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2021-12-08gnu: khmer: Cythonize source files.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (khmer)[source]: Remove generated files. [arguments]: Add phase 'do-use-cython to patch the setup.py to generate cpp files from Cython sources; add 'build-extensions phase; replace 'check phase.
2021-12-08gnu: cwltool: Update to 3.1.20211107152837.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (cwltool): Update to 3.1.20211107152837. [arguments]: Adjust phase 'loosen-version-restrictions; remove trailing #T from build phases; fix /bin/sh invocations in test files.
2021-12-07gnu: newick-utils: Pass -fcommon to compiler.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (newick-utils)[arguments]: Set CFLAGS.
2021-12-07gnu: blasr: Update to 5.3.5.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (blasr): Update to 5.3.5.
2021-12-07gnu: blasr: Remove trailing #T.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (blasr)[arguments]: Remove trailing #T from build phase.
2021-12-07gnu: blasr-libcpp: Update to 5.3.5.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (blasr-libcpp): Update to 5.3.5. [inputs]: Add htslib.
2021-12-07gnu: htseq: Update to 0.12.3.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (htseq): Update to 0.12.3.
2021-12-07gnu: clipper: Update to 2.0.1.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (clipper): Update to 2.0.1. [source]: Add snippet to remove pre-compiled files. [arguments]: Disable tests, delete 'sanity-check phase, and add 'use-python3-for-cython phase.
2021-12-07gnu: pbbam: Update to 1.7.0.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (pbbam): Update to 1.7.0. [arguments]: Remove phase 'find-googletest; add phase 'patch-tests. [propagated-inputs]: Add pbcopper.
2021-12-07gnu: bwa-pssm: Fix build.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (bwa-pssm)[arguments]: Add phase 'patch-C-error.
2021-12-07gnu: Add pbcopper.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (pbcopper): New variable.
2021-12-07gnu: fsom: Build with GCC 6.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (fsom)[native-inputs]: Add gcc-6. [arguments]: Remove trailing #T.
2021-12-07gnu: python-velocyto: Remove generated C files.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (python-velocyto)[source]: Remove all generated .c files.
2021-12-07gnu: python-schema-salad: Update to 8.2.20211116214159.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (python-schema-salad): Update to 8.2.20211116214159. [arguments]: Remove trailing #T. [propagated-inputs]: Replace python-cachecontrol-0.11 with python-cachecontrol. [native-inputs]: Add python-black.
2021-12-07gnu: taxtastic: Update to 0.9.2.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (taxtastic): Update to 0.9.2. [arguments]: Delete 'sanity-check and 'python37-compatibility phases; adjust 'prepare-directory phase.
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.
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