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path: root/gnu/packages/bioinformatics.scm
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2021-08-03gnu: Add r-spectre.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-spectre): New variable.
2021-07-26gnu: Add seqan 3.Ricardo Wurmus
* 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.
2021-07-26gnu: Add segemehl.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (segemehl): New variable.
2021-07-22gnu: python-pysam: Make the check phase honor the tests? argument.Efraim Flashner
* gnu/packages/bioinformatics.scm (python-pysam)[arguments]: Adjust custom 'check phase to skip tests when #:tests is #f.
2021-07-22gnu: python-pysam: Update to 0.16.0.1.Efraim Flashner
* 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.
2021-07-22gnu: Add htslib-1.10.Efraim Flashner
* gnu/packages/bioinformatics.scm (htslib-1.10): New variable.
2021-07-22gnu: python-biopython: Update to 1.73.Efraim Flashner
* gnu/packages/bioinformatics.scm (python-biopython): Update to 1.73.
2021-07-21gnu: Add r-battenberg.Lars-Dominik Braun
* gnu/packages/bioinformatics.scm (r-battenberg): New variable.
2021-07-21gnu: Add r-ascat.Lars-Dominik Braun
* gnu/packages/bioinformatics.scm (r-ascat): New variable.
2021-07-21gnu: Add nanosv.Lars-Dominik Braun
* gnu/packages/bioinformatics.scm (nanosv): New variable.
2021-07-21gnu: Add python-pyvcf.Lars-Dominik Braun
* gnu/packages/bioinformatics.scm (python-pyvcf): New variable.
2021-07-21gnu: checkm: Rename and update to 1.1.3.Lars-Dominik Braun
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.
2021-07-21gnu: Add tombo.Lars-Dominik Braun
* gnu/packages/bioinformatics.scm (tombo): New variable.
2021-07-05gnu: Add ocaml-sqlite3.Julien Lepiller
* 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.
2021-07-01gnu: bioperl-minimal: Avoid top-level cross-module references.Ludovic Courtès
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'.
2021-07-01gnu: Do not import (gnu packages commencement).Ludovic Courtès
Line introduced in 4efbf56e5391dfbb3db3d6cee3138afaccb6cd64. * gnu/packages/bioinformatics.scm: Remove unused (gnu packages commencement) import.
2021-06-22gnu: ensembl-vep: Use a source file-name.Efraim Flashner
* gnu/packages/bioinformatics.scm (ensembl-vep)[source]: Add a file-name field.
2021-06-22gnu: Add perl-cworld-dekker.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (perl-cworld-dekker): New variable.
2021-06-21gnu: Add python-iced.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (python-iced): New variable.
2021-06-14gnu: Add python-cgatcore.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (python-cgatcore): New variable.
2021-06-14gnu: Rename qtbase to qtbase-5.Maxim Cournoyer
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.
2021-06-08gnu: pigx-sars-cov2-ww: Update to 0.0.2.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (pigx-sars-cov2-ww): Update to 0.0.2. [inputs]: Add wget.
2021-06-08gnu: pigx-bsseq: Update to 0.1.5.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (pigx-bsseq): Update to 0.1.5.
2021-06-08gnu: python-hicmatrix: Update to 15.Mădălin Ionel Patrașcu
* 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>
2021-06-08gnu: python-mappy: Move to (gnu packages bioinformatics).Efraim Flashner
* gnu/packages/python-xyz.scm (python-mappy): Move to ... * gnu/packages/bioinformatics.scm: ... here.
2021-06-08gnu: pigx-rnaseq: Update to 0.0.17.Ricardo Wurmus
* 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.
2021-06-07gnu: pigx-rnaseq: Adjust to upgrade of salmon.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (pigx-rnaseq)[arguments]: Add phase "use-latest-salmon".
2021-06-07gnu: salmon: Update to 1.4.0.Ricardo Wurmus
* 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.
2021-06-07gnu: macs: Update to 2.2.7.1.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (macs): Update to 2.2.7.1.
2021-06-07gnu: libgff: Update to 2.0.0.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (libgff): Update to 2.0.0. [home-page]: Update to new home.
2021-06-07gnu: jellyfish: Update to 2.3.0.Ricardo Wurmus
* 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.
2021-06-07gnu: multiqc: Update to 1.10.1.Ricardo Wurmus
* 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.
2021-06-07gnu: python-hic2cool: Update to 0.8.3.Mădălin Ionel Patrașcu
* 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>
2021-06-06gnu: freebayes: Update to 1.3.5.Efraim Flashner
* 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.
2021-06-06gnu: python-cooler: Update to 0.8.11.Mădălin Ionel Patrașcu
* 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.
2021-06-05gnu: pigx-rnaseq: Update to 0.0.13.Ricardo Wurmus
* 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.
2021-06-04gnu: python-scanpy: Update to 1.7.2.Roel Janssen
* gnu/packages/bioinformatics.scm (python-scanpy): Update to 1.7.2.
2021-06-04gnu: Add pigx-sars-cov2-ww.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (pigx-sars-cov2-ww): New variable.
2021-06-03gnu: Add fit-sne.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (fit-sne): New variable.
2021-06-02gnu: Add biobambam2.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (biobambam2): New variable.
2021-06-02gnu: Add libmaus2.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (libmaus2): New variable.
2021-06-01gnu: Add bamutils.Roel Janssen
* gnu/packages/bioinformatics.scm (bamutils): New variable.
2021-05-31gnu: bits: Use git-version and git-file-name.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (bits)[version]: Use git-version. [source]: Use git-file-name.
2021-05-31gnu: piranha: Use git-version.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (piranha)[version]: Use git-version.
2021-05-31gnu: r-chipkernels: Use git-version and git-file-name.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-chipkernels)[version]: Use git-version. [source]: Use git-file-name.
2021-05-31gnu: f-seq: Use git-version and git-file-name.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (f-seq)[version]: Use git-version. [source]: Use git-file-name.
2021-05-31gnu: bismark: Use git-file-name.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (bismark)[source]: Use git-file-name.
2021-05-31gnu: filevercmp: Use git-version.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (filevercmp)[version]: Use git-version; bind "revision" in outer let.
2021-05-31gnu: r-spp: Move to (gnu packages bioconductor).Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-spp): Move from here... * gnu/packages/bioconductor.scm (r-spp): ...to here.
2021-05-31gnu: r-phantompeakqualtools: Let-bind commit, set revision to 1.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-phantompeakqualtools): Bind the commit outside of the package value. [version]: Use git-version. [source]: Use git-file-name.
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