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* 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.
* | gnu: ataqv: Remove references to %outputs and %build-inputs.Ricardo Wurmus2021-12-05
| | | | | | | | | | * gnu/packages/bioinformatics.scm (ataqv)[arguments]: Remove references to %outputs and %build-inputs by using a gexp.
* | gnu: adapterremoval: Remove reference to %outputs.Ricardo Wurmus2021-12-05
| | | | | | | | | | * gnu/packages/bioinformatics.scm (adapterremoval)[arguments]: Remove reference to %outputs by using a gexp.
* | gnu: bbmap: Remove reference to %build-inputs.Ricardo Wurmus2021-12-05
| | | | | | | | | | * gnu/packages/bioinformatics.scm (bbmap)[arguments]: Remove reference to %build-inputs by using a gexp.
* | gnu: intervaltree: Remove reference to %outputs.Ricardo Wurmus2021-12-05
| | | | | | | | | | * gnu/packages/bioinformatics.scm (intervaltree)[arguments]: Remove reference to %outputs by using a gexp.
* | gnu: biobambam2: Remove reference to %build-inputs.Ricardo Wurmus2021-12-05
| | | | | | | | | | * gnu/packages/bioinformatics.scm (biobambam2)[arguments]: Remove reference to %build-inputs by using a gexp.
* | gnu: sjcount: Remove reference to %build-inputs.Ricardo Wurmus2021-12-05
| | | | | | | | | | * gnu/packages/bioinformatics.scm (sjcount)[arguments]: Remove reference to %build-inputs by using a gexp.
* | gnu: sjcount: Remove trailing #T.Ricardo Wurmus2021-12-05
| | | | | | | | | | * gnu/packages/bioinformatics.scm (sjcount)[arguments]: Remove trailing #T from build phases.
* | gnu: dropseq-tools: Remove reference to %build-inputs.Ricardo Wurmus2021-12-05
| | | | | | | | | | * gnu/packages/bioinformatics.scm (dropseq-tools)[arguments]: Remove reference to %build-inputs by using a gexp.
* | gnu: dropseq-tools: Remove trailing #T.Ricardo Wurmus2021-12-05
| | | | | | | | | | | | * gnu/packages/bioinformatics.scm (dropseq-tools)[arguments]: Remove trailing #T from build phases... [source]: ...and from the snippet.
* | gnu: Adjust for python-build-system behavior change.Marius Bakke2021-12-05
| | | | | | | | | | | | | | | | | | | | Commit cb72f9a773e0931ee3758c851d96007ded034e4c changed the semantics of SITE-PACKAGES, but did not adjust all callers. * gnu/packages/bioinformatics.scm (python-pyvcf)[arguments]: Adjust for missing trailing slash. * gnu/packages/maths.scm (nomad-optimizer)[arguments]: Likewise. * gnu/packages/patchutils.scm (patchwork)[arguments]: Likewise.
* | gnu: python-pyvcf: Fix bytecode compilation.Marius Bakke2021-12-05
| | | | | | | | | | * gnu/packages/bioinformatics.scm (python-pyvcf)[arguments]: Add phase to patch sample script.
* | gnu: salmon: Remove reference to %build-inputs.Ricardo Wurmus2021-12-05
| | | | | | | | | | * gnu/packages/bioinformatics.scm (salmon)[arguments]: Use a gexp to remove reference to %build-inputs.
* | gnu: sailfish: Remove references to %build-inputs.Ricardo Wurmus2021-12-04
| | | | | | | | | | * gnu/packages/bioinformatics.scm (sailfish)[arguments]: Use a gexp to remove references to %build-inputs.
* | gnu: sailfish: Simplify snippet.Ricardo Wurmus2021-12-04
| | | | | | | | | | * gnu/packages/bioinformatics.scm (sailfish)[source]: Remove trailing #T from snippet.
* | gnu: piranha: Remove references to %build-inputs.Ricardo Wurmus2021-12-04
| | | | | | | | | | * gnu/packages/bioinformatics.scm (piranha)[arguments]: Use gexp to remove references to %build-inputs.
* | gnu: piranha: Remove trailing #T.Ricardo Wurmus2021-12-04
| | | | | | | | | | * gnu/packages/bioinformatics.scm (piranha)[arguments]: Remove trailing #T from build phases.
* | gnu: emboss: Remove reference to %build-inputs.Ricardo Wurmus2021-12-04
| | | | | | | | | | * gnu/packages/bioinformatics.scm (emboss)[arguments]: Use gexp to remove reference to %build-inputs.
* | gnu: vcftools: Replace references to %outputs.Ricardo Wurmus2021-12-04
| | | | | | | | | | * gnu/packages/bioinformatics.scm (vcftools)[arguments]: Use gexp to remove references to %outputs.
* | gnu: seqan-1: Use gexp for builder.Ricardo Wurmus2021-12-04
| | | | | | | | | | * gnu/packages/bioinformatics.scm (seqan-1)[arguments]: Use a gexp to remove references to %build-inputs and %outputs.
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