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* gnu: tbsp: Update to 1.0.0-2.dc30c03.Ricardo Wurmus2021-12-08
| | | | | | * gnu/packages/bioinformatics.scm (tbsp): Update to 1.0.0-2.dc30c03. [arguments]: Relax requirement on matplot. This may turn out to be a mistake. [inputs]: Replace python-biopython with python-biopython-1.73.
* gnu: mantis: Update to 0.1-2.b6979a2.Ricardo Wurmus2021-12-08
| | | | | | * gnu/packages/bioinformatics.scm (mantis): Update to 0.1-2.b6979a2. [arguments]: Disable the use of SSE4.2 instructions. [native-inputs]: Build with GCC 7.
* gnu: imp: Disable tests.Ricardo Wurmus2021-12-08
| | | | | * gnu/packages/bioinformatics.scm (imp)[arguments]: Disable unreliable test suite.
* gnu: snap-aligner: Update to 2.0.0.Ricardo Wurmus2021-12-08
| | | | * gnu/packages/bioinformatics.scm (snap-aligner): Update to 2.0.0.
* gnu: snap-aligner: Remove trailing #T.Ricardo Wurmus2021-12-08
| | | | | * gnu/packages/bioinformatics.scm (snap-aligner)[arguments]: Remove trailing #T from 'install phase.
* gnu: snap-aligner: Run tests conditionally.Ricardo Wurmus2021-12-08
| | | | | * gnu/packages/bioinformatics.scm (snap-aligner)[arguments]: Respect TESTS? option.
* gnu: khmer: Cythonize source files.Ricardo Wurmus2021-12-08
| | | | | | * 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.
* gnu: cwltool: Update to 3.1.20211107152837.Ricardo Wurmus2021-12-08
| | | | | | * 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.
* gnu: lollypop: Build with libsoup@2.Marius Bakke2021-12-08
| | | | | * gnu/packages/gnome.scm (lollypop)[inputs]: Change from LIBSOUP to LIBSOUP-MINIMAL-2.
* gnu: rhythmbox: Adjust inputs.Marius Bakke2021-12-08
| | | | | * gnu/packages/gnome.scm (rhythmbox)[inputs]: Change from PYTHON2-PYGOBJECT to PYTHON-PYGOBJECT. Add LIBSOUP-MINIMAL-2.
* gnu: labelme: Loosen Python requirements.Marius Bakke2021-12-08
| | | | | * gnu/packages/image-processing.scm (labelme)[arguments]: Patch setup.py so it does not require a specific version of Matplotlib.
* gnu: newick-utils: Pass -fcommon to compiler.Ricardo Wurmus2021-12-07
| | | | * gnu/packages/bioinformatics.scm (newick-utils)[arguments]: Set CFLAGS.
* gnu: blasr: Update to 5.3.5.Ricardo Wurmus2021-12-07
| | | | * gnu/packages/bioinformatics.scm (blasr): Update to 5.3.5.
* gnu: blasr: Remove trailing #T.Ricardo Wurmus2021-12-07
| | | | | * gnu/packages/bioinformatics.scm (blasr)[arguments]: Remove trailing #T from build phase.
* gnu: blasr-libcpp: Update to 5.3.5.Ricardo Wurmus2021-12-07
| | | | | * gnu/packages/bioinformatics.scm (blasr-libcpp): Update to 5.3.5. [inputs]: Add htslib.
* gnu: htseq: Update to 0.12.3.Ricardo Wurmus2021-12-07
| | | | * gnu/packages/bioinformatics.scm (htseq): Update to 0.12.3.
* gnu: clipper: Update to 2.0.1.Ricardo Wurmus2021-12-07
| | | | | | | * 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.
* gnu: pbbam: Update to 1.7.0.Ricardo Wurmus2021-12-07
| | | | | | * gnu/packages/bioinformatics.scm (pbbam): Update to 1.7.0. [arguments]: Remove phase 'find-googletest; add phase 'patch-tests. [propagated-inputs]: Add pbcopper.
* gnu: bwa-pssm: Fix build.Ricardo Wurmus2021-12-07
| | | | | * gnu/packages/bioinformatics.scm (bwa-pssm)[arguments]: Add phase 'patch-C-error.
* gnu: Add pbcopper.Ricardo Wurmus2021-12-07
| | | | * gnu/packages/bioinformatics.scm (pbcopper): New variable.
* gnu: python-ndg-httpsclient: Add missing input.Ricardo Wurmus2021-12-07
| | | | | * gnu/packages/python-web.scm (python-ndg-httpsclient)[propagated-inputs]: Add python-pyasn1.
* gnu: fsom: Build with GCC 6.Ricardo Wurmus2021-12-07
| | | | | * gnu/packages/bioinformatics.scm (fsom)[native-inputs]: Add gcc-6. [arguments]: Remove trailing #T.
* gnu: python-velocyto: Remove generated C files.Ricardo Wurmus2021-12-07
| | | | | * gnu/packages/bioinformatics.scm (python-velocyto)[source]: Remove all generated .c files.
* gnu: python-schema-salad: Update to 8.2.20211116214159.Ricardo Wurmus2021-12-07
| | | | | | | | | * 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.
