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2023-01-15gnu: gdcm: Fix recursive Git source hash.Tobias Geerinckx-Rice
The hash being used covered only the gdcm repository, not the gdcmdata submodule. * gnu/packages/bioinformatics.scm (gdcm)[source]: Update hash. Reported by civodul in #guix.
2023-01-17gnu: gdcm: Update to 3.0.20.Tor-björn Claesson
* gnu/packages/bioinformatics.scm (gdcm): Update to 3.0.20. [home-page, license]: Update. Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2023-01-16gnu: r-cytonorm: Update to 0.0.10-1.166f9ff.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-cytonorm): Update to 0.0.10-1.166f9ff.
2023-01-13gnu: r-signac: Update to 1.9.0-1.af41427.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-signac): Update to 1.9.0-1.af41427. [propagated-inputs]: Remove r-ggforce, r-ggrepel, r-ggseqlogo, r-lsa, r-qlcmatrix, and r-seurat; add r-vctrs.
2023-01-13gnu: python-cellbender: Update source hash.Marius Bakke
The git tag was moved in-place from d82893c05b4e6b912f7f165dc2cd7c36f29cfc52 to d92cfc5a55c8b1771348468035993c52df975170. * gnu/packages/bioinformatics.scm (python-cellbender)[source](sha256): Update.
2023-01-12gnu: Add cellsnp-lite.Simon Tournier
* gnu/packages/bioinformatics.scm (cellsnp-lite): New variable.
2023-01-09gnu: Add r-gg3d.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-gg3d): New variable.
2023-01-08gnu: Move Java XML packages to new module.Ricardo Wurmus
* gnu/packages/xml.scm (java-simple-xml, java-jaxp, java-apache-xml-commons-resolver, java-jaxen, java-xom, java-xsdlib, java-xpp3, java-xmlpull2, java-xmlpull-api-v1, java-dom4j, java-kxml2, java-stax, java-jettison, java-jdom2, java-xstream, java-mxparser): Move these variables from here... * gnu/packages/java-xml.scm: ...to this new file. * gnu/local.mk (GNU_SYSTEM_MODULES): Register new file. * gnu/packages/axoloti.scm, gnu/packages/batik.scm, gnu/packages/bioinformatics.scm, gnu/packages/groovy.scm, gnu/packages/java.scm, gnu/packages/maven.scm: Adjust module imports.
2023-01-08gnu: Add gdcm.Antero Mejr
* gnu/packages/bioinformatics.scm (gdcm): New variable. Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2023-01-07gnu: Use old setuptools in packages that relies on use_2to3 conversion.Marius Bakke
This fixes a regression since 520cdf80581669646ff61e9f18f3b27045556e76 where the use_2to3 functionality was removed from setuptools. * gnu/packages/graph.scm (python-louvain)[native-inputs]: Change from PYTHON-SETUPTOOLS to PYTHON-SETUPTOOLS-57. * gnu/packages/python-check.scm (python-parameterizedtestcase)[native-inputs]: Likewise. * gnu/packages/python-xyz.scm (python-anyjson)[native-inputs]: Add PYTHON-SETUPTOOLS-57. * gnu/packages/bioinformatics.scm (python-pyvcf)[native-inputs]: Change from PYTHON-SETUPTOOLS-FOR-TENSORFLOW to PYTHON-SETUPTOOLS-57.
2023-01-06gnu: bbmap: Update to 39.01.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (bbmap): Update to 39.01.
2023-01-06gnu: bbmap: Use gexp.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (bbmap)[arguments]: Use gexp.
2023-01-06gnu: nanopolish: Drop input labels.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (nanopolish)[inputs]: Drop labels.
2023-01-06gnu: nanopolish: Update to 0.14.0.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (nanopolish): Update to 0.14.0. [source]: Update snippet. [arguments]: Use gexp; use cc-for-target; drop #T from build phases. [inputs]: Add minimap2. [native-inputs]: Add cmake-minimal.
2023-01-06gnu: filtlong: Use Python 3.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (filtlong)[inputs]: Replace python-2 with python-wrapper.
2023-01-06gnu: filtlong: Use gexp.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (filtlong)[arguments]: Use gexp.
2023-01-06gnu: filtlong: Drop input labels.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (filtlong)[inputs]: Drop labels.
2023-01-06gnu: filtlong: Remove trailing #T from build phases.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (filtlong)[arguments]: Remove trailing #T.
2023-01-06gnu: ngless: Use gexp.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (ngless)[arguments]: Use gexp.
2023-01-06gnu: ngless: Remove trailing #T from build phases.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (ngless)[arguments]: Remove trailing #T.
