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2023-11-13gnu: Add r-illuminahumanmethylationepicmanifest.•••* gnu/packages/bioinformatics.scm (r-illuminahumanmethylationepicmanifest): New variable. Change-Id: I9635033ed5e7e44ecfaff76cd002379582900686 Signed-off-by: Ricardo Wurmus <rekado@elephly.net> nafkhamdc
2023-11-04gnu: Add r-ewastools.•••* gnu/packages/bioinformatics.scm (r-ewastools): New variable. Change-Id: I4117dbee188c7d9547fe63b2b89ec9258bbda60b Signed-off-by: Ricardo Wurmus <rekado@elephly.net> Mădălin Ionel Patrașcu
2023-11-04gnu: Add r-dnamcrosshyb.•••* gnu/packages/bioinformatics.scm (r-dnamcrosshyb): New variable. Change-Id: I19e332e6adf0ce9cc721d89bb74a1aa709778873 Signed-off-by: Ricardo Wurmus <rekado@elephly.net> Mădălin Ionel Patrașcu
2023-11-03gnu: r-readwriter: Update to 0.3.2-1.12d32cb.•••* gnu/packages/bioinformatics.scm (r-readwriter): Update to 0.3.2-1.12d32cb. Change-Id: I412190ce94bee4e7b5fce27db7ef8a72188e74f4 Ricardo Wurmus
2023-11-03gnu: Add r-miamiplot.•••* gnu/packages/bioinformatics.scm (r-miamiplot): New variable. Change-Id: I41a3a951c6f1835800301e4c168eeeb0dd299f06 Signed-off-by: Ricardo Wurmus <rekado@elephly.net> Afkhami, Navid
2023-10-31gnu: python-baltica: Add missing R inputs.•••* gnu/packages/bioinformatics.scm (python-baltica)[propagated-inputs]: Add r-biocmanager, r-dplyr, r-genomicranges, r-here, r-openxlsx, r-optparse, r-readr, r-rsamtools, r-stringr, r-tidyr, r-upsetr, and r-yaml. [description]: Add an extra space after a period. Change-Id: I8c1bb556048b406b95e081155a46da17a6be5676 Afkhami, Navid
2023-10-30gnu: Add r-voltron.•••* gnu/packages/bioinformatics.scm (r-voltron): New variable. Change-Id: I5f70cf613bf2c26c4ca119483c9ad3b0beba6502 Ricardo Wurmus
2023-10-22gnu: go-gopkg-in-check-v1: Move to (gnu packages golang-check).•••* gnu/packages/golang.scm (go-gopkg-in-check-v1): Move from here... * gnu/packages/golang-check.scm (go-gopkg-in-check-v1): ... to here. * gnu/packages/bioinformatics.scm: Add (gnu-packages golang-check) to use-module. Signed-off-by: Maxim Cournoyer <maxim.cournoyer@gmail.com> Sharlatan Hellseher
2023-10-22gnu: transanno: Don't set #:tests to #true.•••* gnu/packages/bioinformatics.scm (transanno)[arguments]: Don't set tests unconditionally to #true. Efraim Flashner
2023-10-18Revert "build: cargo-build-system: Disable tests by default."•••This reverts commit 37667443074a6de29f7665868f102111d62f0af9. This change needs more discussion. Efraim Flashner
2023-10-18gnu: transanno: Fix build.•••* gnu/packages/bioinformatics.scm (transanno)[arguments]: Run the test suite. Don't patch Cargo.toml in liftover-rs. Don't patch crate in vendor-dir. [native-inputs]: Add pkg-config. [inputs]: Add xz. Efraim Flashner
2023-10-18build: cargo-build-system: Disable tests by default.•••* guix/build-system/cargo.scm (cargo-build): Disable tests by default. * gnu/packages/admin.scm (greetd, wlgreet, du-dust), * gnu/packages/bioinformatics.scm (circtools, python-gseapy), * gnu/packages/crypto.scm (rust-minisign, b3sum), * gnu/packages/gnome.scm (librsvg), * gnu/packages/python-crypto.scm (python-blake3, python-cryptography-rust), * gnu/packages/python-xyz.scm (python-orjson), * gnu/packages/rust-apps.scm (agate, alfis, bat, diffr, drill, dutree, exa, fd, hexyl, hyperfine, i3status-rust, just, maturin, ripgrep, rot8, rust-swc, rust-cargo-edit, git-interactive-rebase-tool, rust-cbindgen, rust-cbindgen-0.24, rust-cbindgen-0.19, sniffglue, tectonic, treefmt, hex, tokei, vivid, watchexec, rbw, rust-analyzer, rust-cargo-c, rtss, skim, skim-0.7, svd2rust, swayhide, tealdeer, git-absorb, zoxide, htmlq), * gnu/packages/sequoia.scm (sequoia-sqv), * gnu/packages/syndication.scm (newsboat), * gnu/packages/terminals.scm (alacritty), * gnu/packages/text-editors.scm (kak-lsp, parinfer-rust), * gnu/packages/tree-sitter.scm (tree-sitter-cli), * gnu/packages/video.scm (rav1e), * gnu/packages/web.scm (monolith, castor) [arguments]: Enable tests. Efraim Flashner
2023-10-17gnu: Add r-metacell.•••* gnu/packages/bioinformatics.scm (r-metacell): New variable. Afkhami, Navid
2023-09-26multiqc: Don't propagate inputs.•••* gnu/packages/bioinformatics.scm (multiqc)[propagated-inputs]: Move all packages ... [inputs]: ... to here. Efraim Flashner
2023-09-24gnu: python-pygenometracks: Remove syntax error in setup.py.•••* gnu/packages/bioinformatics.scm (python-pygenometracks)[arguments]: Add phase remove-invalid-syntax. Mădălin Ionel Patrașcu
2023-09-24gnu: htslib: Link against htscodecs.•••* 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. Efraim Flashner
2023-09-24gnu: htscodecs: Update to 1.5.1.•••* gnu/packages/bioinformatics.scm (htscodecs): Update to 1.5.1. Efraim Flashner
2023-09-22gnu: wfa2-lib: Mark package as tunable.•••* gnu/packages/bioinformatics.scm (wfa2-lib)[properties]: New field. Efraim Flashner
2023-09-22gnu: python-bwapy: Fix typo.•••* gnu/packages/bioinformatics.scm (python-bwapy)[synopsis]: Fix typo. Marius Bakke
2023-09-22gnu: python-arboreto: Add missing inputs.•••* gnu/packages/bioinformatics.scm (python-arboreto)[propagated-inputs]: Add PYTHON-LZ4 and PYTHON-PYARROW. Marius Bakke
2023-09-20gnu: wfmash: Update to 0.10.5.•••* 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. Efraim Flashner
2023-09-18gnu: python-plastid: Patch it for python 3.10.•••* gnu/packages/bioinformatics.scm (python-plastid)[arguments]: Add new phase 'patch-for-python-3.10. Signed-off-by: Ricardo Wurmus <rekado@elephly.net> Mădălin Ionel Patrașcu
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
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