| Age | Commit message (Expand) | Author |
|---|
| 2020-10-13 | gnu: Remove redundant MariaDB inputs....For well-behaved build systems, including the "dev" output suffices.
* gnu/packages/bioinformatics.scm (kentutils)[inputs]: Remove MARIADB:LIB.
* gnu/packages/cran.scm (r-rmysql)[inputs]: Likewise.
* gnu/packages/databases.scm (python-mysqlclient, soci)[inputs]: Likewise.
* gnu/packages/qt.scm (qt-4, qtbase): Likewise.
* gnu/packages/ruby.scm (ruby-mysql2)[inputs]: Likewise.
| Marius Bakke |
| 2020-10-13 | Merge branch 'master' into staging | Marius Bakke |
| 2020-10-07 | gnu: htslib: Enable support for custom URI schemes....* gnu/packages/bioinformatics.scm (htslib)[arguments]: Enable support for custom URIs.
| Roel Janssen |
| 2020-10-06 | gnu: r-gqtlbase: Update to 1.20.4....* gnu/packages/bioinformatics.scm (r-gqtlbase): Update to 1.20.4.
| Ricardo Wurmus |
| 2020-10-06 | gnu: r-rhdf5: Update to 2.32.3....* gnu/packages/bioinformatics.scm (r-rhdf5): Update to 2.32.3.
| Ricardo Wurmus |
| 2020-10-06 | gnu: r-biocstyle: Update to 2.16.1....* gnu/packages/bioinformatics.scm (r-biocstyle): Update to 2.16.1.
| Ricardo Wurmus |
| 2020-10-05 | Merge branch 'master' into staging | Guillaume Le Vaillant |
| 2020-09-25 | gnu: mafft: Update to 7.471....* gnu/packages/bioinformatics.scm (mafft): Update to 7.471.
Signed-off-by: Mathieu Othacehe <othacehe@gnu.org>
| Mădălin Ionel Patrașcu |
| 2020-09-23 | Merge branch 'staging' into wip-lisp | Guillaume Le Vaillant |
| 2020-09-22 | gnu: mafft: Use HTTPS home page URI....* gnu/packages/bioinformatics.scm (mafft)[home-page, license]: Use HTTPS URI.
| Nicolas Goaziou |
| 2020-09-14 | gnu: r-fithic: Move to (gnu packages bioconductor)....* gnu/packages/bioinformatics.scm (r-fithic): Move from here...
* gnu/packages/bioconductor.scm (r-fithic): ...to here.
Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
| zimoun |
| 2020-09-14 | gnu: r-hitc: Move to (gnu packages bioconductor)....* gnu/packages/bioinformatics.scm (r-hitc): Move from here...
* gnu/packages/bioconductor.scm (r-hitc): ...to here.
Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
| zimoun |
| 2020-09-14 | gnu: r-hdf5array: Move to (gnu packages bioconductor)....* gnu/packages/bioinformatics.scm (r-hdf5array): Move from here...
* gnu/packages/bioconductor.scm (r-hdf5array): ...to here.
Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
| zimoun |
| 2020-09-14 | gnu: r-rhdf5lib: Move to (gnu packages bioconductor)....* gnu/packages/bioinformatics.scm (r-rhdf5lib): Move from here...
* gnu/packages/bioconductor.scm (r-rhdf5lib): ...to here.
Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
| zimoun |
| 2020-09-14 | gnu: r-beachmat: Move to (gnu packages bioconductor)....* gnu/packages/bioinformatics.scm (r-beachmat): Move from here...
* gnu/packages/bioconductor.scm (r-beachmat): ...to here.
Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
| zimoun |
| 2020-09-14 | gnu: r-singlecellexperiment: Move to (gnu packages bioconductor)....* gnu/packages/bioinformatics.scm (r-singlecellexperiment): Move from here...
* gnu/packages/bioconductor.scm (r-singlecellexperiment): ...to here.
Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
| zimoun |
| 2020-09-14 | gnu: r-scater: Move to (gnu packages bioconductor)....* gnu/packages/bioinformatics.scm (r-scater): Move from here...
* gnu/packages/bioconductor.scm (r-scater): ...to here.
Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
| zimoun |
| 2020-09-14 | gnu: r-scran: Move to (gnu packages bioconductor)....* gnu/packages/bioinformatics.scm (r-scran): Move from here...
* gnu/packages/bioconductor.scm (r-scran): ...to here.
Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
| zimoun |
| 2020-09-14 | gnu: r-delayedmatrixstats: Move to (gnu packages bioconductor)....* gnu/packages/bioinformatics.scm (r-delayedmatrixstats): Move from here...
* gnu/packages/bioconductor.scm (r-delayedmatrixstats): ...to here.
Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
| zimoun |
| 2020-09-11 | gnu: r-absfiltergsea: Move to (gnu packages cran)....* gnu/packages/bioinformatics.scm (r-absfiltergsea): Move from here...
* gnu/packages/cran.scm (r-absfiltergsea): ...to here.
Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
| zimoun |
| 2020-09-11 | gnu: r-diversitree: Move to (gnu packages cran)....* gnu/packages/bioinformatics.scm (r-diversitree): Move from here...
* gnu/packages/cran.scm (r-diversitree): ...to here.
Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
| zimoun |
| 2020-09-11 | gnu: r-phangorn: Move to (gnu packages cran)....* gnu/packages/bioinformatics.scm (r-phangorn): Move from here...
* gnu/packages/cran.scm (r-phangorn): ...to here.
Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
| zimoun |
| 2020-09-11 | gnu: r-seurat: Move to (gnu packages cran)....* gnu/packages/bioinformatics.scm (r-seurat): Move from here...
* gnu/packages/cran.scm (r-seurat): ...to here.
Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
| zimoun |
| 2020-09-11 | gnu: r-maldiquant: Move to (gnu packages cran)....* gnu/packages/bioinformatics.scm (r-maldiquant): Move from here...
* gnu/packages/cran.scm (r-maldiquant): ...to here.
Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
| zimoun |
| 2020-09-11 | gnu: r-seqminer: Move to (gnu packages cran)....* gnu/packages/bioinformatics.scm (r-seqminer): Move from here...
* gnu/packages/cran.scm (r-seqminer): ...to here.
Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
| zimoun |
| 2020-09-11 | gnu: r-qtl2: Move to (gnu packages cran)....* gnu/packages/bioinformatics.scm (r-qtl2): Move from here...
* gnu/packages/cran.scm (r-qtl2): ...to here.
Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
| zimoun |
| 2020-09-11 | gnu: r-qtl: Move to (gnu packages cran)....* gnu/packages/bioinformatics.scm (r-qtl): Move from here...
* gnu/packages/cran.scm (r-qtl): ...to here.
Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
| zimoun |
| 2020-09-10 | gnu: Move r-bisquerna....* gnu/packages/bioinformatics.scm (r-bisquerna): Move to ...
* gnu/packages/cran.scm: ... here.
| Roel Janssen |
| 2020-09-09 | Revert "gnu: Add r-loomr."...This reverts commit 1f56ec08af704bdc7aa3e143bf5ce351c5306dea.
This package is not free software.
| Ricardo Wurmus |
| 2020-09-09 | gnu: Add r-bisquerna....* gnu/packages/bioinformatics.scm (r-bisquerna): New variable.
| Roel Janssen |
| 2020-09-09 | gnu: Add r-loomr....* gnu/packages/bioinformatics.scm (r-loomr): New variable.
| Roel Janssen |
| 2020-09-05 | gnu: seqmagick: Update to 0.8.0....* gnu/packages/bioinformatics.scm (seqmagick): Update to 0.8.0.
| Andreas Enge |
| 2020-09-05 | Merge remote-tracking branch 'origin/master' into staging | Efraim Flashner |
| 2020-08-30 | gnu: delly: Update to 0.8.3....* gnu/packages/bioinformatics.scm (delly): Update to 0.8.3.
[inputs]: Order alphabetically.
| Efraim Flashner |
| 2020-08-27 | gnu: vcflib: Install pkgconfig file....* gnu/packages/bioinformatics.scm (vcflib)[arguments]: Adjust custom
'install phase to add vcflib.pc.
| Efraim Flashner |
| 2020-08-27 | gnu: vcflib: Use shared libraries....* gnu/packages/bioinformatics.scm (vcflib)[source]: Add patch. Add
snippet to adjust files for new locations.
