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2024-01-16gnu: python-hicexplorer: Make compatible with latest scipy.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (python-hicexplorer)[arguments]: Add 'scipy-compatibility phase. Change-Id: I31e9058b7fd4ff9245837d5f1cd145b569ec35ad
2024-01-16gnu: python-hicmatrix: Update to 17.1.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (python-hicmatrix): Update to 17.1. [arguments]: Remove. Change-Id: I6b1230d703d0dc1a88ee61a84cc6cd95f7eeb6f9
2024-01-16gnu: scvelo: Make compatible with latest matplotlib.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (scvelo)[arguments]: Add phase 'matplotlib-compatibility. Change-Id: Ia761821c8aa1e516525cff7c680db471a5908e5f
2024-01-16gnu: python-demuxem: Disable tests.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (python-demuxem)[arguments]: Disable tests, because there aren't any. Change-Id: I50364ca6744cf9d2704d4b75a8c79c4fdc4ada6e
2024-01-16gnu: python-cooler: Update to 0.9.1.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (python-cooler): Update to 0.9.1. [build-system]: Use pyproject-build-system. [arguments]: Remove custom build phases; disable tests via #:test-flags. [propagated-inputs]: Remove python-six and python-sparse. [native-inputs]: Remove python-codecov, python-mock, and python-pytest-flake8; add python-coverage, python-hatchling, and python-isort. Change-Id: I48b6a9c07a2bc1c213971585d7191573fd5d5aca
2024-01-16gnu: python-plastid: Update to 0.6.1.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (python-plastid): Update to 0.6.1. [arguments]: Disable four tests. Change-Id: If0225f226e702e89d451e2955d0f76691a8816c0
2024-01-16gnu: cnvkit: Update to 0.9.10.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (cnvkit): Update to 0.9.10. [arguments]: Remove. [inputs]: Add r-minimal. Change-Id: Iaa27fd3dddc507c7a955441f066d4b0e3b8f1757
2024-01-16gnu: python-pegasusio: Disable tests.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (python-pegasusio)[arguments]: Disable tests. Change-Id: I6b32ed416b562b47088dbc34eb7bcb0b8e2cc414
2024-01-16gnu: python-pyani: Disable tests.Ricardo Wurmus
There are none. * gnu/packages/bioinformatics.scm (python-pyani)[arguments]: Disable tests. Change-Id: I6862082c8335e5d487da6d1705ed094922f14e47
2024-01-16gnu: tadbit: Add missing input.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (tadbit)[native-inputs]: Add glib. Change-Id: Ia1f79e2a30f5b57616cf3d1f7b6438f07451fbbf
2024-01-16gnu: python-scanpy: Update to 1.9.6.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (python-scanpy): Update to 1.9.6. [arguments]: Update test flags. [native-inputs]: Add python-hatchling, python-hatch-vcs, and python-pytest-nunit. Change-Id: I6d4dcd267a076c5697ed103650841f520dc9917f
2024-01-12gnu: Add r-azimuth.nafkhamdc
* gnu/packages/bioinformatics.scm (r-azimuth): New variable. Change-Id: I2b0d087378028663ee8d76ced8950f7a9721cb03 Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
2024-01-10gnu: r-signac: Update to 1.12.0-1.8ecdde2.nafkhamdc
* gnu/packages/bioinformatics.scm (r-signac): Update to 1.12.0-1.8ecdde2. Change-Id: Ib852f7a23768383fc62d60577f2aaa893c509317
2024-01-10gnu: Add python-telomerecat.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (python-telomerecat): New variable. Change-Id: Ice4cd367cab677466630f44f6900fc38e3be350c
2024-01-10gnu: Add python-parabam.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (python-parabam): New variable. Change-Id: I66ccf5fd0647f908f1cefd38f0d92e589a81683b
2024-01-05gnu: Add bustools.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (bustools): New variable. Change-Id: I24a936ad1d630663a41855a833e35fb9caa0155c
2024-01-05gnu: Add python-snaptools.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (python-snaptools): New variable. Change-Id: I4f4b32cbbb64472e65d2d88184173b6e1a75e8d2
2024-01-05gnu: Add trinityrnaseq.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (trinityrnaseq): New variable. Change-Id: Ia2c45623576e7e2e51b040b1001b1dd88c1324bb
2024-01-05gnu: scvelo: Disable two broken tests.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (scvelo)[build-system]: Use pyproject-build-system. [arguments]: Disable test_perfect_fit and test_perfect_fit_2d tests because they fail with unexpected results; use G-expression. Change-Id: Ied22a2bc044167012ffaaee15a9626e9f5bccdd5
2024-01-04gnu: python-hicexplorer: Fix build.Troy Figiel
* gnu/packages/bioinformatics.scm (python-hicexplorer)[snippet]: Remove catchall pattern of patch version numbers in setup.py.
2024-01-02gnu: Add cpat.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (cpat): New variable. Change-Id: I7b3acca1bdec2610d7cdaaf6f96440fe000421dd
2024-01-02gnu: Add r-sleuth.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-sleuth): New variable. Change-Id: Ic358945548631fd3ac5de96b2efcf1fd93005898
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.
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