| Age | Commit message (Expand) | Author |
|---|
| 2023-07-18 | gnu: newick-utils: Skip tests on riscv64-linux.•••* gnu/packages/bioinformatics.scm (newick-utils)[arguments]: Skip tests
when building on riscv64-linux.
| 宋文武 |
| 2023-07-17 | gnu: Hide python-bcbio-gff/biopython-1.73.•••To avoid the ambiguous package specification.
* gnu/packages/bioinformatics.scm (python-bcbio-gff/biopython-1.73): Hide
package.
| Christopher Baines |
| 2023-07-15 | gnu: r-pando: Relax requirements.•••* gnu/packages/bioinformatics.scm (r-pando)[arguments]: Patch DESCRIPTION
file.
| Ricardo Wurmus |
| 2023-07-09 | gnu: bwa-pssm: Update home page.•••* gnu/packages/bioinformatics.scm (bwa-pssm)[home-page]: Update.
| Tobias Geerinckx-Rice |
| 2023-07-09 | gnu: blasr-libcpp, blasr: Use Web Archived home pages.•••* gnu/packages/bioinformatics.scm (blasr-libcpp, blasr)[home-page]:
Refer to Web Archive.
| Tobias Geerinckx-Rice |
| 2023-07-12 | gnu: Add r-numbat.•••* gnu/packages/bioinformatics.scm (r-numbat): New variable.
| Ricardo Wurmus |
| 2023-07-12 | gnu: Add r-bpcells.•••* gnu/packages/bioinformatics.scm (r-bpcells): New variable.
| Ricardo Wurmus |
| 2023-07-06 | gnu: r-pando: Fix hash.•••* gnu/packages/bioinformatics.scm (r-pando)[source]: Update hash.
| Ricardo Wurmus |
| 2023-07-06 | gnu: bismark: Update to 0.24.1.•••* gnu/packages/bioinformatics.scm (bismark): Update to 0.24.1.
[source]: Delete bundled plot.ly.
[arguments]: Use plain list; remove trailing #T from build phases; adjust
'replace-plotly.js phase to account for use of script tags; adjust 'install
phase to install documentation in markdown format; add 'configure phase for
replacing references to tools.
[inputs]: Add bowtie, hisat2, minimap2, and samtools.
| Ricardo Wurmus |
| 2023-07-03 | gnu: cutadapt: Update to 4.0.•••* gnu/packages/bioinformatics.scm (cutadapt): Update to 4.0.
[build-system]: Use pyproject-build-system.
[arguments]: Disable a single test; remove 'always-cythonize build phase; add
phase 'fix-test.
[native-inputs]: Add python-pytest-mock and python-pytest-timeout.
| Ricardo Wurmus |
| 2023-07-03 | gnu: python-dnaio: Update to 0.10.0.•••* gnu/packages/bioinformatics.scm (python-dnaio): Update to 0.10.0.
[arguments]: Disable tests, because they don't exist.
[build-system]: Use pyproject-build-system.
[native-inputs]: Add python-setuptools-scm; move python-xopen from here...
[propagated-inputs]: ...to here.
| Ricardo Wurmus |
| 2023-07-03 | gnu: Add r-dtmm.•••* gnu/packages/bioinformatics.scm (r-dtmm): New variable.
| Navid Afkhami |
| 2023-06-29 | gnu: Add rscape.•••* gnu/packages/bioinformatics.scm (rscape): New variable.
Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
| Navid Afkhami |
| 2023-06-29 | gnu: r-pando: Update to 1.0.5.•••* gnu/packages/bioinformatics.scm (r-pando): Update to 1.0.5.
[propagated-inputs]: Remove r-brms and r-xgboost; add r-grr and
r-matrixgenerics.
| Ricardo Wurmus |
| 2023-06-22 | gnu: sambamba: Fix building.•••* gnu/packages/bioinformatics.scm (sambamba)[native-inputs]: Remove
ld-gold-wrapper, bintutils-gold. Remove input labels.
| Efraim Flashner |
| 2023-06-20 | gnu: bioruby: Update to 2.0.4.•••* gnu/packages/bioinformatics.scm (bioruby): Update to 2.0.4.
