| Age | Commit message (Expand) | Author |
|---|
| 2021-12-07 | gnu: blasr-libcpp: Update to 5.3.5.•••* gnu/packages/bioinformatics.scm (blasr-libcpp): Update to 5.3.5.
[inputs]: Add htslib.
| Ricardo Wurmus |
| 2021-12-07 | gnu: htseq: Update to 0.12.3.•••* gnu/packages/bioinformatics.scm (htseq): Update to 0.12.3.
| Ricardo Wurmus |
| 2021-12-07 | gnu: clipper: Update to 2.0.1.•••* 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.
| Ricardo Wurmus |
| 2021-12-07 | gnu: pbbam: Update to 1.7.0.•••* gnu/packages/bioinformatics.scm (pbbam): Update to 1.7.0.
[arguments]: Remove phase 'find-googletest; add phase 'patch-tests.
[propagated-inputs]: Add pbcopper.
| Ricardo Wurmus |
| 2021-12-07 | gnu: bwa-pssm: Fix build.•••* gnu/packages/bioinformatics.scm (bwa-pssm)[arguments]: Add phase
'patch-C-error.
| Ricardo Wurmus |
| 2021-12-07 | gnu: Add pbcopper.•••* gnu/packages/bioinformatics.scm (pbcopper): New variable.
| Ricardo Wurmus |
| 2021-12-07 | gnu: fsom: Build with GCC 6.•••* gnu/packages/bioinformatics.scm (fsom)[native-inputs]: Add gcc-6.
[arguments]: Remove trailing #T.
| Ricardo Wurmus |
| 2021-12-07 | gnu: python-velocyto: Remove generated C files.•••* gnu/packages/bioinformatics.scm (python-velocyto)[source]: Remove all
generated .c files.
| Ricardo Wurmus |
| 2021-12-07 | gnu: python-schema-salad: Update to 8.2.20211116214159.•••* 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.
| Ricardo Wurmus |
| 2021-12-07 | gnu: taxtastic: Update to 0.9.2.•••* gnu/packages/bioinformatics.scm (taxtastic): Update to 0.9.2.
[arguments]: Delete 'sanity-check and 'python37-compatibility phases; adjust
'prepare-directory phase.
| Ricardo Wurmus |
| 2021-12-07 | gnu: taxtastic: Run tests conditionally.•••* gnu/packages/bioinformatics.scm (taxtastic)[arguments]: Respect TESTS?
option.
| Ricardo Wurmus |
| 2021-12-07 | gnu: python-dendropy: Update to 4.5.1.•••* gnu/packages/bioinformatics.scm (python-dendropy): Update to 4.5.1.
[arguments]: Skip failing tests.
| Ricardo Wurmus |
| 2021-12-07 | gnu: python-cooler: Use python-cytoolz-for-cooler.•••* gnu/packages/bioinformatics.scm (python-cooler)[propagated-inputs]: Replace
python-cytoolz with python-cytoolz-for-cooler.
| Ricardo Wurmus |
| 2021-12-07 | gnu: phylip: Update to 3.697.•••* gnu/packages/bioinformatics.scm (phylip): Update to 3.697.
| Ricardo Wurmus |
| 2021-12-07 | gnu: phylip: Pass -fcommon to compiler.•••* gnu/packages/bioinformatics.scm (phylip)[arguments]: Set CFLAGS.
| Ricardo Wurmus |
| 2021-12-07 | gnu: phylip: Remove trailing #T.•••* gnu/packages/bioinformatics.scm (phylip)[arguments]: Remove trailing #T from
build phases.
| Ricardo Wurmus |
| 2021-12-07 | gnu: subread: Remove trailing #T.•••* gnu/packages/bioinformatics.scm (subread)[arguments]: Remove trailing #T
from build phases.
| Ricardo Wurmus |
| 2021-12-07 | gnu: subread: Update to 2.0.3.•••* gnu/packages/bioinformatics.scm (subread): Update to 2.0.3.
| Ricardo Wurmus |
| 2021-12-07 | gnu: subread: Update home page..•••* gnu/packages/bioinformatics.scm (subread)[home-page]: Use new home page.
| Ricardo Wurmus |
| 2021-12-07 | gnu: subread: Pass -fcommon to compiler.•••* gnu/packages/bioinformatics.scm (subread)[arguments]: Add -fcommon to flags.
| Ricardo Wurmus |
| 2021-12-07 | gnu: hisat: Update to 0.1.6.•••* gnu/packages/bioinformatics.scm (hisat): Update to 0.1.6.
| Ricardo Wurmus |
| 2021-12-07 | gnu: hisat: Remove trailing #T.•••* gnu/packages/bioinformatics.scm (hisat)[arguments]: Remove trailing #T from
build phase.
| Ricardo Wurmus |
| 2021-12-07 | gnu: hisat: Remove invalid characters.•••* gnu/packages/bioinformatics.scm (hisat)[arguments]: Remove curly quotes.
| Ricardo Wurmus |
| 2021-12-07 | gnu: crossmap: Update to 0.6.1.•••* gnu/packages/bioinformatics.scm (crossmap): Update to 0.6.1.
[source]: Add snippet to remove generated files.
| Ricardo Wurmus |
| 2021-12-07 | gnu: Remove python2-bx-python.•••* gnu/packages/bioinformatics.scm (python2-bx-python): Delete variable.
| Ricardo Wurmus |
| 2021-12-07 | gnu: python-bx-python: Update to 0.8.12.•••* 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.
| Ricardo Wurmus |
| 2021-12-07 | gnu: Remove pbtranscript-tofu.•••Upstream has disappeared and it depends on Python 2, which is no longer
supported.
