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2023-07-18gnu: texlive-latex-examplep -> texlive-examplep.•••* gnu/packages/tex.scm (texlive-examplep): New variable. (texlive-latex-examplep): Deprecate variable. * gnu/packages/bioinformatics.scm (discrover)[native-inputs]: Use new name. Nicolas Goaziou
2023-07-18gnu: texlive-latex-verbatimbox -> texlive-verbatimbox.•••* gnu/packages/tex.scm (texlive-verbatimbox): New variable. (texlive-latex-verbatimbox): Deprecate variable. * gnu/packages/bioinformatics.scm (discrover)[native-inputs]: Use new name. Nicolas Goaziou
2023-07-18gnu: texlive-fonts-ec -> texlive-ec.•••* gnu/packages/tex.scm (texlive-ec): New variable. (texlive-fonts-ec): Deprecate variable. (lyx): (biber): * gnu/packages/python-xyz.scm (python-pypandoc): * gnu/packages/statistics.scm (r-with-tests): * doc/build.scm (pdf-manual): * gnu/packages/bioinformatics.scm (discrover): (phyml): (velvet): * gnu/packages/chemistry.scm (yaehmop): * gnu/packages/chez.scm (stex-bootstrap): * gnu/packages/ocaml.scm (unison): (ocaml-bibtex2html): * gnu/packages/plotutils.scm (asymptote): Use new name. Nicolas Goaziou
2023-07-18gnu: texlive-latex-psfrag -> texlive-psfrag.•••* gnu/packages/tex.scm (texlive-psfrag): New variable. (texlive-latex-psfrag): Deprecate variable. (texlive-pstool): * gnu/packages/bioinformatics.scm (phyml): Use new name. Nicolas Goaziou
2023-07-18gnu: texlive-latex-natbib -> texlive-natbib.•••* gnu/packages/tex.scm (texlive-natbib): New variable. (texlive-latex-natbib): Deprecate variable. (texlive-apacite): * gnu/packages/bioinformatics.scm (discrover): * gnu/packages/maths.scm (hypre): Use new name. Nicolas Goaziou
2023-07-18gnu: newick-utils: Skip tests on riscv64-linux.•••* gnu/packages/bioinformatics.scm (newick-utils)[arguments]: Skip tests when building on riscv64-linux. 宋文武
2023-07-17gnu: 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
2023-07-15gnu: r-pando: Relax requirements.•••* gnu/packages/bioinformatics.scm (r-pando)[arguments]: Patch DESCRIPTION file. Ricardo Wurmus
2023-07-09gnu: bwa-pssm: Update home page.•••* gnu/packages/bioinformatics.scm (bwa-pssm)[home-page]: Update. Tobias Geerinckx-Rice
2023-07-09gnu: blasr-libcpp, blasr: Use Web Archived home pages.•••* gnu/packages/bioinformatics.scm (blasr-libcpp, blasr)[home-page]: Refer to Web Archive. Tobias Geerinckx-Rice
2023-07-12gnu: Add r-numbat.•••* gnu/packages/bioinformatics.scm (r-numbat): New variable. Ricardo Wurmus
2023-07-12gnu: Add r-bpcells.•••* gnu/packages/bioinformatics.scm (r-bpcells): New variable. Ricardo Wurmus
2023-07-06gnu: r-pando: Fix hash.•••* gnu/packages/bioinformatics.scm (r-pando)[source]: Update hash. Ricardo Wurmus
2023-07-06gnu: 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
2023-07-03gnu: 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
2023-07-03gnu: 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
2023-07-03gnu: Add r-dtmm.•••* gnu/packages/bioinformatics.scm (r-dtmm): New variable. Navid Afkhami
2023-06-29gnu: Add rscape.•••* gnu/packages/bioinformatics.scm (rscape): New variable. Signed-off-by: Ricardo Wurmus <rekado@elephly.net> Navid Afkhami
2023-06-29gnu: 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
2023-06-22gnu: sambamba: Fix building.•••* gnu/packages/bioinformatics.scm (sambamba)[native-inputs]: Remove ld-gold-wrapper, bintutils-gold. Remove input labels. Efraim Flashner
2023-06-20gnu: bioruby: Update to 2.0.4.•••* gnu/packages/bioinformatics.scm (bioruby): Update to 2.0.4. [arguments]: Update style. Christopher Baines
