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2023-09-14gnu: perl-cworld-dekker: Drop labels from inputs.•••* gnu/packages/bioinformatics.scm (perl-cworld-dekker)[arguments]: Use G-expression and avoid references to labeled inputs. [inputs]: Drop labels. Ricardo Wurmus
2023-09-13gnu: python-hicmatrix: Remove custom 'check phase.•••* gnu/packages/bioinformatics.scm (python-hicmatrix)[arguments]: Remove custom 'check phase. Ricardo Wurmus
2023-09-13gnu: python-hicmatrix: Remove syntax error in setup.py.•••* gnu/packages/bioinformatics.scm (python-hicmatrix)[arguments]: Add phase remove-invalid-syntax. Signed-off-by: Ricardo Wurmus <rekado@elephly.net> Mădălin Ionel Patrașcu
2023-09-12gnu: Add python-peaks2utr.•••* gnu/packages/bioinformatics.scm (python-peaks2utr): New variable. Ricardo Wurmus
2023-09-12gnu: macs: Update to 2.2.9.1.•••* 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. Ricardo Wurmus
2023-09-12gnu: python-cgatcore: Update to 0.6.15.•••* gnu/packages/bioinformatics.scm (python-cgatcore): Update to 0.6.15. Signed-off-by: Christopher Baines <mail@cbaines.net> Hilton Chain
2023-09-02gnu: r-chromunity: Update to 0.0.2-1.712e56c.•••* gnu/packages/bioinformatics.scm (r-chromunity): Update to 0.0.2-1.712e56c. [propagated-inputs]: Add r-bsgenome-hsapiens-ucsc-hg38; remove r-skitools. Navid Afkhami
2023-08-28gnu: Add python-scdamandtools.•••* gnu/packages/bioinformatics.scm (python-scdamandtools): New variable. Signed-off-by: Ricardo Wurmus <rekado@elephly.net> Navid Afkhami
2023-08-27gnu: vbz-compression: Update to 1.0.3.•••* gnu/packages/bioinformatics.scm (vbz-compression): Update to 1.0.3. Signed-off-by: Christopher Baines <mail@cbaines.net> Greg Hogan
2023-08-10gnu: plink: Build with GCC 8.•••* gnu/packages/bioinformatics.scm (plink)[native-inputs]: Add gcc-8. Ricardo Wurmus
2023-08-04gnu: r-liana: Update to 0.1.11-1.10d8177.•••* gnu/packages/bioinformatics.scm (r-liana): Update to 0.1.11-1.10d8177. Ricardo Wurmus
2023-07-30gnu: mash: Fix build.•••* gnu/packages/bioinformatics.scm (mash)[arguments]: Add a new 'bootstrap phase. Tobias Geerinckx-Rice
2023-07-30gnu: mash: Update package style.•••* gnu/packages/bioinformatics.scm (mash)[arguments]: Consolidate similar SUBSTITUTE* calls. Don't explicitly return #t from phases. Tobias Geerinckx-Rice
2023-08-01gnu: Add python-baltica.•••* gnu/packages/bioinformatics.scm (python-baltica): New variable. Navid Afkhami
2023-07-31gnu: Add python-liana-py.•••* gnu/packages/bioinformatics.scm (python-liana-py): New variable. Signed-off-by: Ricardo Wurmus <rekado@elephly.net> Navid Afkhami
2023-07-31gnu: python-decoupler-py: Update to 1.5.0-1.459b235.•••* 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> Navid Afkhami
2023-07-23gnu: fuse@3: Bind to default FUSE variable.•••* 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. Tobias Geerinckx-Rice
2023-07-21gnu: newick-utils: Skip tests when cross-compiling.•••* gnu/packages/bioinformatics.scm (newick-utils)[arguments]: Adjust #: tests? to skip tests when cross-compiling. Efraim Flashner
2023-07-18gnu: discrover: Fix build.•••* gnu/packages/bioinformatics.scm (discrover)[native-inputs]: Add TEXLIVE-FORLOOP, TEXLIVE-LISTOFITEMS, TEXLIVE-READARRAY. Nicolas Goaziou
2023-07-18gnu: Rationalize texlive-updmap.cfg and texlive-tiny inputs.•••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. Nicolas Goaziou
2023-07-18gnu: phyml: Fix build.•••* gnu/packages/bioinformatics.scm (phyml)[native-inputs]: Add TEXLIVE-INFWARERR, TEXLIVE-KVOPTIONS and TEXLIVE-PDFTEXCMDS. Nicolas Goaziou
2023-07-18gnu: velvet: Improve package style.•••* gnu/packages/bioinformatics.scm (velvet)[arguments]: Use G-expressions. [native-inputs]: Remove label. Nicolas Goaziou
2023-07-18gnu: velvet: Fix error when building documentation.•••* gnu/packages/bioinformatics.scm (velvet)[native-inputs]: Add TEXLIVE-GRFEXT, TEXLIVE-INFWARERR, TEXLIVE-KVOPTIONS and TEXLIVE-KPDFTEXCMDS. Nicolas Goaziou
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
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