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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.
2021-12-08gnu: lollypop: Build with libsoup@2.Marius Bakke
* gnu/packages/gnome.scm (lollypop)[inputs]: Change from LIBSOUP to LIBSOUP-MINIMAL-2.
2021-12-08gnu: rhythmbox: Adjust inputs.Marius Bakke
* gnu/packages/gnome.scm (rhythmbox)[inputs]: Change from PYTHON2-PYGOBJECT to PYTHON-PYGOBJECT. Add LIBSOUP-MINIMAL-2.
2021-12-08gnu: labelme: Loosen Python requirements.Marius Bakke
* gnu/packages/image-processing.scm (labelme)[arguments]: Patch setup.py so it does not require a specific version of Matplotlib.
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: python-ndg-httpsclient: Add missing input.Ricardo Wurmus
* gnu/packages/python-web.scm (python-ndg-httpsclient)[propagated-inputs]: Add python-pyasn1.
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: Add python-cytoolz-for-cooler.Ricardo Wurmus
* gnu/packages/python-xyz.scm (python-cytoolz-for-cooler): New variable.
2021-12-07gnu: python-sparse: Update to 0.13.0.Ricardo Wurmus
* gnu/packages/python-xyz.scm (python-sparse): Update to 0.13.0.
2021-12-07gnu: python-dask: Update to 2021.11.2.Ricardo Wurmus
* gnu/packages/python-xyz.scm (python-dask): Update to 2021.11.2. [source]: Fetch from github. [arguments]: Remove phase 'disable-broken-tests.
2021-12-07gnu: python-dask: Run tests conditionally.Ricardo Wurmus
* gnu/packages/python-xyz.scm (python-dask)[arguments]: Respect TESTS? option.
2021-12-07gnu: python-dask: Add missing input for tests.Ricardo Wurmus
* gnu/packages/python-xyz.scm (python-dask)[native-inputs]: Add python-pytest-rerunfailures.
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: python-pytest-console-scripts: Update to 1.2.1.Ricardo Wurmus
* gnu/packages/python-check.scm (python-pytest-console-scripts): Update to 1.2.1.
2021-12-07gnu: Add python-pytest-rerunfailures.Ricardo Wurmus
* gnu/packages/python-check.scm (python-pytest-rerunfailures): New variable.
2021-12-07gnu: mcl: Add -fcommon to compiler flags.Ricardo Wurmus
* gnu/packages/machine-learning.scm (mcl)[arguments]: Set CFLAGS.
2021-12-07gnu: python-cytoolz: Update to 0.11.2.Ricardo Wurmus
* gnu/packages/python-xyz.scm (python-cytoolz): Update to 0.11.2. [source]: Add snippet.
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: helm: Fix build with GCC 9 and later.Pierre Langlois
* gnu/packages/music.scm (helm)[origin]: Add patch. * gnu/packages/patches/helm-fix-gcc-9-build.patch: New file. * gnu/local.mk (dist_patch_DATA): Register it.
2021-12-06gnu: patchwork: Adjust for python-build-system change.Marius Bakke
This is a follow-up to commit db5646d957895944007c1bb44fcd998ea392f168, et.al. * gnu/packages/patchutils.scm (patchwork)[arguments]: Adapt one more site-packages call.
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.
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