| Age | Commit message (Expand) | Author |
|---|
| 2021-07-26 | gnu: Add seqan 3....* gnu/packages/bioinformatics.scm (seqan): Rename this variable...
(seqan-2): ...to this.
(seqan): New variable for seqan3.
(flexbar)[native-inputs]: Update name for seqan 2.
| Ricardo Wurmus |
| 2021-07-26 | gnu: Add segemehl....* gnu/packages/bioinformatics.scm (segemehl): New variable.
| Ricardo Wurmus |
| 2021-07-22 | gnu: python-pysam: Make the check phase honor the tests? argument....* gnu/packages/bioinformatics.scm (python-pysam)[arguments]: Adjust
custom 'check phase to skip tests when #:tests is #f.
| Efraim Flashner |
| 2021-07-22 | gnu: python-pysam: Update to 0.16.0.1....* gnu/packages/bioinformatics.scm (python-pysam): Update to 0.16.0.1.
[arguments]: Update custom 'check phase.
[propagated-inputs]: Replace htslib-1.9 with 1.10.
[native-inputs]: Add python-pytest. Replace samtools-1.9 with 1.10,
bcftools-1.9 with 1.10.
(bcftools-1.9): Replace with bcftools-1.10.
[native-inputs]: Replace htslib-1.9 with 1.10.
(samtools-1.9): Replace with samtools-1.10.
[inputs]: Replace htslib-1.9 with 1.10.
| Efraim Flashner |
| 2021-07-22 | gnu: Add htslib-1.10....* gnu/packages/bioinformatics.scm (htslib-1.10): New variable.
| Efraim Flashner |
| 2021-07-22 | gnu: python-biopython: Update to 1.73....* gnu/packages/bioinformatics.scm (python-biopython): Update to 1.73.
| Efraim Flashner |
| 2021-07-21 | gnu: Add r-battenberg....* gnu/packages/bioinformatics.scm (r-battenberg): New variable.
| Lars-Dominik Braun |
| 2021-07-21 | gnu: Add r-ascat....* gnu/packages/bioinformatics.scm (r-ascat): New variable.
| Lars-Dominik Braun |
| 2021-07-21 | gnu: Add nanosv....* gnu/packages/bioinformatics.scm (nanosv): New variable.
| Lars-Dominik Braun |
| 2021-07-21 | gnu: Add python-pyvcf....* gnu/packages/bioinformatics.scm (python-pyvcf): New variable.
| Lars-Dominik Braun |
| 2021-07-21 | gnu: checkm: Rename and update to 1.1.3....Renamed from python2-checkm-genome to checkm to better reflect its
status as standalone-application and support for Python 3.
* gnu/packages/bioinformatics.scm (python2-checkm-genome): Redirect to…
(checkm): …here and update to 1.1.3.
[propagated-inputs]: Move to inputs.
[inputs]: Use Python 3 dependencies.
[home-page]: Point to real home-page.
| Lars-Dominik Braun |
| 2021-07-21 | gnu: Add tombo....* gnu/packages/bioinformatics.scm (tombo): New variable.
| Lars-Dominik Braun |
| 2021-07-05 | gnu: Add ocaml-sqlite3....* gnu/packages/ocaml.scm (ocaml-sqlite3): New variable.
(ocaml4.07-sqlite3): Inherit from ocaml-sqlite3.
* gnu/packages/bioinformatics.scm (pplacer): Also use package-with-ocaml4.07
with ocaml-sqlite3.
| Julien Lepiller |
| 2021-07-01 | gnu: bioperl-minimal: Avoid top-level cross-module references....This could lead to circular reference breakage.
* gnu/packages/bioinformatics.scm (bioperl-minimal): Move top-level
references to perl-* variables and their transitive inputs to
'arguments' and 'inputs'.
| Ludovic Courtès |
| 2021-07-01 | gnu: Do not import (gnu packages commencement)....Line introduced in 4efbf56e5391dfbb3db3d6cee3138afaccb6cd64.