[inputs]: Add fastahack, smithwaterman, tabixpp, xz.
[native-inputs]: Add pkg-config. Remove the package-source of fastahack,
fsom, smithwaterman, tabixpp.
[arguments]: Remove make-flags. Add custom phase to add the output lib
directory to the rpath. Adjust custom 'unpack-submodule-sources for the
change in native-inputs. Adjust custom 'install phase to also install
libraries and headers.
* gnu/packages/patches/vcflib-use-shared-libraries.patch: New file.
* gnu/local.mk (dist_patch_DATA): Register it.
| Efraim Flashner |
| 2020-08-27 | gnu: fastahack: Install pkgconfig file....* gnu/packages/bioinformatics.scm (fastahack)[arguments]: Adjust custom
'install phase to add fastahack.pc.
| Efraim Flashner |
| 2020-08-27 | gnu: fastahack: Build and install shared library and headers....* gnu/packages/bioinformatics.scm (fastahack)[arguments]: Add phase to
build PIE objects. Add custom phase to build dynamic library. Adjust
custom 'install phase to install shared library and headers.
| Efraim Flashner |
| 2020-08-27 | gnu: smithwaterman: Install pkgconfig file....* gnu/packages/bioinformatics.scm (smithwaterman)[arguments]: Adjust
custom 'install phase to add smithwaterman.pc file.
| Efraim Flashner |
| 2020-08-27 | gnu: smithwaterman: Build and install shared library and headers....* gnu/packages/bioinformatics.scm (smithwaterman)[arguments]: Add custom
phase to build PIE objects. Add custom 'build-dynamic phase to build
dynamic library. Adjust custom 'install phase to install shared library
and headers.
| Efraim Flashner |
| 2020-08-27 | gnu: tabixpp: Install pkgconfig file....* gnu/packages/bioinformatics.scm (tabixpp)[arguments]: Adjust custom
'install phase to add tabixpp.pc file.
| Efraim Flashner |
| 2020-08-27 | gnu: tabixpp: Build and install shared library and headers....* gnu/packages/bioinformatics.scm (tabixpp)[arguments]: Adjust custom
'build phase to build shared library. Adjust custom 'install phase to
install libraries and header.
| Efraim Flashner |
| 2020-08-20 | gnu: r-complexheatmap: Update to 2.4.3....* gnu/packages/bioinformatics.scm (r-complexheatmap): Update to 2.4.3.
| Ricardo Wurmus |
| 2020-08-20 | gnu: r-gage: Update to 2.38.3....* gnu/packages/bioinformatics.scm (r-gage): Update to 2.38.3.
[propagated-inputs]: Add r-go-db.
| Ricardo Wurmus |
| 2020-08-20 | gnu: r-annotationhub: Update to 2.20.2....* gnu/packages/bioinformatics.scm (r-annotationhub): Update to 2.20.2.
| Ricardo Wurmus |
| 2020-08-20 | gnu: r-delayedarray: Update to 0.14.1....* gnu/packages/bioinformatics.scm (r-delayedarray): Update to 0.14.1.
| Ricardo Wurmus |
| 2020-08-20 | gnu: r-annotationdbi: Update to 1.50.3....* gnu/packages/bioinformatics.scm (r-annotationdbi): Update to 1.50.3.
| Ricardo Wurmus |
| 2020-08-20 | gnu: r-biocviews: Update to 1.56.2....* gnu/packages/bioinformatics.scm (r-biocviews): Update to 1.56.2.
| Ricardo Wurmus |
| 2020-08-19 | gnu: pigx-chipseq: Update to 0.0.43....* gnu/packages/bioinformatics.scm (pigx-chipseq): Update to 0.0.43.
| Ricardo Wurmus |
| 2020-08-18 | gnu: bowtie1: Add missing Python input....Reported-by: Marcel Schilling <marcel.schilling@mdc-berlin.de>
* gnu/packages/bioinformatics.scm (bowtie1)[inputs]: Add python-wrapper.
| Ricardo Wurmus |