2023-06-09gnu: Add python-mudata.•••* gnu/packages/bioinformatics.scm (python-mudata): New variable. Signed-off-by: Ricardo Wurmus <rekado@elephly.net> Navid Afkhami
2023-06-09gnu: Add python-mofax.•••* gnu/packages/bioinformatics.scm (python-mofax): New variable. Signed-off-by: Ricardo Wurmus <rekado@elephly.net> Navid Afkhami
2023-06-06gnu: Add python-decoupler-py.•••* gnu/packages/bioinformatics.scm (python-decoupler-py): New variable. Co-authored-by: Ricardo Wurmus <rekado@elephly.net>. Navid Afkhami
2023-06-05gnu: 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
2023-06-05gnu: Add python-bulkvis.•••* gnu/packages/bioinformatics.scm (python-bulkvis): New variable. Co-authored-by: Ricardo Wurmus <rekado@elephly.net> Navid Afkhami
2023-06-05gnu: Add python-readpaf.•••* gnu/packages/bioinformatics.scm (python-readpaf): New variable. Navid Afkhami
2023-06-02gnu: Add r-singlet.•••* gnu/packages/bioinformatics.scm (r-singlet): New variable. Ricardo Wurmus
2023-06-02gnu: Add python-cell2cell.•••* gnu/packages/bioinformatics.scm (python-cell2cell): New variable. Signed-off-by: Ricardo Wurmus <rekado@elephly.net> Navid Afkhami
2023-06-02gnu: Add java-maxent.•••* gnu/packages/bioinformatics.scm (java-maxent): New variable. Ricardo Wurmus
2023-06-01gnu: Add python-pyani.•••* gnu/packages/bioinformatics.scm (python-pyani): New variable. Ricardo Wurmus
2023-06-01gnu: Add python-illumina-utils.•••* gnu/packages/bioinformatics.scm (python-illumina-utils): New variable. Ricardo Wurmus
2023-06-01gnu: Add python-ete3.•••* gnu/packages/bioinformatics.scm (python-ete3): New variable. Ricardo Wurmus
2023-05-26gnu: Add python-gseapy.•••* gnu/packages/bioinformatics.scm (python-gseapy): New variable. Ricardo Wurmus
2023-05-19gnu: java-picard-1.113: Drop input package labels.•••* gnu/packages/bioinformatics.scm (java-picard-1.113)[inputs]: Drop labels. Ricardo Wurmus
2023-05-19gnu: 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
2023-05-14gnu: discrover: Remove package labels.•••* gnu/packages/bioinformatics.scm (discrover)[native-inputs]: Remove package labels. Ricardo Wurmus
2023-05-14gnu: 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
2023-05-14gnu: delly: Simplify.•••* gnu/packages/bioinformatics.scm (delly)[source]: Simplify snippet. [arguments]: Do not use quasiquote; simplify 'install-templates phase. Ricardo Wurmus
2023-05-14gnu: 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
2023-05-14gnu: 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
2023-05-14gnu: 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
2023-05-12gnu: jamm: Use G-expression.•••* gnu/packages/bioinformatics.scm (jamm)[arguments]: Use G-expression. Ricardo Wurmus
2023-05-12gnu: 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
2023-05-12gnu: multichoose: Clean up.•••* gnu/packages/bioinformatics.scm (multichoos): Fix indentation. [arguments]: Use G-expression. Ricardo Wurmus
2023-05-12gnu: samblaster: Update to 0.1.26.•••* gnu/packages/bioinformatics.scm (samblaster): Update to 0.1.26. Ricardo Wurmus
2023-05-12gnu: 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
2023-05-12gnu: 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
2023-05-12gnu: methyldackel: Simplify arguments.•••* gnu/packages/bioinformatics.scm (methyldackel)[arguments]: Use list, drop argument list. [native-inputs]: Drop package label. Ricardo Wurmus
2023-05-12gnu: phast: Simplify by using G-expression.•••* gnu/packages/bioinformatics.scm (phast)[arguments]: Use G-expression and drop trailing #T from build phases. Ricardo Wurmus
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