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2023-09-26multiqc: Don't propagate inputs.Efraim Flashner
* gnu/packages/bioinformatics.scm (multiqc)[propagated-inputs]: Move all packages ... [inputs]: ... to here.
2023-09-24gnu: python-pygenometracks: Remove syntax error in setup.py.Mădălin Ionel Patrașcu
* gnu/packages/bioinformatics.scm (python-pygenometracks)[arguments]: Add phase remove-invalid-syntax.
2023-09-24gnu: htslib: Link against htscodecs.Efraim Flashner
* gnu/packages/bioinformatics.scm (htslib)[source]: Add snippet to remove bundled htscodecs. [arguments]: Add configure-flag to link against htscodecs. [propagated-inputs]: Add htscodecs. (htslib-1.14, htslib-1.12): Use bundled htscodecs.
2023-09-24gnu: htscodecs: Update to 1.5.1.Efraim Flashner
* gnu/packages/bioinformatics.scm (htscodecs): Update to 1.5.1.
2023-09-22gnu: wfa2-lib: Mark package as tunable.Efraim Flashner
* gnu/packages/bioinformatics.scm (wfa2-lib)[properties]: New field.
2023-09-22gnu: python-bwapy: Fix typo.Marius Bakke
* gnu/packages/bioinformatics.scm (python-bwapy)[synopsis]: Fix typo.
2023-09-22gnu: python-arboreto: Add missing inputs.Marius Bakke
* gnu/packages/bioinformatics.scm (python-arboreto)[propagated-inputs]: Add PYTHON-LZ4 and PYTHON-PYARROW.
2023-09-20gnu: wfmash: Update to 0.10.5.Efraim Flashner
* gnu/packages/bioinformatics.scm (wfmash): Update to 0.10.5. [source]: Update to changes in source code. [arguments]: Add configure-flag to enable more features. [native-inputs]: Add pkg-config.
2023-09-18gnu: python-plastid: Patch it for python 3.10.Mădălin Ionel Patrașcu
* gnu/packages/bioinformatics.scm (python-plastid)[arguments]: Add new phase 'patch-for-python-3.10. Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
2023-09-14gnu: perl-cworld-dekker: Drop labels from inputs.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (perl-cworld-dekker)[arguments]: Use G-expression and avoid references to labeled inputs. [inputs]: Drop labels.
2023-09-13gnu: python-hicmatrix: Remove custom 'check phase.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (python-hicmatrix)[arguments]: Remove custom 'check phase.
2023-09-13gnu: python-hicmatrix: Remove syntax error in setup.py.Mădălin Ionel Patrașcu
* gnu/packages/bioinformatics.scm (python-hicmatrix)[arguments]: Add phase remove-invalid-syntax. Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
2023-09-12gnu: Add python-peaks2utr.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (python-peaks2utr): New variable.
2023-09-12gnu: macs: Update to 2.2.9.1.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (macs): Update to 2.2.9.1. [build-system]: Use pyproject-build-system. [arguments]: Remove custom 'check phase. [native-inputs]: Move python-cython from here... [inputs]: ...and python-numpy from here... [propagated-inputs]: ...to here.
2023-09-12gnu: python-cgatcore: Update to 0.6.15.Hilton Chain
* gnu/packages/bioinformatics.scm (python-cgatcore): Update to 0.6.15. Signed-off-by: Christopher Baines <mail@cbaines.net>
2023-09-02gnu: r-chromunity: Update to 0.0.2-1.712e56c.Navid Afkhami
* gnu/packages/bioinformatics.scm (r-chromunity): Update to 0.0.2-1.712e56c. [propagated-inputs]: Add r-bsgenome-hsapiens-ucsc-hg38; remove r-skitools.
2023-08-28gnu: Add python-scdamandtools.Navid Afkhami
* gnu/packages/bioinformatics.scm (python-scdamandtools): New variable. Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
2023-08-27gnu: vbz-compression: Update to 1.0.3.Greg Hogan
* gnu/packages/bioinformatics.scm (vbz-compression): Update to 1.0.3. Signed-off-by: Christopher Baines <mail@cbaines.net>
2023-08-10gnu: plink: Build with GCC 8.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (plink)[native-inputs]: Add gcc-8.
2023-08-04gnu: r-liana: Update to 0.1.11-1.10d8177.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-liana): Update to 0.1.11-1.10d8177.
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>
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