[arguments]: Update style.
| Christopher Baines |
| 2023-06-09 | gnu: Add python-mudata.•••* gnu/packages/bioinformatics.scm (python-mudata): New variable.
Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
| Navid Afkhami |
| 2023-06-09 | gnu: Add python-mofax.•••* gnu/packages/bioinformatics.scm (python-mofax): New variable.
Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
| Navid Afkhami |
| 2023-06-06 | gnu: Add python-decoupler-py.•••* gnu/packages/bioinformatics.scm (python-decoupler-py): New variable.
Co-authored-by: Ricardo Wurmus <rekado@elephly.net>.
| Navid Afkhami |
| 2023-06-05 | gnu: python-bulkvis: Reference upstream issue.•••* gnu/packages/bioinformatics.scm (python-bulkvis)[arguments]: Add comment
with link to upstream issue for bokeh compatibility patch.
| Ricardo Wurmus |
| 2023-06-05 | gnu: Add python-bulkvis.•••* gnu/packages/bioinformatics.scm (python-bulkvis): New variable.
Co-authored-by: Ricardo Wurmus <rekado@elephly.net>
| Navid Afkhami |
| 2023-06-05 | gnu: Add python-readpaf.•••* gnu/packages/bioinformatics.scm (python-readpaf): New variable.
| Navid Afkhami |
| 2023-06-02 | gnu: Add r-singlet.•••* gnu/packages/bioinformatics.scm (r-singlet): New variable.
| Ricardo Wurmus |
| 2023-06-02 | gnu: Add python-cell2cell.•••* gnu/packages/bioinformatics.scm (python-cell2cell): New variable.
Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
| Navid Afkhami |
| 2023-06-02 | gnu: Add java-maxent.•••* gnu/packages/bioinformatics.scm (java-maxent): New variable.
| Ricardo Wurmus |
| 2023-06-01 | gnu: Add python-pyani.•••* gnu/packages/bioinformatics.scm (python-pyani): New variable.
| Ricardo Wurmus |
| 2023-06-01 | gnu: Add python-illumina-utils.•••* gnu/packages/bioinformatics.scm (python-illumina-utils): New variable.
| Ricardo Wurmus |
| 2023-06-01 | gnu: Add python-ete3.•••* gnu/packages/bioinformatics.scm (python-ete3): New variable.
| Ricardo Wurmus |
| 2023-05-26 | gnu: Add python-gseapy.•••* gnu/packages/bioinformatics.scm (python-gseapy): New variable.
| Ricardo Wurmus |
| 2023-05-19 | gnu: java-picard-1.113: Drop input package labels.•••* gnu/packages/bioinformatics.scm (java-picard-1.113)[inputs]: Drop labels.
| Ricardo Wurmus |
| 2023-05-19 | gnu: java-picard-1.113: Drop trailing #T from build phases.•••* gnu/packages/bioinformatics.scm (java-picard-1.113)[arguments]: Remove
trailing #T from build phases.
| Ricardo Wurmus |
| 2023-05-14 | gnu: discrover: Remove package labels.•••* gnu/packages/bioinformatics.scm (discrover)[native-inputs]: Remove package
labels.
| Ricardo Wurmus |
| 2023-05-14 | gnu: diamond: Update to 2.1.6.•••* gnu/packages/bioinformatics.scm (diamond): Update to 2.1.6.
[arguments]: Do not disable tests; pass configure flag to avoid SSE4 and AVX2
in the interest of compatibility.
[license]: Set to GPLv3+.
| Ricardo Wurmus |
| 2023-05-14 | gnu: delly: Simplify.•••* gnu/packages/bioinformatics.scm (delly)[source]: Simplify snippet.
[arguments]: Do not use quasiquote; simplify 'install-templates phase.
| Ricardo Wurmus |
| 2023-05-14 | gnu: python-pybigwig: Update to 0.3.22.•••* gnu/packages/bioinformatics.scm (python-pybigwig): Update to 0.3.22.
[source]: Simplify snippet.
[arguments]: Explicitly disable tests; simplify 'link-with-libBigWig phase.