* gnu/packages/bioinformatics.scm: Remove unused (gnu packages
commencement) import.
| Ludovic Courtès |
| 2021-06-22 | gnu: ensembl-vep: Use a source file-name....* gnu/packages/bioinformatics.scm (ensembl-vep)[source]: Add a file-name
field.
| Efraim Flashner |
| 2021-06-22 | gnu: Add perl-cworld-dekker....* gnu/packages/bioinformatics.scm (perl-cworld-dekker): New variable.
| Ricardo Wurmus |
| 2021-06-21 | gnu: Add python-iced....* gnu/packages/bioinformatics.scm (python-iced): New variable.
| Ricardo Wurmus |
| 2021-06-14 | gnu: Add python-cgatcore....* gnu/packages/bioinformatics.scm (python-cgatcore): New variable.
| Ricardo Wurmus |
| 2021-06-14 | gnu: Rename qtbase to qtbase-5....This change was automated via the following command:
$ git ls-files | xargs sed -i 's/,qtbase)/,qtbase-5)/g'
$ git ls-files | xargs sed -i 's/inherit qtbase)/inherit qtbase-5)/g'
$ git ls-files | xargs sed -i 's/package-version qtbase)/package-version qtbase-5)/g'
$ git checkout etc # to clear some spurious changes
This is done so the qtbase package can be upgraded to version 6 in the
following commit.
| Maxim Cournoyer |
| 2021-06-08 | gnu: pigx-sars-cov2-ww: Update to 0.0.2....* gnu/packages/bioinformatics.scm (pigx-sars-cov2-ww): Update to 0.0.2.
[inputs]: Add wget.
| Ricardo Wurmus |
| 2021-06-08 | gnu: pigx-bsseq: Update to 0.1.5....* gnu/packages/bioinformatics.scm (pigx-bsseq): Update to 0.1.5.
| Ricardo Wurmus |
| 2021-06-08 | gnu: python-hicmatrix: Update to 15....* gnu/packages/bioinformatics.scm (python-hicmatrix): Update to 15.
[arguments]: Enabled tests. Remove 'relax-requirements phase.
[native-inputs]: Add python-pytest.
Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
| Mădălin Ionel Patrașcu |
| 2021-06-08 | gnu: python-mappy: Move to (gnu packages bioinformatics)....* gnu/packages/python-xyz.scm (python-mappy): Move to ...
* gnu/packages/bioinformatics.scm: ... here.
| Efraim Flashner |
| 2021-06-08 | gnu: pigx-rnaseq: Update to 0.0.17....* gnu/packages/bioinformatics.scm (pigx-rnaseq): Update to 0.0.17.
[arguments]: Remove "use-latest-salmon" phase; add "set-timezone" phase.
[inputs]: Replace r-gprofiler with r-gprofiler2; add r-ggpubr and
python-deeptools.
[native-inputs]: Add tzdata.
| Ricardo Wurmus |
| 2021-06-07 | gnu: pigx-rnaseq: Adjust to upgrade of salmon....* gnu/packages/bioinformatics.scm (pigx-rnaseq)[arguments]: Add phase
"use-latest-salmon".
| Ricardo Wurmus |
| 2021-06-07 | gnu: salmon: Update to 1.4.0....* gnu/packages/bioinformatics.scm (salmon): Update to 1.4.0.
[arguments]: Remove unnecessary flags, add other soon-to-be-unnecessary flags;
remove "prepare-rapmap" phase, add "prepare-pufferfish" phase, add
"fix-error-message-in-tests" phase, simplify "use-system-libraries" phase.
[inputs]: Add curl and pufferfish sources; remove libdivsufsort and rapmap
sources.
| Ricardo Wurmus |
| 2021-06-07 | gnu: macs: Update to 2.2.7.1....* gnu/packages/bioinformatics.scm (macs): Update to 2.2.7.1.
| Ricardo Wurmus |
| 2021-06-07 | gnu: libgff: Update to 2.0.0....* gnu/packages/bioinformatics.scm (libgff): Update to 2.0.0.
[home-page]: Update to new home.
| Ricardo Wurmus |
| 2021-06-07 | gnu: jellyfish: Update to 2.3.0....* gnu/packages/bioinformatics.scm (jellyfish): Update to 2.3.0.
[arguments]: Disable SSE to avoid tuning to the build node's CPU.
[native-inputs]: Replace python-2 with python-wrapper.
[license]: Update.
| Ricardo Wurmus |
| 2021-06-07 | gnu: multiqc: Update to 1.10.1....* gnu/packages/bioinformatics.scm (multiqc): Update to 1.10.1.
[arguments]: Remove build phase "relax-requirements"; replace "check" phase.
[propagated-inputs]: Add python-coloredlogs, python-future, python-networkx,
and python-rich; remove python-nose.
[native-inputs]: Add python-pytest and the test suite.
| Ricardo Wurmus |
| 2021-06-07 | gnu: python-hic2cool: Update to 0.8.3....* gnu/packages/bioinformatics.scm (python-hic2cool): Update to 0.8.3.
[source]: Download using git-fetch.
[arguments]: Enable tests. Add phase to make test data writable.
