| Age | Commit message (Expand) | Author |
|---|---|---|
| 2021-12-05 | gnu: sjcount: Remove trailing #T.•••* gnu/packages/bioinformatics.scm (sjcount)[arguments]: Remove trailing #T from build phases. | Ricardo Wurmus |
| 2021-12-05 | 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 | 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 | 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 | gnu: python-pyvcf: Fix bytecode compilation.•••* gnu/packages/bioinformatics.scm (python-pyvcf)[arguments]: Add phase to patch sample script. | Marius Bakke |
| 2021-12-05 | gnu: minimap2: Update to 2.23.•••* gnu/packages/bioinformatics.scm (minimap2): Update to 2.23. | Efraim Flashner |
| 2021-12-05 | gnu: salmon: Remove reference to %build-inputs.•••* gnu/packages/bioinformatics.scm (salmon)[arguments]: Use a gexp to remove reference to %build-inputs. | Ricardo Wurmus |
| 2021-12-04 | 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 | gnu: sailfish: Simplify snippet.•••* gnu/packages/bioinformatics.scm (sailfish)[source]: Remove trailing #T from snippet. | Ricardo Wurmus |
| 2021-12-04 | 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 | gnu: piranha: Remove trailing #T.•••* gnu/packages/bioinformatics.scm (piranha)[arguments]: Remove trailing #T from build phases. | Ricardo Wurmus |
| 2021-12-04 | 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 | gnu: vcftools: Replace references to %outputs.•••* gnu/packages/bioinformatics.scm (vcftools)[arguments]: Use gexp to remove references to %outputs. | Ricardo Wurmus |
| 2021-12-04 | 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 | gnu: seqan-2: Use gexp for builder.•••* gnu/packages/bioinformatics.scm (seqan-2)[arguments]: Use a gexp to remove references to %build-inputs and %outputs. | Ricardo Wurmus |
| 2021-12-04 | gnu: sra-tools: Remove references to %build-inputs.•••* gnu/packages/bioinformatics.scm (sra-tools)[arguments]: Use a gexp instead of referencing %build-inputs. | Ricardo Wurmus |
| 2021-12-04 | gnu: preseq: Remove references to %outputs and %build-inputs.•••* gnu/packages/bioinformatics.scm (preseq)[arguments]: Replace references to %outputs and %build-inputs by using a gexp. | Ricardo Wurmus |
| 2021-12-04 | gnu: preseq: Simplify snippet.•••* gnu/packages/bioinformatics.scm (preseq)[source]: Simplify snippet. | Ricardo Wurmus |
| 2021-12-04 | gnu: plink-ng: Enable tests.•••* gnu/packages/bioinformatics.scm (plink-ng)[arguments]: Replace 'check phase to run tests; do not disable tests via arguments. [native-inputs]: Add diffutils, plink, and python. | Ricardo Wurmus |
| 2021-12-04 | gnu: plink-ng: Replace reference to %outputs.•••* gnu/packages/bioinformatics.scm (plink-ng)[arguments]: Remove reference to %outputs by using a gexp. | Ricardo Wurmus |
| 2021-12-04 | gnu: plink: Remove reference to %build-inputs.•••* gnu/packages/bioinformatics.scm (plink)[arguments]: Use a gexp to replace reference to %build-inputs. | Ricardo Wurmus |
| 2021-12-04 | gnu: plink: Remove trailing #T.•••* gnu/packages/bioinformatics.scm (plink)[arguments]: Remove trailing #T from build phase. | Ricardo Wurmus |
| 2021-12-04 | gnu: rsem: Update to 1.3.3.•••* gnu/packages/bioinformatics.scm (rsem): Update to 1.3.3. [arguments]: Build with gnu++11 standard; patch sources for compatibility. | Ricardo Wurmus |
| 2021-12-04 | gnu: rsem: Remove trailing #T.•••* gnu/packages/bioinformatics.scm (rsem)[arguments]: Remove trailing #T from build phases. | Ricardo Wurmus |
| 2021-12-04 | gnu: rsem: Remove references to %build-inputs.•••* gnu/packages/bioinformatics.scm (rsem)[arguments]: Use a gexp. | Ricardo Wurmus |
| 2021-12-04 | gnu: rsem: Remove trailing #T from snippet.•••* gnu/packages/bioinformatics.scm (rsem)[source]: Remove trailing #T. | Ricardo Wurmus |
| 2021-12-04 | gnu: prodigal: Remove reference to %outputs.•••* gnu/packages/bioinformatics.scm (prodigal)[arguments]: Remove reference to %outputs by using a gexp. | Ricardo Wurmus |
