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2023-07-30gnu: mash: Fix build.Tobias Geerinckx-Rice
* gnu/packages/bioinformatics.scm (mash)[arguments]: Add a new 'bootstrap phase.
2023-07-30gnu: mash: Update package style.Tobias Geerinckx-Rice
* gnu/packages/bioinformatics.scm (mash)[arguments]: Consolidate similar SUBSTITUTE* calls. Don't explicitly return #t from phases.
2023-08-01gnu: Add python-baltica.Navid Afkhami
* gnu/packages/bioinformatics.scm (python-baltica): New variable.
2023-07-31gnu: Add python-liana-py.Navid Afkhami
* gnu/packages/bioinformatics.scm (python-liana-py): New variable. Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
2023-07-31gnu: python-decoupler-py: Update to 1.5.0-1.459b235.Navid Afkhami
* gnu/packages/bioinformatics.scm (python-decoupler-py): Update to 1.5.0-1.459b235. [arguments]: Disable two more tests. Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
2023-07-23gnu: fuse@3: Bind to default FUSE variable.Tobias Geerinckx-Rice
* gnu/packages/linux.scm (fuse): Rename this… (fuse-2): …to this, and… (fuse-3): …rename this… (fuse): …to this! (fuse-static): Rename this… (fuse-2-static): …to this. Adjust all users.
2023-07-21gnu: newick-utils: Skip tests when cross-compiling.Efraim Flashner
* gnu/packages/bioinformatics.scm (newick-utils)[arguments]: Adjust #: tests? to skip tests when cross-compiling.
2023-07-18gnu: discrover: Fix build.Nicolas Goaziou
* gnu/packages/bioinformatics.scm (discrover)[native-inputs]: Add TEXLIVE-FORLOOP, TEXLIVE-LISTOFITEMS, TEXLIVE-READARRAY.
2023-07-18gnu: Rationalize texlive-updmap.cfg and texlive-tiny inputs.Nicolas Goaziou
TEXLIVE-UPDMAP.CFG and TEXLIVE-TINY should only be used as native inputs. Also remove texlive packages already provided by them. * doc/build.scm (pdf-manual): * gnu/packages/algebra.scm (pari-gp): * gnu/packages/bioinformatics.scm (discrover): (phyml): (velvet): * gnu/packages/chemistry.scm (yaehmop): * gnu/packages/chez.scm (stex-bootstrap): (chez-web): (chez-sockets): * gnu/packages/cran.scm (r-prereg): * gnu/packages/docbook.scm (dblatex): * gnu/packages/emacs-xyz.scm (emacs-auctex): * gnu/packages/engineering.scm (fastcap): * gnu/packages/fsf.scm (book-faif): * gnu/packages/graphviz.scm (dot2tex): * gnu/packages/maths.scm (hypre): * gnu/packages/ocaml.scm (unison): (ocaml-bibtex2html): * gnu/packages/plotutils.scm (asymptote): * gnu/packages/python-xyz.scm (python-nbconvert): (python-pypandoc): * gnu/packages/radio.scm (gnuradio): (libosmo-dsp): * gnu/packages/statistics.scm (r-with-tests): * gnu/packages/tex.scm (texlive-makecmds): (texlive-innerscript): (teximpatient): (texlive-xkeyval): Remove texlive packages already provided by TEXLIVE-UPDMAP.CFG. Don't add TEXLIVE-TINY or TEXLIVE-UPDMAP.CFG as inputs.
2023-07-18gnu: phyml: Fix build.Nicolas Goaziou
* gnu/packages/bioinformatics.scm (phyml)[native-inputs]: Add TEXLIVE-INFWARERR, TEXLIVE-KVOPTIONS and TEXLIVE-PDFTEXCMDS.
2023-07-18gnu: velvet: Improve package style.Nicolas Goaziou
* gnu/packages/bioinformatics.scm (velvet)[arguments]: Use G-expressions. [native-inputs]: Remove label.
2023-07-18gnu: velvet: Fix error when building documentation.Nicolas Goaziou
* gnu/packages/bioinformatics.scm (velvet)[native-inputs]: Add TEXLIVE-GRFEXT, TEXLIVE-INFWARERR, TEXLIVE-KVOPTIONS and TEXLIVE-KPDFTEXCMDS.
2023-07-18gnu: texlive-latex-examplep -> texlive-examplep.Nicolas Goaziou
* gnu/packages/tex.scm (texlive-examplep): New variable. (texlive-latex-examplep): Deprecate variable. * gnu/packages/bioinformatics.scm (discrover)[native-inputs]: Use new name.
2023-07-18gnu: texlive-latex-verbatimbox -> texlive-verbatimbox.Nicolas Goaziou
* gnu/packages/tex.scm (texlive-verbatimbox): New variable. (texlive-latex-verbatimbox): Deprecate variable. * gnu/packages/bioinformatics.scm (discrover)[native-inputs]: Use new name.
2023-07-18gnu: texlive-fonts-ec -> texlive-ec.Nicolas Goaziou
* 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.
2023-07-18gnu: texlive-latex-psfrag -> texlive-psfrag.Nicolas Goaziou
* gnu/packages/tex.scm (texlive-psfrag): New variable. (texlive-latex-psfrag): Deprecate variable. (texlive-pstool): * gnu/packages/bioinformatics.scm (phyml): Use new name.
2023-07-18gnu: texlive-latex-natbib -> texlive-natbib.Nicolas Goaziou
* 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.
2023-07-18gnu: newick-utils: Skip tests on riscv64-linux.宋文武
* gnu/packages/bioinformatics.scm (newick-utils)[arguments]: Skip tests when building on riscv64-linux.
2023-07-17gnu: Hide python-bcbio-gff/biopython-1.73.Christopher Baines
To avoid the ambiguous package specification. * gnu/packages/bioinformatics.scm (python-bcbio-gff/biopython-1.73): Hide package.
2023-07-15gnu: r-pando: Relax requirements.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-pando)[arguments]: Patch DESCRIPTION file.
2023-07-09gnu: bwa-pssm: Update home page.Tobias Geerinckx-Rice
* gnu/packages/bioinformatics.scm (bwa-pssm)[home-page]: Update.
2023-07-09gnu: blasr-libcpp, blasr: Use Web Archived home pages.Tobias Geerinckx-Rice
* gnu/packages/bioinformatics.scm (blasr-libcpp, blasr)[home-page]: Refer to Web Archive.
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+.
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