Age | Commit message (Expand) | Author |
2020-12-23 | gnu: discrover: Use new texlive package names....* gnu/packages/bioinformatics.scm (discrover)[native-inputs]: Replace
"texlive-fonts-cm" and "texlive-fonts-amsfonts" with their new names
"texlive-cm" and "texlive-amsfonts", respectively.
| Ricardo Wurmus |
2020-12-23 | gnu: discrover: Remove obsolete build phase....* gnu/packages/bioinformatics.scm (discrover)[arguments]: Remove obsolete
build phase setenv-HOME.
| Ricardo Wurmus |
2020-11-26 | Merge branch 'master' into staging | Marius Bakke |
2020-11-24 | gnu: tadbit: Update to 1.0.1....* gnu/packages/bioinformatics.scm (tadbit): Update to 1.0.1.
[arguments]: Remove #:tests? and #:python arguments.
[phases]{fix-problems-with-setup.py}: Remove no longer needed steps.
{check}: Override phase.
[native-inputs]: Add glib and pkg-config.
[inputs]: Add python-future and python-h5py.
| Maxim Cournoyer |
2020-11-24 | gnu: imp: Migrate to Python 3....* gnu/packages/bioinformatics.scm (imp)
[arguments]: Enable tests by removing the #:tests? argument.
Specify the arguments to pass to the ctest test running via the
#:configure-flags argument.
[inputs]: Add cgal and opencv. Remove python-2. Move swig to...
[native-inputs]: ...here. Add python-wrapper.
[propagated-inputs]: Replace python2-numpy, python2-scipy, python2-pandas,
python2-scikit-learn and python2-networkx by python-numpy, python-scipy,
python-pandas, python-scikit-learn and python-networkx, respectively.
| Maxim Cournoyer |
2020-11-23 | Merge branch 'master' into staging | Marius Bakke |
2020-11-23 | gnu: Add cwltool....* gnu/packages/bioinformatics.scm (cwltool): New variable.
| Efraim Flashner |
2020-11-23 | gnu: Add python-schema-salad....* gnu/packages/bioinformatics.scm (python-schema-salad): New variable.
| Efraim Flashner |
2020-11-15 | Merge branch 'master' into staging | Marius Bakke |
2020-11-15 | gnu: methyldackel: Update to 0.5.1....* gnu/packages/bioinformatics.scm (methyldackel): Update to 0.5.1.
[arguments]: Link with libbigwig.
[inputs]: Add curl and libbigwig; replace htslib with htslib-1.9.
| Ricardo Wurmus |
2020-11-13 | gnu: Fix build for python-pysam....* gnu/packages/bioinformatics.scm (python-pysam): Use htslib-1.9,
samtools-1.9, and bcftools-1.9.
| Roel Janssen |
2020-11-13 | gnu: Add bcftools-1.9....* gnu/packages/bioinformatics.scm (bcftools-1.9): New variable.
| Roel Janssen |
2020-11-13 | gnu: bedtools: Use samtools-1.9....The build for bedtools with samtools 1.11 triggers a testsuite
failure which is reported here:
https://github.com/arq5x/bedtools2/issues/814
* gnu/packages/bioinformatics.scm (bedtools): Use samtools-1.9.
| Roel Janssen |
2020-11-13 | gnu: Add samtools-1.9....* gnu/packages/bioinformatics.scm (samtools-1.9): New variable.
| Roel Janssen |
2020-11-13 | gnu: Add htslib-1.9....* gnu/packages/bioinformatics.scm (htslib-1.9): New variable.
| Roel Janssen |
2020-11-11 | Merge branch 'master' into staging | Marius Bakke |
2020-11-09 | gnu: macs: Remove generated code....* gnu/packages/bioinformatics.scm (macs)[source]: Add snippet to remove
cython generated code.
[native-inputs]: Add python-cython.
| Efraim Flashner |
2020-11-09 | gnu: macs: Update check phase....* gnu/packages/bioinformatics.scm (macs)[arguments]: Don't delete 'check
phase before using custom 'check phase.
| Efraim Flashner |
2020-11-09 | gnu: macs: Update source, home-page URIs....* gnu/packages/bioinformatics.scm (macs)[source, home-page]: Update
URIs to new location.
| Efraim Flashner |
2020-11-07 | Merge branch 'master' into staging... Conflicts:
gnu/local.mk
gnu/packages/gdb.scm
gnu/packages/lisp-xyz.scm
gnu/packages/web-browsers.scm
| Marius Bakke |
2020-10-29 | gnu: Update samtools to 1.11....* gnu/packages/bioinformatics.scm (samtools): Update to 1.11.
| Roel Janssen |
2020-10-29 | gnu: Update bcftools to 1.11....* gnu/packages/bioinformatics.scm (bcftools): Update to 1.11.
| Roel Janssen |
2020-10-29 | gnu: Update htslib to 1.11....* gnu/packages/bioinformatics.scm (htslib): Update to 1.11.
| Roel Janssen |
2020-10-23 | gnu: imp: Update to 2.13.0....* gnu/packages/bioinformatics.scm (imp): Update to 2.13.0.
| Ludovic Courtès |
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 |