[propagated-inputs]: Add python-h5py, python-numpy, python-pandas,
python-scipy.
Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
| Mădălin Ionel Patrașcu |
| 2021-06-06 | gnu: freebayes: Update to 1.3.5....* gnu/packages/bioinformatics.scm (freebayes): Update to 1.3.5.
[source]: Remove patch.
[arguments]: Adjust custom 'patch-source phase for changes in source.
[inputs]: Remove zlib.
* gnu/packages/patches/freebayes-devendor-deps.patch: Remove file.
* gnu/local.mk (dist_patch_DATA): Remove it.
| Efraim Flashner |
| 2021-06-06 | gnu: python-cooler: Update to 0.8.11....* gnu/packages/bioinformatics.scm (python-cooler): Update to 0.8.11.
[arguments]: Add build phase "patch-tests"; replace "check" phase.
[native-inputs]: Add python-codecov, python-pytest-cov, and
python-pytest-flake8.
[propagated-inputs]: Add python-six and python-sparse.
| Mădălin Ionel Patrașcu |
| 2021-06-05 | gnu: pigx-rnaseq: Update to 0.0.13....* gnu/packages/bioinformatics.scm (pigx-rnaseq): Update to 0.0.13.
[arguments]: Remove obsolete substitutions.
[inputs]: Remove fastqc and trim-galore; add hisat2 and fastp.
| Ricardo Wurmus |
| 2021-06-04 | gnu: python-scanpy: Update to 1.7.2....* gnu/packages/bioinformatics.scm (python-scanpy): Update to 1.7.2.
| Roel Janssen |
| 2021-06-04 | gnu: Add pigx-sars-cov2-ww....* gnu/packages/bioinformatics.scm (pigx-sars-cov2-ww): New variable.
| Ricardo Wurmus |
| 2021-06-03 | gnu: Add fit-sne....* gnu/packages/bioinformatics.scm (fit-sne): New variable.
| Ricardo Wurmus |
| 2021-06-02 | gnu: Add biobambam2....* gnu/packages/bioinformatics.scm (biobambam2): New variable.
| Ricardo Wurmus |
| 2021-06-02 | gnu: Add libmaus2....* gnu/packages/bioinformatics.scm (libmaus2): New variable.
| Ricardo Wurmus |
| 2021-06-01 | gnu: Add bamutils....* gnu/packages/bioinformatics.scm (bamutils): New variable.
| Roel Janssen |
| 2021-05-31 | gnu: bits: Use git-version and git-file-name....* gnu/packages/bioinformatics.scm (bits)[version]: Use git-version.
[source]: Use git-file-name.
| Ricardo Wurmus |
| 2021-05-31 | gnu: piranha: Use git-version....* gnu/packages/bioinformatics.scm (piranha)[version]: Use git-version.
| Ricardo Wurmus |
| 2021-05-31 | gnu: r-chipkernels: Use git-version and git-file-name....* gnu/packages/bioinformatics.scm (r-chipkernels)[version]: Use git-version.
[source]: Use git-file-name.
| Ricardo Wurmus |
| 2021-05-31 | gnu: f-seq: Use git-version and git-file-name....* gnu/packages/bioinformatics.scm (f-seq)[version]: Use git-version.
[source]: Use git-file-name.
| Ricardo Wurmus |
| 2021-05-31 | gnu: bismark: Use git-file-name....* gnu/packages/bioinformatics.scm (bismark)[source]: Use git-file-name.
| Ricardo Wurmus |
| 2021-05-31 | gnu: filevercmp: Use git-version....* gnu/packages/bioinformatics.scm (filevercmp)[version]: Use git-version; bind
"revision" in outer let.
| Ricardo Wurmus |
| 2021-05-31 | gnu: r-spp: Move to (gnu packages bioconductor)....* gnu/packages/bioinformatics.scm (r-spp): Move from here...
* gnu/packages/bioconductor.scm (r-spp): ...to here.
| Ricardo Wurmus |
| 2021-05-31 | gnu: r-phantompeakqualtools: Let-bind commit, set revision to 1....* gnu/packages/bioinformatics.scm (r-phantompeakqualtools): Bind the commit
outside of the package value.
[version]: Use git-version.
[source]: Use git-file-name.
| Ricardo Wurmus |
| 2021-05-31 | gnu: r-methylkit: Move to (gnu packages bioconductor)....* gnu/packages/bioinformatics.scm (r-methylkit): Move from here...
* gnu/packages/bioconductor.scm (r-methylkit): ...to here.
| zimoun |
