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path: root/gnu/packages/bioinformatics.scm
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2021-12-07gnu: taxtastic: Run tests conditionally.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (taxtastic)[arguments]: Respect TESTS? option.
2021-12-07gnu: python-dendropy: Update to 4.5.1.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (python-dendropy): Update to 4.5.1. [arguments]: Skip failing tests.
2021-12-07gnu: python-cooler: Use python-cytoolz-for-cooler.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (python-cooler)[propagated-inputs]: Replace python-cytoolz with python-cytoolz-for-cooler.
2021-12-07gnu: phylip: Update to 3.697.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (phylip): Update to 3.697.
2021-12-07gnu: phylip: Pass -fcommon to compiler.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (phylip)[arguments]: Set CFLAGS.
2021-12-07gnu: phylip: Remove trailing #T.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (phylip)[arguments]: Remove trailing #T from build phases.
2021-12-07gnu: subread: Remove trailing #T.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (subread)[arguments]: Remove trailing #T from build phases.
2021-12-07gnu: subread: Update to 2.0.3.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (subread): Update to 2.0.3.
2021-12-07gnu: subread: Update home page..Ricardo Wurmus
* gnu/packages/bioinformatics.scm (subread)[home-page]: Use new home page.
2021-12-07gnu: subread: Pass -fcommon to compiler.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (subread)[arguments]: Add -fcommon to flags.
2021-12-07gnu: hisat: Update to 0.1.6.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (hisat): Update to 0.1.6.
2021-12-07gnu: hisat: Remove trailing #T.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (hisat)[arguments]: Remove trailing #T from build phase.
2021-12-07gnu: hisat: Remove invalid characters.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (hisat)[arguments]: Remove curly quotes.
2021-12-07gnu: crossmap: Update to 0.6.1.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (crossmap): Update to 0.6.1. [source]: Add snippet to remove generated files.
2021-12-07gnu: Remove python2-bx-python.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (python2-bx-python): Delete variable.
2021-12-07gnu: python-bx-python: Update to 0.8.12.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (python-bx-python): Update to 0.8.12. [propagated-inputs]: Remove python-six. [arguments]: Remove. Tests are still not run, though.
2021-12-07gnu: Remove pbtranscript-tofu.Ricardo Wurmus
Upstream has disappeared and it depends on Python 2, which is no longer supported. * gnu/packages/bioinformatics.scm (pbtranscript-tofu): Remove variable.
2021-12-07gnu: python-pyfit-sne: Update to 1.2.1.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (python-pyfit-sne): Update to 1.2.1. [arguments]: Disable tests explicitly.
2021-12-06gnu: f-seq: Update name of commons-cli JAR.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (f-seq)[arguments]: Use new name of commons-cli JAR.
2021-12-06gnu: f-seq: Remove trailing #T.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (f-seq)[arguments]: Remove trailing #T from build phase.
2021-12-06gnu: f-seq: Simplify snippet.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (f-seq)[source]: Simplify snippet.
2021-12-05Merge remote-tracking branch 'origin/master' into core-updates-frozenRicardo Wurmus
2021-12-05gnu: python-bwapy: Remove sanity-check.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (python-bwapy)[arguments]: Add phase 'relax-requirements to accept a slightly older version of wheel; remove the 'sanity-check phase.
2021-12-05gnu: Remove python2-plastid.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (python2-plastid): Remove variable.
2021-12-05gnu: Remove python2-twobitreader.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (python2-twobitreader): Remove variable.
2021-12-05gnu: python-bbknn: Fix sanity-check phase.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (python-bbknn)[arguments]: Add phase 'do-not-fail-to-find-sklearn, which prevents the 'sanity-check phase from failing.
2021-12-05gnu: python-bbknn: Add missing input.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (python-bbknn)[propagated-inputs]: Add python-scikit-learn.
2021-12-05gnu: velvet: Add missing TeX package.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (velvet)[native-inputs]: Add texlive-fonts-ec.
2021-12-05gnu: velvet: Remove trailing #T.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (velvet)[arguments]: Remove trailing #T from build phases.
2021-12-05gnu: python-bwapy: Remove pre-built object files.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (python-bwapy)[source]: Remove all .o files in a snippet.
2021-12-05gnu: metabat: Remove trailing #T.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (metabat)[arguments]: Remove trailing #T from build phases.
2021-12-05gnu: kraken2: Remove reference to %outputs.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (kraken2)[arguments]: Remove reference to %outputs by using a gexp.
2021-12-05gnu: methyldackel: Remove reference to %outputs.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (methyldackel)[arguments]: Remove reference to %outputs by using a gexp.
2021-12-05gnu: phast: Remove reference to %outputs.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (phast)[arguments]: Remove reference to %outputs by using a gexp.
2021-12-05gnu: libsbml: Remove references to %build-inputs.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (libsbml)[arguments]: Remove references to %build-inputs by using a gexp.
2021-12-05gnu: ataqv: Remove references to %outputs and %build-inputs.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (ataqv)[arguments]: Remove references to %outputs and %build-inputs by using a gexp.
2021-12-05gnu: adapterremoval: Remove reference to %outputs.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (adapterremoval)[arguments]: Remove reference to %outputs by using a gexp.
2021-12-05gnu: bbmap: Remove reference to %build-inputs.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (bbmap)[arguments]: Remove reference to %build-inputs by using a gexp.
2021-12-05gnu: intervaltree: Remove reference to %outputs.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (intervaltree)[arguments]: Remove reference to %outputs by using a gexp.
2021-12-05gnu: biobambam2: Remove reference to %build-inputs.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (biobambam2)[arguments]: Remove reference to %build-inputs by using a gexp.
2021-12-05gnu: sjcount: Remove reference to %build-inputs.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (sjcount)[arguments]: Remove reference to %build-inputs by using a gexp.
2021-12-05gnu: sjcount: Remove trailing #T.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (sjcount)[arguments]: Remove trailing #T from build phases.
2021-12-05gnu: dropseq-tools: Remove reference to %build-inputs.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (dropseq-tools)[arguments]: Remove reference to %build-inputs by using a gexp.
2021-12-05gnu: dropseq-tools: Remove trailing #T.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (dropseq-tools)[arguments]: Remove trailing #T from build phases... [source]: ...and from the snippet.
2021-12-05gnu: Adjust for python-build-system behavior change.Marius Bakke
Commit cb72f9a773e0931ee3758c851d96007ded034e4c changed the semantics of SITE-PACKAGES, but did not adjust all callers. * gnu/packages/bioinformatics.scm (python-pyvcf)[arguments]: Adjust for missing trailing slash. * gnu/packages/maths.scm (nomad-optimizer)[arguments]: Likewise. * gnu/packages/patchutils.scm (patchwork)[arguments]: Likewise.
2021-12-05gnu: python-pyvcf: Fix bytecode compilation.Marius Bakke
* gnu/packages/bioinformatics.scm (python-pyvcf)[arguments]: Add phase to patch sample script.
2021-12-05gnu: minimap2: Update to 2.23.Efraim Flashner
* gnu/packages/bioinformatics.scm (minimap2): Update to 2.23.
2021-12-05gnu: salmon: Remove reference to %build-inputs.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (salmon)[arguments]: Use a gexp to remove reference to %build-inputs.
2021-12-04gnu: sailfish: Remove references to %build-inputs.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (sailfish)[arguments]: Use a gexp to remove references to %build-inputs.
2021-12-04gnu: sailfish: Simplify snippet.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (sailfish)[source]: Remove trailing #T from snippet.
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