2023-01-04gnu: bamtools: Build shared libraries.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (bamtools)[arguments]: Build shared libraries instead of static libs.
2023-01-04gnu: Add scallop.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (scallop): New variable.
2023-01-03gnu: Add python-bcbio-gff.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (python-bcbio-gff): New variable.
2022-12-30gnu: Add r-domultibarheatmap.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-domultibarheatmap): New variable.
2022-12-28gnu: r-giotto: Update to 1.1.2-1.3c8067c.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-giotto): Update to 1.1.2-1.3c8067c.
2022-12-22gnu: Add r-bedtorch.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-bedtorch): New variable.
2022-12-22gnu: Add r-rhtslib12.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-rhtslib12): New variable.
2022-12-22gnu: Add wiggletools.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (wiggletools): New variable.
2022-12-22gnu: Add python-episcanpy.Navid Afkhami
* gnu/packages/bioinformatics.scm (python-episcanpy): New variable. Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
2022-12-22gnu: Add python-bamnostic.Navid Afkhami
* gnu/packages/bioinformatics.scm (python-bamnostic): New variable. Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
2022-12-21gnu: Add vembrane.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (vembrane): New variable.
2022-12-21gnu: python-plastid: Update to 0.6.0.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (python-plastid): Update to 0.6.0. [source]: Fetch from git repository. [build-system]: Use pyproject-build-system. [arguments]: Enable tests; add build phases 'unpack-test-data and 'build-extensions. [inputs]: Add openssl. [native-inputs]: Add test data.
2022-12-21gnu: python-pysam: Update to 0.20.0.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (python-pysam): Update to 0.20.0. [build-system]: Use pyproject-build-system.
2022-12-21gnu: htslib: Update to 1.16.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (htslib): Update to 1.16.
2022-12-21gnu: pbbam: Use htslib 1.14.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (pbbam)[propagated-inputs]: Replace htslib with htslib-1.14.
2022-12-21gnu: Add htslib-1.14.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (htslib-1.14): New variable.
2022-12-18gnu: python-scanpy: Use pyproject-build-system.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (python-scanpy)[build-system]: Use pyproject-build-system. [arguments]: Remove custom 'build and 'install phases; move pytest arguments to #:test-flags; add 'pretend-version phase; replace custom 'check phase with 'delete-bad-tests phase.
2022-12-18gnu: python-multivelo: Simplify with pyproject-build-system.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (python-multivelo)[build-system]: Use pyproject-build-system. [arguments]: Remove custom 'build and 'install phases.
2022-12-14gnu: bedtools-2.18: Use gexp.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (bedtools-2.18)[arguments]: Use gexp. [native-inputs]: Drop package label.
2022-12-13gnu: bedops: Update to 2.4.41.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (bedops): Update to 2.4.41. [arguments]: Remove trailing #T from build phases; do not set BINDIR in make-flags; set CC; replace 'install phase. [native-inputs]: Add diffutils, perl, and which.
2022-12-13gnu: tophat: Remove trailing #T from build phases and snippet.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (tophat)[source]: Remove trailing #T from snippet. [arguments]: Remove trailing #T from build phases.
2022-12-13gnu: python-bx-python: Update to 0.9.0.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (python-bx-python): Update to 0.9.0. [build-system]: Use pyproject-build-system. [arguments]: Add phase 'build-extensions and 'disable-cython-doctests. [native-inputs]: Replace python-nose with python-pytest.
2022-12-13gnu: bioawk: Use gexp.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (bioawk)[arguments]: Use gexp and simplify 'install phase.
2022-12-13gnu: blasr-libcpp: Remove trailing #T from build phases.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (blasr-libcpp)[arguments]: Remove trailing #T from build phases.
2022-12-13gnu: pbbam: Drop input labels.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (pbbam)[native-inputs]: Drop labels.
2022-12-13gnu: pbbam: Update to 2.1.0.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (pbbam): Update to 2.1.0.
2022-12-13gnu: pbcopper: Update to 2.0.0.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (pbcopper): Update to 2.0.0.
2022-12-13gnu: bedtools: Remove unnecessary quasiquotation.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (bedtools)[arguments]: Remove quasiquote. [native-inputs]: Drop input label.
2022-12-13gnu: bamutils: Update to 1.0.15.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (bamutils): Update to 1.0.15. [arguments]: Remove quasiquoting; remove USER_WARNINGS from make-flags. [native-inputs]: Update libstatgen.
2022-12-13gnu: bamtools: Update to 2.5.2.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (bamtools): Update to 2.5.2. [arguments]: Enable tests; remove extra phases. [inputs]: Add jsoncpp. [native-inputs]: Add pkg-config.
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