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2023-07-12gnu: Add r-numbat.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-numbat): New variable.
2023-07-12gnu: Add r-bpcells.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-bpcells): New variable.
2023-07-06gnu: r-pando: Fix hash.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-pando)[source]: Update hash.
2023-07-06gnu: bismark: Update to 0.24.1.Ricardo Wurmus
* 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.
2023-07-03gnu: cutadapt: Update to 4.0.Ricardo Wurmus
* 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.
2023-07-03gnu: python-dnaio: Update to 0.10.0.Ricardo Wurmus
* 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.
2023-07-03gnu: Add r-dtmm.Navid Afkhami
* gnu/packages/bioinformatics.scm (r-dtmm): New variable.
2023-06-29gnu: Add rscape.Navid Afkhami
* gnu/packages/bioinformatics.scm (rscape): New variable. Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
2023-06-29gnu: r-pando: Update to 1.0.5.Ricardo Wurmus
* 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.
2023-06-22gnu: sambamba: Fix building.Efraim Flashner
* gnu/packages/bioinformatics.scm (sambamba)[native-inputs]: Remove ld-gold-wrapper, bintutils-gold. Remove input labels.
2023-06-20gnu: bioruby: Update to 2.0.4.Christopher Baines
* gnu/packages/bioinformatics.scm (bioruby): Update to 2.0.4. [arguments]: Update style.
2023-06-09gnu: Add python-mudata.Navid Afkhami
* gnu/packages/bioinformatics.scm (python-mudata): New variable. Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
2023-06-09gnu: Add python-mofax.Navid Afkhami
* gnu/packages/bioinformatics.scm (python-mofax): New variable. Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
2023-06-06gnu: Add python-decoupler-py.Navid Afkhami
* gnu/packages/bioinformatics.scm (python-decoupler-py): New variable. Co-authored-by: Ricardo Wurmus <rekado@elephly.net>.
2023-06-05gnu: python-bulkvis: Reference upstream issue.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (python-bulkvis)[arguments]: Add comment with link to upstream issue for bokeh compatibility patch.
2023-06-05gnu: Add python-bulkvis.Navid Afkhami
* gnu/packages/bioinformatics.scm (python-bulkvis): New variable. Co-authored-by: Ricardo Wurmus <rekado@elephly.net>
2023-06-05gnu: Add python-readpaf.Navid Afkhami
* gnu/packages/bioinformatics.scm (python-readpaf): New variable.
2023-06-02gnu: Add r-singlet.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-singlet): New variable.
2023-06-02gnu: Add python-cell2cell.Navid Afkhami
* gnu/packages/bioinformatics.scm (python-cell2cell): New variable. Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
2023-06-02gnu: Add java-maxent.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (java-maxent): New variable.
2023-06-01gnu: Add python-pyani.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (python-pyani): New variable.
2023-06-01gnu: Add python-illumina-utils.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (python-illumina-utils): New variable.
2023-06-01gnu: Add python-ete3.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (python-ete3): New variable.
2023-05-26gnu: Add python-gseapy.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (python-gseapy): New variable.
2023-05-19gnu: java-picard-1.113: Drop input package labels.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (java-picard-1.113)[inputs]: Drop labels.
2023-05-19gnu: java-picard-1.113: Drop trailing #T from build phases.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (java-picard-1.113)[arguments]: Remove trailing #T from build phases.
2023-05-14gnu: discrover: Remove package labels.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (discrover)[native-inputs]: Remove package labels.
2023-05-14gnu: diamond: Update to 2.1.6.Ricardo Wurmus
* 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+.
2023-05-14gnu: delly: Simplify.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (delly)[source]: Simplify snippet. [arguments]: Do not use quasiquote; simplify 'install-templates phase.
2023-05-14gnu: python-pybigwig: Update to 0.3.22.Ricardo Wurmus
* 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.
2023-05-14gnu: codingquarry: Use G-expression.Ricardo Wurmus
* 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.
2023-05-14gnu: blast+: Update to 2.14.0.Ricardo Wurmus
* 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.
2023-05-12gnu: jamm: Use G-expression.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (jamm)[arguments]: Use G-expression.
2023-05-12gnu: arriba: Use SEARCH-INPUT-FILE and -DIRECTORY.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (arriba)[arguments]: Use SEARCH-INPUT-DIRECTORY and SEARCH-INPUT-FILE; use G-expression; drop trailing #T from build phases.
2023-05-12gnu: multichoose: Clean up.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (multichoos): Fix indentation. [arguments]: Use G-expression.
2023-05-12gnu: samblaster: Update to 0.1.26.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (samblaster): Update to 0.1.26.
2023-05-12gnu: samblaster: Simplify.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (samblaster): Fix indentation. [arguments]: Use G-expression; drop trailing #T from 'install phase. [description]: Use double spacing between all sentences.
2023-05-12gnu: methyldackel: Update to 0.6.1.Ricardo Wurmus
* 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.
2023-05-12gnu: methyldackel: Simplify arguments.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (methyldackel)[arguments]: Use list, drop argument list. [native-inputs]: Drop package label.
2023-05-12gnu: phast: Simplify by using G-expression.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (phast)[arguments]: Use G-expression and drop trailing #T from build phases.
2023-05-12gnu: ribotaper: Simplify with G-expression.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (ribotaper)[arguments]: Use G-expression and drop trailing #T from build phase.
2023-05-12gnu: sra-tools: Do link with libxml2.Ricardo Wurmus
* 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.
2023-05-12gnu: ncbi-vdb: Ensure that vdb-sqlite is installed.Ricardo Wurmus
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.
2023-05-12gnu: Add python-mgatk.Mădălin Ionel Patrașcu
* gnu/packages/bioinformatics.scm (python-mgatk): New variable. Co-authored-by: Ricardo Wurmus <rekado@elephly.net>
2023-05-08gnu: Add homer.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (homer): New variable.
2023-05-05Revert "gnu: Add python-gimmemotifs."Ricardo Wurmus
This reverts commit dc8b3ebe5d4ba2a39c12f62d836963ffee1e4b47. python-gimmemotifs is not usable without proprietary third-party tools.
2023-05-05gnu: Add python-gimmemotifs.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (python-gimmemotifs): New variable.
2023-05-05gnu: Add python-biofluff.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (python-biofluff): New variable.
2023-05-05gnu: Add python-genomepy.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (python-genomepy): New variable.
2023-05-05gnu: Add python-logomaker.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (python-logomaker): New variable.
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