| Commit message (Expand) | Author | Age | Files | Lines |
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| * | gnu: java-picard-1.113: Use ant/java8.•••* gnu/packages/bioinformatics.scm (java-picard-1.113)[arguments]: Use
ant/java8.
[inputs]: Replace ant with ant/java8.
| Ricardo Wurmus | 2020-12-01 | 1 | -1/+2 |
| * | gnu: pigx-chipseq: Update to 0.0.51.•••* gnu/packages/bioinformatics.scm (pigx-chipseq): Update to 0.0.51.
[inputs]: Add r-corrplot, r-deseq2, r-dt, r-ggrepel, r-gprofiler2, r-pheatmap,
and r-rsubread.
| Ricardo Wurmus | 2020-11-30 | 1 | -8/+15 |
| * | gnu: pigx-scrnaseq: Update to 1.1.7.•••* gnu/packages/bioinformatics.scm (pigx-scrnaseq): Update to 1.1.7.
| Ricardo Wurmus | 2020-11-30 | 1 | -2/+2 |
| * | Merge branch 'master' into staging | Marius Bakke | 2020-11-26 | 1 | -26/+53 |
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| | * | 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 | 1 | -15/+18 |
| | * | 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 | 2020-11-24 | 1 | -11/+35 |
| * | | Merge branch 'master' into staging | Marius Bakke | 2020-11-23 | 1 | -1/+131 |
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| | * | gnu: Add cwltool.•••* gnu/packages/bioinformatics.scm (cwltool): New variable.
| Efraim Flashner | 2020-11-23 | 1 | -0/+91 |
| | * | gnu: Add python-schema-salad.•••* gnu/packages/bioinformatics.scm (python-schema-salad): New variable.
| Efraim Flashner | 2020-11-23 | 1 | -1/+40 |
| * | | Merge branch 'master' into staging | Marius Bakke | 2020-11-15 | 1 | -7/+70 |
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| | * | 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 | 2020-11-15 | 1 | -3/+6 |
| | * | 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 | 1 | -1/+1 |
| | * | gnu: Add bcftools-1.9.•••* gnu/packages/bioinformatics.scm (bcftools-1.9): New variable.
| Roel Janssen | 2020-11-13 | 1 | -2/+24 |
| | * | 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 | 1 | -1/+1 |
| | * | gnu: Add samtools-1.9.•••* gnu/packages/bioinformatics.scm (samtools-1.9): New variable.
| Roel Janssen | 2020-11-13 | 1 | -0/+25 |
| | * | gnu: Add htslib-1.9.•••* gnu/packages/bioinformatics.scm (htslib-1.9): New variable.
| Roel Janssen | 2020-11-13 | 1 | -0/+13 |
| * | | Merge branch 'master' into staging | Marius Bakke | 2020-11-11 | 1 | -9/+23 |
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| | * | 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 | 1 | -2/+15 |
| | * | 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 | 1 | -5/+6 |
| | * | gnu: macs: Update source, home-page URIs.•••* gnu/packages/bioinformatics.scm (macs)[source, home-page]: Update
URIs to new location.
| Efraim Flashner | 2020-11-09 | 1 | -2/+2 |
| * | | 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 | 2020-11-07 | 1 | -10/+11 |
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| | * | gnu: Update samtools to 1.11.•••* gnu/packages/bioinformatics.scm (samtools): Update to 1.11.
| Roel Janssen | 2020-10-29 | 1 | -3/+3 |
| | * | gnu: Update bcftools to 1.11.•••* gnu/packages/bioinformatics.scm (bcftools): Update to 1.11.
| Roel Janssen | 2020-10-29 | 1 | -3/+3 |
| | * | gnu: Update htslib to 1.11.•••* gnu/packages/bioinformatics.scm (htslib): Update to 1.11.
| Roel Janssen | 2020-10-29 | 1 | -2/+2 |
| | * | gnu: imp: Update to 2.13.0.•••* gnu/packages/bioinformatics.scm (imp): Update to 2.13.0.
