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* | 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: 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: 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.
* | gnu: Remove pbtranscript-tofu.Ricardo Wurmus2021-12-07
| | | | | | | | | | | | | | Upstream has disappeared and it depends on Python 2, which is no longer supported. * gnu/packages/bioinformatics.scm (pbtranscript-tofu): Remove variable.
* | gnu: python-pyfit-sne: Update to 1.2.1.Ricardo Wurmus2021-12-07
| | | | | | | | | | * gnu/packages/bioinformatics.scm (python-pyfit-sne): Update to 1.2.1. [arguments]: Disable tests explicitly.
* | gnu: f-seq: Update name of commons-cli JAR.Ricardo Wurmus2021-12-06
| | | | | | | | | | * gnu/packages/bioinformatics.scm (f-seq)[arguments]: Use new name of commons-cli JAR.
* | gnu: f-seq: Remove trailing #T.Ricardo Wurmus2021-12-06
| | | | | | | | | | * gnu/packages/bioinformatics.scm (f-seq)[arguments]: Remove trailing #T from build phase.
* | gnu: f-seq: Simplify snippet.Ricardo Wurmus2021-12-06
| | | | | | | | * gnu/packages/bioinformatics.scm (f-seq)[source]: Simplify snippet.
* | Merge remote-tracking branch 'origin/master' into core-updates-frozenRicardo Wurmus2021-12-05
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| * gnu: minimap2: Update to 2.23.Efraim Flashner2021-12-05
| | | | | | | | * gnu/packages/bioinformatics.scm (minimap2): Update to 2.23.
| * gnu: pigx-sars-cov2-ww: Update to 0.0.4.Ricardo Wurmus2021-12-04
| | | | | | | | | | * gnu/packages/bioinformatics.scm (pigx-sars-cov2-ww): Update to 0.0.4. [inputs]: Add bbmap, bedtools, fastp, ivar, and r-r-utils.
| * gnu: imp: Update to 2.15.0.Ricardo Wurmus2021-12-03
| | | | | | | | | | * gnu/packages/bioinformatics.scm (imp): Update to 2.15.0. [arguments]: Disable one more test.
| * gnu: python-ont-fast5-api: Update to 4.0.0.Ricardo Wurmus2021-12-03
| | | | | | | | | | | | | | | | * gnu/packages/bioinformatics.scm (python-ont-fast5-api): Update to 4.0.0. [source]: Remove bundled plugin binaries. [arguments]: Install plugin from inputs. [inputs]: Add vbz-compression. [propagated-inputs]: Remove python-six; add python-packaging.
| * gnu: Add vbz-compression.Ricardo Wurmus2021-12-03
| | | | | | | | * gnu/packages/bioinformatics.scm (vbz-compression): New variable.
| * gnu: ivar: Disable parallel tests.Ricardo Wurmus2021-12-03
| | | | | | | | * gnu/packages/bioinformatics.scm (ivar)[arguments]: Disable parallel tests.
| * gnu: Remove python2-biom-format.Ricardo Wurmus2021-12-03
| | | | | | | | | | | | | | | | There are no users of this variant, and the current version of biom-format does not support Python 2. * gnu/packages/bioinformatics.scm (python2-biom-format): Remove variable. (python-biom-format)[properties]: Remove field.
| * gnu: ribodiff: Remove trailing #T.Ricardo Wurmus2021-12-02
| | | | | | | | | | * gnu/packages/bioinformatics.scm (ribodiff)[arguments]: Remove trailing #T from build phase.
| * gnu: ribodiff: Disable broken test.Ricardo Wurmus2021-12-02
| | | | | | | | | | * gnu/packages/bioinformatics.scm (ribodiff)[arguments]: Add build phase 'disable-plot-test.
| * gnu: khmer: Fix build with Python 3.8.Ricardo Wurmus2021-12-02
| | | | | | | | | | | | * gnu/packages/bioinformatics.scm (khmer)[source]: Remove trailing #T. [arguments]: Remove trailing #T from build phases; add build phase 'python-3.8-compatibility.
| * gnu: python-biom-format: Update to 2.1.10.Ricardo Wurmus2021-12-02
| | | | | | | | | | | | | | | | * gnu/packages/bioinformatics.scm (python-biom-format): Update to 2.1.10. [source]: Simplify snippet. [arguments]: Add phase 'relax; remove trailing #T from other build phases. [propagated-inputs]: Add python-anndata; replace python-pandas-0.25 with python-pandas.
