| Age | Commit message (Expand) | Author |
|---|---|---|
| 2021-12-08 | gnu: khmer: Cythonize source files....* 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. | Ricardo Wurmus |
| 2021-12-08 | gnu: cwltool: Update to 3.1.20211107152837....* 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. | Ricardo Wurmus |
| 2021-12-07 | gnu: newick-utils: Pass -fcommon to compiler....* gnu/packages/bioinformatics.scm (newick-utils)[arguments]: Set CFLAGS. | Ricardo Wurmus |
| 2021-12-07 | gnu: blasr: Update to 5.3.5....* gnu/packages/bioinformatics.scm (blasr): Update to 5.3.5. | Ricardo Wurmus |
| 2021-12-07 | gnu: blasr: Remove trailing #T....* gnu/packages/bioinformatics.scm (blasr)[arguments]: Remove trailing #T from build phase. | Ricardo Wurmus |
| 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 |
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