| Age | Commit message (Expand) | Author |
|---|
| 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 |
| 2023-05-05 | Revert "gnu: Add python-gimmemotifs."...This reverts commit dc8b3ebe5d4ba2a39c12f62d836963ffee1e4b47.
python-gimmemotifs is not usable without proprietary third-party tools.
| Ricardo Wurmus |
| 2023-05-05 | gnu: Add python-gimmemotifs....* gnu/packages/bioinformatics.scm (python-gimmemotifs): New variable.
| Ricardo Wurmus |
| 2023-05-05 | gnu: Add python-biofluff....* gnu/packages/bioinformatics.scm (python-biofluff): New variable.
| Ricardo Wurmus |
| 2023-05-05 | gnu: Add python-genomepy....* gnu/packages/bioinformatics.scm (python-genomepy): New variable.
| Ricardo Wurmus |
| 2023-05-05 | gnu: Add python-logomaker....* gnu/packages/bioinformatics.scm (python-logomaker): New variable.
| Ricardo Wurmus |
| 2023-05-05 | gnu: python-pyfaidx: Update to 0.7.2.1....* gnu/packages/bioinformatics.scm (python-pyfaidx): Update to 0.7.2.1.
[build-system]: Use pyproject-build-system.
[arguments]: Ignore tests that require large downloads.
[native-inputs]: Remove python-six; add python-fsspec, python-pytest,
python-pytest-cov, python-mock, and python-numpy.
| Ricardo Wurmus |
| 2023-05-04 | gnu: python-screed: Update to 1.1.2....* gnu/packages/bioinformatics.scm (python-screed): Update to 1.1.2.
[build-system]: Use pyproject-build-system.
[native-inputs]: Remove python-pytest.
[inputs]: Remove python-bz2file.
Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
| Mădălin Ionel Patrașcu |
| 2023-05-04 | gnu: Add python-goatools....* gnu/packages/bioinformatics.scm (python-goatools): New variable.
Co-authored-by: Ricardo Wurmus <rekado@elephly.net>
| Navid Afkhami |
| 2023-05-03 | gnu: pigx-sars-cov-2: Update to 0.0.9....* gnu/packages/bioinformatics.scm (pigx-sars-cov-2): Update to 0.0.9.
| Ricardo Wurmus |
| 2023-05-03 | gnu: Add fanc....* gnu/packages/bioinformatics.scm (fanc): New variable.
| Ricardo Wurmus |
| 2023-04-29 | gnu: r-tictoc: Update to 1.2....* gnu/packages/bioinformatics.scm (r-tictoc): Update to 1.2.
| Ricardo Wurmus |
| 2023-04-27 | gnu: gdcm: Disable dependent tests....* gnu/packages/bioinformatics.scm (gdcm)[arguments]: Disable tests that depend
on the output of a disabled test.
| Ricardo Wurmus |
| 2023-04-27 | gnu: freebayes: Update to 1.3.7....* gnu/packages/bioinformatics.scm (freebayes): Update to 1.3.7.
[arguments]: Do not use "grep -P" in tests; drop trailing #T.
| Ricardo Wurmus |
