.scm
gnu/packages/mail.scm
gnu/packages/sdl.scm
gnu/packages/texinfo.scm
gnu/packages/tls.scm
gnu/packages/version-control.scm
| Marius Bakke |
| 2020-04-05 | gnu: python-intervaltree: Update to 3.0.2....* gnu/packages/bioinformatics.scm (python-intervaltree): Update to 3.0.2.
[arguments]: Don't skip the tests, work around the problematic
sanity-check instead.
| Jakub Kądziołka |
| 2020-04-03 | gnu: sailfish: Fix build failure....* gnu/packages/bioinformatics.scm (sailfish)[arguments]: Prepend to
CPLUS_INCLUDE_PATH instead of overriding it.
| Marius Bakke |
| 2020-04-01 | gnu: r-biomart: Update to 2.42.1....* gnu/packages/bioinformatics.scm (r-biomart): Update to 2.42.1.
[native-inputs]: Add r-knitr.
| Ricardo Wurmus |
| 2020-04-01 | gnu: r-genomeinfodb: Update to 1.22.1....* gnu/packages/bioinformatics.scm (r-genomeinfodb): Update to 1.22.1.
[native-inputs]: Add r-knitr.
| Ricardo Wurmus |
| 2020-03-27 | Merge branch 'master' into core-updates... Conflicts:
gnu/packages/icu4c.scm
gnu/packages/man.scm
gnu/packages/python-xyz.scm
guix/scripts/environment.scm
guix/scripts/pack.scm
guix/scripts/package.scm
guix/scripts/pull.scm
guix/store.scm
| Marius Bakke |
| 2020-03-26 | gnu: Update sambamba to 0.7.1....* gnu/packages/bioinformatics.scm (sambamba): Update to 0.7.1;
Remove unneeded undead input.
| Roel Janssen |
| 2020-03-24 | gnu: r-tximport: Update to 1.14.2....* gnu/packages/bioinformatics.scm (r-tximport): Update to 1.14.2.
[native-inputs]: Add r-knitr.
| Ricardo Wurmus |
| 2020-03-22 | gnu: edirect: Install more programs....* gnu/packages/bioinformatics.scm (edirect)[arguments]: Add
'patch-programs phase to work around not finding binaries in the PATH.
Rewrite 'install phase to install many more scripts. Rewrite
'wrap-program to wrap more scripts with more programs.
[inputs]: Add edirect-go-programs.
[native-search-paths]: New field.
| Efraim Flashner |
| 2020-03-22 | gnu: Add edirect-go-programs....* gnu/packages/bioinformatics.scm (edirect-go-programs): New variable.
(edirect)[source]: Adjust snippet to not use non-free software.
| Efraim Flashner |
| 2020-03-18 | Merge branch 'master' into core-updates | Marius Bakke |
| 2020-03-14 | Merge branch 'master' into core-updates | Marius Bakke |
| 2020-03-17 | gnu: pigx-scrnaseq: Update to 1.1.4....* gnu/packages/bioinformatics.scm (pigx-scrnaseq): Update to 1.1.4.
| Ricardo Wurmus |
| 2020-03-16 | gnu: star: Update to 2.7.3a....* gnu/packages/bioinformatics.scm (star): Update to 2.7.3a.
| Ricardo Wurmus |
| 2020-03-13 | gnu: salmon: Adjust for C_INCLUDE_PATH changes....* gnu/packages/bioinformatics.scm (salmon)[arguments]: Append Eigen headers to
C_INCLUDE_PATH instead of CPATH.
| Marius Bakke |
| 2020-03-12 | gnu: edirect: Update to 13.3.20200128....* gnu/packages/bioinformatics.scm (edirect): Update to 13.3.20200128.
[source]: Remove bundled certificate authority tarball.
| Efraim Flashner |
| 2020-03-12 | gnu: r-qtl: Update to 1.46-2....* gnu/packages/bioinformatics.scm (r-qtl): Update to 1.46-2.
| Ricardo Wurmus |
| 2020-03-11 | gnu: python-pybedtools: Update to 0.8.1....* gnu/packages/bioinformatics.scm (python-pybedtools): Update to 0.8.1.
[arguments]: Add another test to the 'disable-broken-tests phase.
(python2-pybedtools)[native-inputs]: Add python2-pathlib.
| Efraim Flashner |
| 2020-03-11 | gnu: python-pyfaidx: Update to 0.5.8....* gnu/packages/bioinformatics.scm (python-pyfaidx): Update to 0.5.8.
| Efraim Flashner |
| 2020-03-11 | gnu: Add python2-pyfaidx....* gnu/packages/bioinformatics.scm (python2-pyfaidx): New variable.
| Efraim Flashner |
| 2020-03-10 | gnu: java-forester-1.005: Update source URI....* gnu/packages/bioinformatics.scm (java-forester-1.005)[source]: Update URI.
[native-inputs]: Wrap long line.
| Björn Höfling |
| 2020-03-09 | gnu: Fix build of python-velocyto....* gnu/packages/bioinformatics.scm (python-velocyto): Add python-joblib to
native-inputs to make the test suite run succesfully.
| Roel Janssen |
| 2020-03-08 | gnu: ngless: Update to 1.1.0....* gnu/packages/bioinformatics.scm (ngless): Update to 1.1.0.
| Ricardo Wurmus |
| 2020-03-08 | gnu: taxtastic: Update to 0.8.11....* gnu/packages/bioinformatics.scm (taxtastic): Update to 0.8.11.
[source]: Fetch from Github.
[arguments]: Build with default Python; add phases 'prepare-directory,
'python37-compatibility, and update 'check phase.
[propagated-inputs]: Replace Python 2 variants with Python 3 variants.
| Ricardo Wurmus |