* gnu/packages/bioinformatics.scm (pbtranscript-tofu): Remove variable.
| Ricardo Wurmus |
| 2021-12-07 | gnu: python-pyfit-sne: Update to 1.2.1.•••* gnu/packages/bioinformatics.scm (python-pyfit-sne): Update to 1.2.1.
[arguments]: Disable tests explicitly.
| Ricardo Wurmus |
| 2021-12-06 | gnu: f-seq: Update name of commons-cli JAR.•••* gnu/packages/bioinformatics.scm (f-seq)[arguments]: Use new name of
commons-cli JAR.
| Ricardo Wurmus |
| 2021-12-06 | gnu: f-seq: Remove trailing #T.•••* gnu/packages/bioinformatics.scm (f-seq)[arguments]: Remove trailing #T from
build phase.
| Ricardo Wurmus |
| 2021-12-06 | gnu: f-seq: Simplify snippet.•••* gnu/packages/bioinformatics.scm (f-seq)[source]: Simplify snippet.
| Ricardo Wurmus |
| 2021-12-05 | Merge remote-tracking branch 'origin/master' into core-updates-frozen | Ricardo Wurmus |
| 2021-12-05 | gnu: python-bwapy: Remove sanity-check.•••* gnu/packages/bioinformatics.scm (python-bwapy)[arguments]: Add phase
'relax-requirements to accept a slightly older version of wheel; remove the
'sanity-check phase.
| Ricardo Wurmus |
| 2021-12-05 | gnu: Remove python2-plastid.•••* gnu/packages/bioinformatics.scm (python2-plastid): Remove variable.
| Ricardo Wurmus |
| 2021-12-05 | gnu: Remove python2-twobitreader.•••* gnu/packages/bioinformatics.scm (python2-twobitreader): Remove variable.
| Ricardo Wurmus |
| 2021-12-05 | gnu: python-bbknn: Fix sanity-check phase.•••* gnu/packages/bioinformatics.scm (python-bbknn)[arguments]: Add phase
'do-not-fail-to-find-sklearn, which prevents the 'sanity-check phase from
failing.
| Ricardo Wurmus |
| 2021-12-05 | gnu: python-bbknn: Add missing input.•••* gnu/packages/bioinformatics.scm (python-bbknn)[propagated-inputs]: Add
python-scikit-learn.
| Ricardo Wurmus |
| 2021-12-05 | gnu: velvet: Add missing TeX package.•••* gnu/packages/bioinformatics.scm (velvet)[native-inputs]: Add
texlive-fonts-ec.
| Ricardo Wurmus |
| 2021-12-05 | gnu: velvet: Remove trailing #T.•••* gnu/packages/bioinformatics.scm (velvet)[arguments]: Remove trailing #T from
build phases.
| Ricardo Wurmus |
| 2021-12-05 | gnu: python-bwapy: Remove pre-built object files.•••* gnu/packages/bioinformatics.scm (python-bwapy)[source]: Remove all .o files
in a snippet.
| Ricardo Wurmus |
| 2021-12-05 | gnu: metabat: Remove trailing #T.•••* gnu/packages/bioinformatics.scm (metabat)[arguments]: Remove trailing #T
from build phases.
| Ricardo Wurmus |
| 2021-12-05 | gnu: kraken2: Remove reference to %outputs.•••* gnu/packages/bioinformatics.scm (kraken2)[arguments]: Remove reference to
%outputs by using a gexp.
| Ricardo Wurmus |
| 2021-12-05 | gnu: methyldackel: Remove reference to %outputs.•••* gnu/packages/bioinformatics.scm (methyldackel)[arguments]: Remove reference
to %outputs by using a gexp.
| Ricardo Wurmus |
| 2021-12-05 | gnu: phast: Remove reference to %outputs.•••* gnu/packages/bioinformatics.scm (phast)[arguments]: Remove reference to
%outputs by using a gexp.
| Ricardo Wurmus |
| 2021-12-05 | gnu: libsbml: Remove references to %build-inputs.•••* gnu/packages/bioinformatics.scm (libsbml)[arguments]: Remove references to
%build-inputs by using a gexp.
| Ricardo Wurmus |
| 2021-12-05 | gnu: ataqv: Remove references to %outputs and %build-inputs.•••* gnu/packages/bioinformatics.scm (ataqv)[arguments]: Remove references to
%outputs and %build-inputs by using a gexp.
| Ricardo Wurmus |
| 2021-12-05 | gnu: adapterremoval: Remove reference to %outputs.•••* gnu/packages/bioinformatics.scm (adapterremoval)[arguments]: Remove
reference to %outputs by using a gexp.
| Ricardo Wurmus |
| 2021-12-05 | gnu: bbmap: Remove reference to %build-inputs.•••* gnu/packages/bioinformatics.scm (bbmap)[arguments]: Remove reference to
%build-inputs by using a gexp.
| Ricardo Wurmus |
| 2021-12-05 | gnu: intervaltree: Remove reference to %outputs.•••* gnu/packages/bioinformatics.scm (intervaltree)[arguments]: Remove reference
to %outputs by using a gexp.
| Ricardo Wurmus |
| 2021-12-05 | gnu: biobambam2: Remove reference to %build-inputs.•••* gnu/packages/bioinformatics.scm (biobambam2)[arguments]: Remove reference to
%build-inputs by using a gexp.
| Ricardo Wurmus |
