| Commit message (Expand) | Author | Age | Files | Lines | |
|---|---|---|---|---|---|
| * | Merge remote-tracking branch 'origin/master' into core-updates-frozen | Ricardo Wurmus | 2021-12-05 | 1 | -130/+164 |
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| | * | gnu: minimap2: Update to 2.23.•••* gnu/packages/bioinformatics.scm (minimap2): Update to 2.23. | Efraim Flashner | 2021-12-05 | 1 | -2/+2 |
| | * | gnu: pigx-sars-cov2-ww: Update to 0.0.4.•••* gnu/packages/bioinformatics.scm (pigx-sars-cov2-ww): Update to 0.0.4. [inputs]: Add bbmap, bedtools, fastp, ivar, and r-r-utils. | Ricardo Wurmus | 2021-12-04 | 1 | -2/+7 |
| | * | gnu: imp: Update to 2.15.0.•••* gnu/packages/bioinformatics.scm (imp): Update to 2.15.0. [arguments]: Disable one more test. | Ricardo Wurmus | 2021-12-03 | 1 | -3/+5 |
| | * | gnu: python-ont-fast5-api: Update to 4.0.0.•••* 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. | Ricardo Wurmus | 2021-12-03 | 1 | -3/+18 |
| | * | gnu: Add vbz-compression.•••* gnu/packages/bioinformatics.scm (vbz-compression): New variable. | Ricardo Wurmus | 2021-12-03 | 1 | -0/+37 |
| | * | gnu: ivar: Disable parallel tests.•••* gnu/packages/bioinformatics.scm (ivar)[arguments]: Disable parallel tests. | Ricardo Wurmus | 2021-12-03 | 1 | -0/+1 |
| | * | gnu: Remove python2-biom-format.•••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. | Ricardo Wurmus | 2021-12-03 | 1 | -17/+1 |
| | * | gnu: ribodiff: Remove trailing #T.•••* gnu/packages/bioinformatics.scm (ribodiff)[arguments]: Remove trailing #T from build phase. | Ricardo Wurmus | 2021-12-02 | 1 | -2/+1 |
| | * | gnu: ribodiff: Disable broken test.•••* gnu/packages/bioinformatics.scm (ribodiff)[arguments]: Add build phase 'disable-plot-test. | Ricardo Wurmus | 2021-12-02 | 1 | -0/+5 |
| | * | gnu: khmer: Fix build with Python 3.8.•••* gnu/packages/bioinformatics.scm (khmer)[source]: Remove trailing #T. [arguments]: Remove trailing #T from build phases; add build phase 'python-3.8-compatibility. | Ricardo Wurmus | 2021-12-02 | 1 | -6/+9 |
| | * | gnu: python-biom-format: Update to 2.1.10.•••* 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. | Ricardo Wurmus | 2021-12-02 | 1 | -15/+16 |
| | * | gnu: pardre: Update to 2.2.5.•••* gnu/packages/bioinformatics.scm (pardre): Update to 2.2.5. [arguments]: Remove trailing #T and update comment about tests. | Ricardo Wurmus | 2021-12-02 | 1 | -7/+5 |
| | * | gnu: pardre: Use C++ bindings for MPI.•••* gnu/packages/bioinformatics.scm (pardre)[inputs]: Replace openmpi with openmpi-c++. | Ricardo Wurmus | 2021-12-02 | 1 | -1/+1 |
| | * | gnu: Add python-mygene.•••* gnu/packages/bioinformatics.scm (python-mygene): New variable. | Ricardo Wurmus | 2021-12-02 | 1 | -0/+21 |
| | * | gnu: Add python-biothings-client.•••* gnu/packages/bioinformatics.scm (python-biothings-client): New variable. | Ricardo Wurmus | 2021-12-02 | 1 | -0/+19 |
| | * | gnu: Remove couger.•••This package has been moved to the Guix Past channel. * gnu/packages/bioinformatics.scm (couger): Remove variable. | Ricardo Wurmus | 2021-12-02 | 1 | -71/+0 |
| | * | gnu: r-umi4cpackage: Embed references to perl and bowtie2.•••* 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. | Ricardo Wurmus | 2021-11-30 | 1 | -1/+16 |
| * | | 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 | 1 | -0/+10 |
| * | | gnu: Remove python2-plastid.•••* gnu/packages/bioinformatics.scm (python2-plastid): Remove variable. | Ricardo Wurmus | 2021-12-05 | 1 | -3/+0 |
| * | | gnu: Remove python2-twobitreader.•••* gnu/packages/bioinformatics.scm (python2-twobitreader): Remove variable. | Ricardo Wurmus | 2021-12-05 | 1 | -3/+0 |
| * | | 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 | 1 | -1/+8 |
| * | | gnu: python-bbknn: Add missing input.•••* gnu/packages/bioinformatics.scm (python-bbknn)[propagated-inputs]: Add python-scikit-learn. | Ricardo Wurmus | 2021-12-05 | 1 | -0/+1 |
| * | | gnu: velvet: Add missing TeX package.•••* gnu/packages/bioinformatics.scm (velvet)[native-inputs]: Add texlive-fonts-ec. | Ricardo Wurmus | 2021-12-05 | 1 | -1/+2 |