| * gnu: pardre: Update to 2.2.5.Ricardo Wurmus2021-12-02
| | | | | | | | | | * gnu/packages/bioinformatics.scm (pardre): Update to 2.2.5. [arguments]: Remove trailing #T and update comment about tests.
| * gnu: pardre: Use C++ bindings for MPI.Ricardo Wurmus2021-12-02
| | | | | | | | | | * gnu/packages/bioinformatics.scm (pardre)[inputs]: Replace openmpi with openmpi-c++.
| * gnu: Add python-mygene.Ricardo Wurmus2021-12-02
| | | | | | | | * gnu/packages/bioinformatics.scm (python-mygene): New variable.
| * gnu: Add python-biothings-client.Ricardo Wurmus2021-12-02
| | | | | | | | * gnu/packages/bioinformatics.scm (python-biothings-client): New variable.
| * gnu: Remove couger.Ricardo Wurmus2021-12-02
| | | | | | | | | | | | This package has been moved to the Guix Past channel. * gnu/packages/bioinformatics.scm (couger): Remove variable.
| * gnu: r-umi4cpackage: Embed references to perl and bowtie2.Ricardo Wurmus2021-11-30
| | | | | | | | | | | | | | * gnu/packages/bioinformatics.scm (r-umi4cpackage)[arguments]: Add build phases to patch calls of bowtie2 and perl. [inputs]: Add perl and bowtie. [synopsis]: Remove trailing period.
* | gnu: python-bwapy: Remove sanity-check.Ricardo Wurmus2021-12-05
| | | | | | | | | | | | * gnu/packages/bioinformatics.scm (python-bwapy)[arguments]: Add phase 'relax-requirements to accept a slightly older version of wheel; remove the 'sanity-check phase.
* | gnu: Remove python2-plastid.Ricardo Wurmus2021-12-05
| | | | | | | | * gnu/packages/bioinformatics.scm (python2-plastid): Remove variable.
* | gnu: Remove python2-twobitreader.Ricardo Wurmus2021-12-05
| | | | | | | | * gnu/packages/bioinformatics.scm (python2-twobitreader): Remove variable.
* | gnu: python-bbknn: Fix sanity-check phase.Ricardo Wurmus2021-12-05
| | | | | | | | | | | | * gnu/packages/bioinformatics.scm (python-bbknn)[arguments]: Add phase 'do-not-fail-to-find-sklearn, which prevents the 'sanity-check phase from failing.
* | gnu: python-bbknn: Add missing input.Ricardo Wurmus2021-12-05
| | | | | | | | | | * gnu/packages/bioinformatics.scm (python-bbknn)[propagated-inputs]: Add python-scikit-learn.
* | gnu: velvet: Add missing TeX package.Ricardo Wurmus2021-12-05
| | | | | | | | | | * gnu/packages/bioinformatics.scm (velvet)[native-inputs]: Add texlive-fonts-ec.
* | gnu: velvet: Remove trailing #T.Ricardo Wurmus2021-12-05
| | | | | | | | | | * gnu/packages/bioinformatics.scm (velvet)[arguments]: Remove trailing #T from build phases.
* | gnu: python-bwapy: Remove pre-built object files.Ricardo Wurmus2021-12-05
| | | | | | | | | | * gnu/packages/bioinformatics.scm (python-bwapy)[source]: Remove all .o files in a snippet.
* | gnu: metabat: Remove trailing #T.Ricardo Wurmus2021-12-05
| | | | | | | | | | * gnu/packages/bioinformatics.scm (metabat)[arguments]: Remove trailing #T from build phases.
* | gnu: kraken2: Remove reference to %outputs.Ricardo Wurmus2021-12-05
| | | | | | | | | | * gnu/packages/bioinformatics.scm (kraken2)[arguments]: Remove reference to %outputs by using a gexp.
* | gnu: methyldackel: Remove reference to %outputs.Ricardo Wurmus2021-12-05
| | | | | | | | | | * gnu/packages/bioinformatics.scm (methyldackel)[arguments]: Remove reference to %outputs by using a gexp.
* | gnu: phast: Remove reference to %outputs.Ricardo Wurmus2021-12-05
| | | | | | | | | | * gnu/packages/bioinformatics.scm (phast)[arguments]: Remove reference to %outputs by using a gexp.
* | gnu: libsbml: Remove references to %build-inputs.Ricardo Wurmus2021-12-05
| | | | | | | | | | * gnu/packages/bioinformatics.scm (libsbml)[arguments]: Remove references to %build-inputs by using a gexp.
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