* gnu: taxtastic: Update to 0.9.2.Ricardo Wurmus2021-12-07
| | | | | | * gnu/packages/bioinformatics.scm (taxtastic): Update to 0.9.2. [arguments]: Delete 'sanity-check and 'python37-compatibility phases; adjust 'prepare-directory phase.
* gnu: taxtastic: Run tests conditionally.Ricardo Wurmus2021-12-07
| | | | | * gnu/packages/bioinformatics.scm (taxtastic)[arguments]: Respect TESTS? option.
* gnu: python-dendropy: Update to 4.5.1.Ricardo Wurmus2021-12-07
| | | | | * gnu/packages/bioinformatics.scm (python-dendropy): Update to 4.5.1. [arguments]: Skip failing tests.
* gnu: python-cooler: Use python-cytoolz-for-cooler.Ricardo Wurmus2021-12-07
| | | | | * gnu/packages/bioinformatics.scm (python-cooler)[propagated-inputs]: Replace python-cytoolz with python-cytoolz-for-cooler.
* gnu: Add python-cytoolz-for-cooler.Ricardo Wurmus2021-12-07
| | | | * gnu/packages/python-xyz.scm (python-cytoolz-for-cooler): New variable.
* gnu: python-sparse: Update to 0.13.0.Ricardo Wurmus2021-12-07
| | | | * gnu/packages/python-xyz.scm (python-sparse): Update to 0.13.0.
* gnu: python-dask: Update to 2021.11.2.Ricardo Wurmus2021-12-07
| | | | | | * gnu/packages/python-xyz.scm (python-dask): Update to 2021.11.2. [source]: Fetch from github. [arguments]: Remove phase 'disable-broken-tests.
* gnu: python-dask: Run tests conditionally.Ricardo Wurmus2021-12-07
| | | | * gnu/packages/python-xyz.scm (python-dask)[arguments]: Respect TESTS? option.
* gnu: python-dask: Add missing input for tests.Ricardo Wurmus2021-12-07
| | | | | * gnu/packages/python-xyz.scm (python-dask)[native-inputs]: Add python-pytest-rerunfailures.
* gnu: phylip: Update to 3.697.Ricardo Wurmus2021-12-07
| | | | * gnu/packages/bioinformatics.scm (phylip): Update to 3.697.
* gnu: phylip: Pass -fcommon to compiler.Ricardo Wurmus2021-12-07
| | | | * gnu/packages/bioinformatics.scm (phylip)[arguments]: Set CFLAGS.
* gnu: phylip: Remove trailing #T.Ricardo Wurmus2021-12-07
| | | | | * gnu/packages/bioinformatics.scm (phylip)[arguments]: Remove trailing #T from build phases.
* gnu: subread: Remove trailing #T.Ricardo Wurmus2021-12-07
| | | | | * gnu/packages/bioinformatics.scm (subread)[arguments]: Remove trailing #T from build phases.
* gnu: subread: Update to 2.0.3.Ricardo Wurmus2021-12-07
| | | | * gnu/packages/bioinformatics.scm (subread): Update to 2.0.3.
* gnu: subread: Update home page..Ricardo Wurmus2021-12-07
| | | | * gnu/packages/bioinformatics.scm (subread)[home-page]: Use new home page.
* gnu: subread: Pass -fcommon to compiler.Ricardo Wurmus2021-12-07
| | | | * gnu/packages/bioinformatics.scm (subread)[arguments]: Add -fcommon to flags.
* gnu: python-pytest-console-scripts: Update to 1.2.1.Ricardo Wurmus2021-12-07
| | | | | * gnu/packages/python-check.scm (python-pytest-console-scripts): Update to 1.2.1.
* gnu: Add python-pytest-rerunfailures.Ricardo Wurmus2021-12-07
| | | | * gnu/packages/python-check.scm (python-pytest-rerunfailures): New variable.
* gnu: mcl: Add -fcommon to compiler flags.Ricardo Wurmus2021-12-07
| | | | * gnu/packages/machine-learning.scm (mcl)[arguments]: Set CFLAGS.
* gnu: python-cytoolz: Update to 0.11.2.Ricardo Wurmus2021-12-07
| | | | | * gnu/packages/python-xyz.scm (python-cytoolz): Update to 0.11.2. [source]: Add snippet.
* gnu: hisat: Update to 0.1.6.Ricardo Wurmus2021-12-07
| | | | * gnu/packages/bioinformatics.scm (hisat): Update to 0.1.6.
* gnu: hisat: Remove trailing #T.Ricardo Wurmus2021-12-07
| | | | | * gnu/packages/bioinformatics.scm (hisat)[arguments]: Remove trailing #T from build phase.
* gnu: hisat: Remove invalid characters.Ricardo Wurmus2021-12-07
| | | | * gnu/packages/bioinformatics.scm (hisat)[arguments]: Remove curly quotes.
* gnu: crossmap: Update to 0.6.1.Ricardo Wurmus2021-12-07
| | | | | * gnu/packages/bioinformatics.scm (crossmap): Update to 0.6.1. [source]: Add snippet to remove generated files.
* gnu: Remove python2-bx-python.Ricardo Wurmus2021-12-07
| | | | * gnu/packages/bioinformatics.scm (python2-bx-python): Delete variable.
* gnu: python-bx-python: Update to 0.8.12.Ricardo Wurmus2021-12-07
| | | | | | * 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.
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