| 2021-12-04 | gnu: prank: Bind INPUTS in 'install phase.•••* gnu/packages/bioinformatics.scm (prank)[arguments]: Bind INPUTS in 'install phase to remove references to %build-inputs. | Ricardo Wurmus |
| 2021-12-04 | gnu: prank: Remove trailing #T.•••* gnu/packages/bioinformatics.scm (prank)[arguments]: Remove trailing #T from build phases. | Ricardo Wurmus |
| 2021-12-04 | 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 | gnu: mash: Replace references to %build-inputs.•••* gnu/packages/bioinformatics.scm (mash)[arguments]: Use a gexp. | Ricardo Wurmus |
| 2021-12-04 | gnu: mash: Move htslib and capnproto to regular inputs.•••* gnu/packages/bioinformatics.scm (mash)[native-inputs]: Move htslib and capnproto from here... [inputs]: ...to here. | Ricardo Wurmus |
| 2021-12-04 | gnu: mash: Simplify snippet.•••* gnu/packages/bioinformatics.scm (mash)[snippet]: Simplify. | Ricardo Wurmus |
| 2021-12-04 | gnu: mafft: Remove trailing #T.•••* gnu/packages/bioinformatics.scm (mafft)[arguments]: Remove trailing #T from build phase. | Ricardo Wurmus |
| 2021-12-04 | gnu: mafft: Replace references to %build-inputs and %outputs.•••* gnu/packages/bioinformatics.scm (mafft)[arguments]: Replace references to %outputs with a gexp; replace reference to %build-inputs in the 'wrap-programs phase by binding INPUTS. | Ricardo Wurmus |
| 2021-12-04 | gnu: jellyfish: Replace reference to %outputs.•••* gnu/packages/bioinformatics.scm (jellyfish)[arguments]: Use a gexp. | Ricardo Wurmus |
| 2021-12-04 | gnu: fastp: Replace reference to %outputs.•••* gnu/packages/bioinformatics.scm (fastp)[arguments]: Use a gexp. | Ricardo Wurmus |
| 2021-12-04 | gnu: java-picard: Replace reference to %build-inputs.•••* gnu/packages/bioinformatics.scm (java-picard): Use a gexp. | Ricardo Wurmus |
| 2021-12-04 | gnu: java-htsjdk: Replace reference to %outputs.•••* gnu/packages/bioinformatics.scm (java-htsjdk)[arguments]: Use a gexp. | Ricardo Wurmus |
| 2021-12-04 | gnu: fxtract: Replace reference to %outputs.•••* gnu/packages/bioinformatics.scm (fxtract)[arguments]: Use a gexp. | Ricardo Wurmus |
| 2021-12-04 | gnu: delly: Replace reference to %outputs.•••* gnu/packages/bioinformatics.scm (delly)[arguments]: Replace reference to %outputs with a gexp. | Ricardo Wurmus |
| 2021-12-03 | gnu: libbigwig: Replace reference to %outputs.•••* gnu/packages/bioinformatics.scm (libbigwig)[arguments]: Replace reference to %outputs with a gexp. | Ricardo Wurmus |
| 2021-12-03 | gnu: cd-hit: Replace reference to %outputs.•••* gnu/packages/bioinformatics.scm (cd-hit)[arguments]: Replace reference to %outputs with gexp. | Ricardo Wurmus |
| 2021-12-03 | gnu: bowtie1: Replace reference to %outputs.•••* gnu/packages/bioinformatics.scm (bowtie1)[arguments]: Remove reference to %outputs by using a gexp. | Ricardo Wurmus |
| 2021-12-03 | gnu: bowtie: Remove reference to %outputs.•••* gnu/packages/bioinformatics.scm (bowtie)[arguments]: Replace reference to %outputs with a gexp. | Ricardo Wurmus |
| 2021-12-03 | gnu: bless: Remove reference to %build-inputs.•••* gnu/packages/bioinformatics.scm (bless)[arguments]: Replace reference to %build-inputs with a gexp. Use the dynamic library of zlib while we're at it. [inputs]: Remove zlib:static. | Ricardo Wurmus |
| 2021-12-03 | gnu: bless: Remove trailing #T from snippet and build phases.•••* gnu/packages/bioinformatics.scm (bless)[source, arguments]: Remove all trailing #Ts. | Ricardo Wurmus |
| 2021-12-03 | gnu: bedtools: Remove reference to %outputs.•••* gnu/packages/bioinformatics.scm (bedtools)[arguments]: Use a gexp instead of referencing %outputs. | Ricardo Wurmus |
| 2021-12-03 | gnu: qtltools: Replace references to %build-inputs.•••* gnu/packages/bioinformatics.scm (qtltools)[arguments]: Use a gexp instead of referencing %build-inputs. | Ricardo Wurmus |
| 2021-12-03 | gnu: imp: Update to 2.15.0.•••* gnu/packages/bioinformatics.scm (imp): Update to 2.15.0. [arguments]: Disable one more test. | Ricardo Wurmus |
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