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2024-01-02gnu: Add r-wasabi.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-wasabi): New variable. Change-Id: I5ce6c47f1fb3b1d5dfedd0977e53cb70ce379077
2024-01-02gnu: Add r-projectils.Mădălin Ionel Patrașcu
* gnu/packages/bioinformatics.scm (r-projectils): New variable. Change-Id: Ia975cfcb9c79e59b029c6839dc87b5dcb89bf72a
2024-01-02gnu: Add r-stacas.Mădălin Ionel Patrașcu
* gnu/packages/bioinformatics.scm (r-stacas): New variable. Change-Id: I258a315465ed88b8013d26a36718250c950aa107
2024-01-01gnu: r-seurat-utils: Update to 2.5.0-1.c0374cc.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-seurat-utils): Update to 2.5.0-1.c0374cc. [propagated-inputs]: Add r-databaselinke-r, r-enhancedvolcano, r-foreach, r-job, r-magrittr, r-pheatmap, r-plotly, r-qs, r-rstudioapi, and r-tidyverse. Change-Id: Iea2df8205357e7717c0adec00f6852794817d295
2024-01-01gnu: Add r-databaselinke-r.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-databaselinke-r): New variable. Change-Id: I0cfcb5b6810b7afebbb9ccb02aafcce05507536c
2023-12-25gnu: Add lammps-serial.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (lammps-serial): New variable. Change-Id: Ifd189a28f423e43ddda8654f758486737eef4a3c
2023-12-25gnu: Add lammps.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (lammps): New variable. Change-Id: Ic9745a623300b82b7fb1417437220415305e7332
2023-12-19gnu: r-sccustomize: Update to 2.0.1-1.3973745.nafkhamdc
* gnu/packages/bioinformatics.scm (r-sccustomize): Update to 2.0.1-1.3973745. Change-Id: I4e4b499a658eaed0396263d1d9fd277a541a13d9 Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
2023-12-15gnu: pyscenic: Update to 0.11.2-1.5f170fd.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (pyscenic): Update to 0.11.2-1.5f170fd. [build-system]: Use pyproject-build-system. [arguments]: Patch setup.py. [propagated-inputs]: Add python-pyarrow. Change-Id: I3acd7c921c2c44741c0afd0bbda011f63ed14c42
2023-12-15gnu: python-ctxcore: Update to 0.2.0.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (python-ctxcore): Update to 0.2.0. [build-system]: Use pyproject-build-system. [propagated-inputs]: Replace python-pyarrow-0.16 with python-pyarrow. Change-Id: I3f72f9872b438c0a624d23becb5d7828f1986da7
2023-12-15gnu: r-readwriter: Update to 1.5.3-1.91373c4.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-readwriter): Update to 1.5.3-1.91373c4. [propagated-inputs]: Remove r-gdata. Change-Id: Ice16d3b07d7446ca864fd30e46110c9060b83081
2023-12-15gnu: r-stringendo: Update to 0.6.0.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-stringendo): Update to 0.6.0. [propagated-inputs]: Remove r-devtools and r-usethis; add r-clipr. Change-Id: Iff4a841beb51558ba7d5d8e87ee56e7c3f2b2710
2023-12-15gnu: r-liana: Add missing inputs.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-liana)[propagated-inputs]: Add r-basilisk and r-basilisk-utils. Change-Id: I5dce058a446245e6797cca1c35485f38b3da819a
2023-11-13gnu: Add r-illuminahumanmethylationepicmanifest.nafkhamdc
* gnu/packages/bioinformatics.scm (r-illuminahumanmethylationepicmanifest): New variable. Change-Id: I9635033ed5e7e44ecfaff76cd002379582900686 Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
2023-11-04gnu: Add r-ewastools.Mădălin Ionel Patrașcu
* gnu/packages/bioinformatics.scm (r-ewastools): New variable. Change-Id: I4117dbee188c7d9547fe63b2b89ec9258bbda60b Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
2023-11-04gnu: Add r-dnamcrosshyb.Mădălin Ionel Patrașcu
* gnu/packages/bioinformatics.scm (r-dnamcrosshyb): New variable. Change-Id: I19e332e6adf0ce9cc721d89bb74a1aa709778873 Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
2023-11-03gnu: r-readwriter: Update to 0.3.2-1.12d32cb.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-readwriter): Update to 0.3.2-1.12d32cb. Change-Id: I412190ce94bee4e7b5fce27db7ef8a72188e74f4
2023-11-03gnu: Add r-miamiplot.Afkhami, Navid
* gnu/packages/bioinformatics.scm (r-miamiplot): New variable. Change-Id: I41a3a951c6f1835800301e4c168eeeb0dd299f06 Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
2023-10-31gnu: python-baltica: Add missing R inputs.Afkhami, Navid
* 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
2023-10-30gnu: Add r-voltron.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-voltron): New variable. Change-Id: I5f70cf613bf2c26c4ca119483c9ad3b0beba6502
2023-10-22gnu: go-gopkg-in-check-v1: Move to (gnu packages golang-check).Sharlatan Hellseher
* 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>
2023-10-22gnu: transanno: Don't set #:tests to #true.Efraim Flashner
* gnu/packages/bioinformatics.scm (transanno)[arguments]: Don't set tests unconditionally to #true.
2023-10-18Revert "build: cargo-build-system: Disable tests by default."Efraim Flashner
This reverts commit 37667443074a6de29f7665868f102111d62f0af9. This change needs more discussion.
2023-10-18gnu: transanno: Fix build.Efraim Flashner
* 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.
2023-10-18build: cargo-build-system: Disable tests by default.Efraim Flashner
* 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.
2023-10-17gnu: Add r-metacell.Afkhami, Navid
* gnu/packages/bioinformatics.scm (r-metacell): New variable.
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>
generated by cgit v1.2.3 (git 2.46.2) at 2024-12-29 13:45:45 +0000