| Ludovic Courtès | 2020-10-23 | 1 | -2/+3 |
| * | | 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 | 1 | -1/+0 |
| * | | Merge branch 'master' into staging | Marius Bakke | 2020-10-13 | 1 | -6/+13 |
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| | * | gnu: htslib: Enable support for custom URI schemes.•••* gnu/packages/bioinformatics.scm (htslib)[arguments]: Enable support for custom URIs.
| Roel Janssen | 2020-10-07 | 1 | -0/+7 |
| | * | gnu: r-gqtlbase: Update to 1.20.4.•••* gnu/packages/bioinformatics.scm (r-gqtlbase): Update to 1.20.4.
| Ricardo Wurmus | 2020-10-06 | 1 | -2/+2 |
| | * | gnu: r-rhdf5: Update to 2.32.3.•••* gnu/packages/bioinformatics.scm (r-rhdf5): Update to 2.32.3.
| Ricardo Wurmus | 2020-10-06 | 1 | -2/+2 |
| | * | gnu: r-biocstyle: Update to 2.16.1.•••* gnu/packages/bioinformatics.scm (r-biocstyle): Update to 2.16.1.
| Ricardo Wurmus | 2020-10-06 | 1 | -2/+2 |
| * | | Merge branch 'master' into staging | Guillaume Le Vaillant | 2020-10-05 | 1 | -342/+5 |
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| | * | 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 | 2020-09-25 | 1 | -3/+3 |
| | * | gnu: mafft: Use HTTPS home page URI.•••* gnu/packages/bioinformatics.scm (mafft)[home-page, license]: Use HTTPS URI.
| Nicolas Goaziou | 2020-09-22 | 1 | -2/+2 |
| | * | 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 | 1 | -26/+0 |
| | * | 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 | 1 | -29/+0 |
| | * | 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 | 1 | -30/+0 |
| | * | 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 | 1 | -82/+0 |
| | * | 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 | 1 | -25/+0 |
| | * | 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 | 1 | -29/+0 |
| | * | 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 | 1 | -37/+0 |
| | * | 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 | 1 | -43/+0 |
| | * | 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 | 2020-09-14 | 1 | -36/+0 |
| * | | Merge branch 'staging' into wip-lisp | Guillaume Le Vaillant | 2020-09-23 | 1 | -1/+1 |
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| | * | Merge remote-tracking branch 'origin/master' into staging | Efraim Flashner | 2020-09-05 | 1 | -111/+303 |
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| | * | | gnu: check: Update to 0.15.1.•••* gnu/packages/check.scm (check): Update to 0.15.1.
(check-0.14): New public variable.
* gnu/packages/backup.scm (burp)[native-inputs]: Change from CHECK to
CHECK-0.14.
* gnu/packages/bioinformatics.scm (libsbml)[native-inputs]: Likewise.
* gnu/packages/databases.scm (recutils)[native-inputs]: Likewise.
* gnu/packages/electronics.scm (libsigrokdecode)[native-inputs]: Likewise.
* gnu/packages/enlightenment.scm (efl, edi)[native-inputs]: Likewise.
* gnu/packages/gnome.scm (gdm)[inputs]: Likewise.
* gnu/packages/gtk.scm (girara)[native-inputs]: Likewise.
* gnu/packages/messaging.scm (pidgin)[native-inputs]: Likewise.
* gnu/packages/networking.scm (iodine)[native-inputs]: Likewise.
* gnu/packages/pulseaudio.scm (pulseaudio)[native-inputs]: Likewise.
* gnu/packages/sssd.scm (sssd)[native-inputs]: Likewise.
* gnu/packages/web.scm (libwapcaplet)[native-inputs]: Likewise.
| Marius Bakke | 2020-07-25 | 1 | -1/+1 |
| * | | | 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 | 1 | -27/+0 |
| * | | | 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 | 1 | -31/+0 |
| * | | | 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 | 1 | -28/+0 |
| * | | | 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 | 1 | -65/+0 |