| * | | gnu: velvet: Remove trailing #T.•••* gnu/packages/bioinformatics.scm (velvet)[arguments]: Remove trailing #T from build phases. | Ricardo Wurmus | 2021-12-05 | 1 | -6/+3 |
| * | | 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 | 1 | -1/+4 |
| * | | gnu: metabat: Remove trailing #T.•••* gnu/packages/bioinformatics.scm (metabat)[arguments]: Remove trailing #T from build phases. | Ricardo Wurmus | 2021-12-05 | 1 | -4/+2 |
| * | | 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 | 1 | -3/+3 |
| * | | 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 | 1 | -4/+3 |
| * | | 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 | 1 | -2/+2 |
| * | | 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 | 1 | -7/+7 |
| * | | 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 | 1 | -5/+5 |
| * | | 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 | 1 | -3/+3 |
| * | | 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 | 1 | -3/+3 |
| * | | 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 | 1 | -3/+3 |
| * | | gnu: biobambam2: Remove reference to %build-inputs.•••* gnu/packages/bioinformatics.scm (biobambam2)[arguments]: Remove reference to %build-inputs by using a gexp. | Ricardo Wurmus | 2021-12-05 | 1 | -2/+2 |
| * | | gnu: sjcount: Remove reference to %build-inputs.•••* gnu/packages/bioinformatics.scm (sjcount)[arguments]: Remove reference to %build-inputs by using a gexp. | Ricardo Wurmus | 2021-12-05 | 1 | -3/+3 |
| * | | gnu: sjcount: Remove trailing #T.•••* gnu/packages/bioinformatics.scm (sjcount)[arguments]: Remove trailing #T from build phases. | Ricardo Wurmus | 2021-12-05 | 1 | -4/+2 |
| * | | gnu: dropseq-tools: Remove reference to %build-inputs.•••* gnu/packages/bioinformatics.scm (dropseq-tools)[arguments]: Remove reference to %build-inputs by using a gexp. | Ricardo Wurmus | 2021-12-05 | 1 | -3/+3 |
| * | | gnu: dropseq-tools: Remove trailing #T.•••* gnu/packages/bioinformatics.scm (dropseq-tools)[arguments]: Remove trailing #T from build phases... [source]: ...and from the snippet. | Ricardo Wurmus | 2021-12-05 | 1 | -8/+4 |
| * | | gnu: Adjust for python-build-system behavior change.•••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. | Marius Bakke | 2021-12-05 | 1 | -2/+1 |
| * | | gnu: python-pyvcf: Fix bytecode compilation.•••* gnu/packages/bioinformatics.scm (python-pyvcf)[arguments]: Add phase to patch sample script. | Marius Bakke | 2021-12-05 | 1 | -0/+6 |
| * | | gnu: salmon: Remove reference to %build-inputs.•••* gnu/packages/bioinformatics.scm (salmon)[arguments]: Use a gexp to remove reference to %build-inputs. | Ricardo Wurmus | 2021-12-05 | 1 | -9/+9 |
| * | | gnu: sailfish: Remove references to %build-inputs.•••* gnu/packages/bioinformatics.scm (sailfish)[arguments]: Use a gexp to remove references to %build-inputs. | Ricardo Wurmus | 2021-12-04 | 1 | -17/+17 |
| * | | gnu: sailfish: Simplify snippet.•••* gnu/packages/bioinformatics.scm (sailfish)[source]: Remove trailing #T from snippet. | Ricardo Wurmus | 2021-12-04 | 1 | -4/+2 |
| * | | gnu: piranha: Remove references to %build-inputs.•••* gnu/packages/bioinformatics.scm (piranha)[arguments]: Use gexp to remove references to %build-inputs. | Ricardo Wurmus | 2021-12-04 | 1 | -4/+4 |
| * | | gnu: piranha: Remove trailing #T.•••* gnu/packages/bioinformatics.scm (piranha)[arguments]: Remove trailing #T from build phases. | Ricardo Wurmus | 2021-12-04 | 1 | -4/+2 |
| * | | gnu: emboss: Remove reference to %build-inputs.•••* gnu/packages/bioinformatics.scm (emboss)[arguments]: Use gexp to remove reference to %build-inputs. | Ricardo Wurmus | 2021-12-04 | 1 | -2/+2 |
| * | | gnu: vcftools: Replace references to %outputs.•••* gnu/packages/bioinformatics.scm (vcftools)[arguments]: Use gexp to remove references to %outputs. | Ricardo Wurmus | 2021-12-04 | 1 | -5/+5 |
| * | | gnu: seqan-1: Use gexp for builder.•••* gnu/packages/bioinformatics.scm (seqan-1)[arguments]: Use a gexp to remove references to %build-inputs and %outputs. | Ricardo Wurmus | 2021-12-04 | 1 | -12/+11 |
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