[build-system]: Use pyproject-build-system.
| Ricardo Wurmus |
| 2023-05-14 | gnu: codingquarry: Use G-expression.•••* gnu/packages/bioinformatics.scm (codingquarry)[arguments]: Use G-expression
to simplify 'install phase. Install files to /share/codingquarry prefix.
[native-search-paths]: Adjust prefix.
[native-inputs]: Move python-2 from here...
[inputs]: ...to here.
| Ricardo Wurmus |
| 2023-05-14 | gnu: blast+: Update to 2.14.0.•••* gnu/packages/bioinformatics.scm (blast+): Update to 2.14.0.
[arguments]: Remove trailing #T from build phases; let WHICH* return #FALSE on
failure; use G-expression.
[inputs]: Drop package labels.
| Ricardo Wurmus |
| 2023-05-12 | gnu: jamm: Use G-expression.•••* gnu/packages/bioinformatics.scm (jamm)[arguments]: Use G-expression.
| Ricardo Wurmus |
| 2023-05-12 | gnu: arriba: Use SEARCH-INPUT-FILE and -DIRECTORY.•••* gnu/packages/bioinformatics.scm (arriba)[arguments]:
Use SEARCH-INPUT-DIRECTORY and SEARCH-INPUT-FILE; use G-expression; drop
trailing #T from build phases.
| Ricardo Wurmus |
| 2023-05-12 | gnu: multichoose: Clean up.•••* gnu/packages/bioinformatics.scm (multichoos): Fix indentation.
[arguments]: Use G-expression.
| Ricardo Wurmus |
| 2023-05-12 | gnu: samblaster: Update to 0.1.26.•••* gnu/packages/bioinformatics.scm (samblaster): Update to 0.1.26.
| Ricardo Wurmus |
| 2023-05-12 | gnu: samblaster: Simplify.•••* gnu/packages/bioinformatics.scm (samblaster): Fix indentation.
[arguments]: Use G-expression; drop trailing #T from 'install phase.
[description]: Use double spacing between all sentences.
| Ricardo Wurmus |
| 2023-05-12 | gnu: methyldackel: Update to 0.6.1.•••* gnu/packages/bioinformatics.scm (methyldackel): Update to 0.6.1.
[arguments]: Set LIBBIGWIG variable instead of patching Makefile.
[inputs]: Replace htslib-1.9 with htslib.
| Ricardo Wurmus |
| 2023-05-12 | gnu: methyldackel: Simplify arguments.•••* gnu/packages/bioinformatics.scm (methyldackel)[arguments]: Use list, drop
argument list.
[native-inputs]: Drop package label.
| Ricardo Wurmus |
| 2023-05-12 | gnu: phast: Simplify by using G-expression.•••* gnu/packages/bioinformatics.scm (phast)[arguments]: Use G-expression and
drop trailing #T from build phases.
| Ricardo Wurmus |
| 2023-05-12 | gnu: ribotaper: Simplify with G-expression.•••* gnu/packages/bioinformatics.scm (ribotaper)[arguments]: Use G-expression and
drop trailing #T from build phase.
| Ricardo Wurmus |
| 2023-05-12 | gnu: sra-tools: Do link with libxml2.•••* gnu/packages/bioinformatics.scm (sra-tools)[arguments]: Use G-expression for
clarity; drop trailing #T from build phases; modify 'configure phase to
dynamically link with libxml2.
[inputs]: Drop package labels; add libxml2.
| Ricardo Wurmus |
| 2023-05-12 | gnu: ncbi-vdb: Ensure that vdb-sqlite is installed.•••The most important change here is the addition of the 'install-libs phase.
All other changes are just the result of switching to G-expressions.
* gnu/packages/bioinformatics.scm (ncbi-vdb)[arguments]: Add 'install-libs
phase; use G-expression; drop trailing #T from build phases.
[inputs]: Drop package labels.
| Ricardo Wurmus |
| 2023-05-12 | gnu: Add python-mgatk.•••* gnu/packages/bioinformatics.scm (python-mgatk): New variable.
Co-authored-by: Ricardo Wurmus <rekado@elephly.net>
| Mădălin Ionel Patrașcu |
| 2023-05-08 | gnu: Add homer.•••* gnu/packages/bioinformatics.scm (homer): New variable.
| Ricardo Wurmus |
