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2024-12-03gnu: r-circus: Add missing input.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-circus)[native-inputs]: Add r-testthat. Change-Id: I7178baece0a8134923fd550e2f1cc303f32aaaea
2024-12-03gnu: Remove r-numbat.Ricardo Wurmus
This is a duplicate of a package in (gnu packages bioconductor). * gnu/packages/bioinformatics.scm (r-numbat): Delete variable. Change-Id: Ic1f5d9779a594432a0dd8bd0be9059423a2f5b34
2024-12-03gnu: r-spectre: Disable tests.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-spectre)[arguments]: Disable tests. Change-Id: I7978b05d0c1c2de3ada6b1b490ae36b28171f17c
2024-12-03gnu: r-gchain: Add missing inputs.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-gchain)[native-inputs]: Add r-pwalign and r-testthat. [arguments]: Add phase 'skip-bad-tests. Change-Id: Ia11c6e50e0d2886762ec551df3e5d73ef98547f8
2024-12-03gnu: r-seraster: Add missing input.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-seraster)[native-inputs]: Add r-testthat. Change-Id: I88fb4a51831aff1b08437ef08adb62e344185a07
2024-12-03gnu: r-gtrack: Add missing input.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-gtrack)[native-inputs]: Add r-testthat. Change-Id: I7b0cad1b8fd27d88ff766c5a46bd01dae2933422
2024-12-03gnu: r-doubletcollection: Add missing input and disable tests.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-doubletcollection)[native-inputs]: Add r-testthat. [arguments]: Disable tests. Change-Id: I8802f703ecfd8d69e6e457cffb28e34d3f4f2b06
2024-12-03gnu: r-pando: Add missing inputs and disable tests.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-pando)[native-inputs]: Add r-bsgenome-hsapiens-ucsc-hg38, r-devtools, r-doparallel, and r-ensdb-hsapiens-v86. [arguments]: Disable tests. Change-Id: Ic66679e2b8c4cdb9835ce08dc4dbb0a42e35e291
2024-12-03gnu: r-anpan: Add missing input.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-anpan)[native-inputs]: Add r-testthat. Change-Id: I69be3fa82db5f9c4e1302c9a3bd2d4f5253bde13
2024-12-03gnu: r-hdwgcna: Add missing inputs.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-hdwgcna)[native-inputs]: Add r-devtools and r-testthat. Change-Id: I553d4fc2f1a682e5d552862c5e50a31140528073
2024-12-03gnu: r-ewastools: Add missing inputs.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-ewastools)[native-inputs]: Add r-enmix, r-illuminahumanmethylationepicanno-ilm10b4-hg19, r-minfi, r-stringi, and r-testthat. Change-Id: I8ba2b1c46a4898b27874a7dc8648bb142f4b5a70
2024-12-03gnu: r-bamutils: Add test inputs and disable tests.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-bamutils)[arguments]: Disable tests. [native-inputs]: Add r-testthat and samtools. Change-Id: I781c38fb59355a51f2cd27a833d7ed5dbe5277ab
2024-12-03gnu: r-bamutils: Update to 0.0.0.9000-2.0a7d2d9.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-bamutils): Update to 0.0.0.9000-2.0a7d2d9. Change-Id: I04e86c2ff1059f23a34615ac6067926cdd9cb355
2024-12-03gnu: r-dropbead: Disable tests.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-dropbead)[native-inputs]: Add r-data-table. [arguments]: Disable tests. Change-Id: I48c74a7b4253695ab5c877f6f1cebdca6ed42cb7
2024-12-03gnu: r-sleuth: Disable tests.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-sleuth)[native-inputs]: Add r-testthat. [arguments]: Disable tests. Change-Id: Ib060eb18f8964212eb38b7025a35c16f0aca97b9
2024-12-03gnu: r-ggsankey: Add missing inputs.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-ggsankey)[native-inputs]: Add r-testthat. Change-Id: Iaafb75cc47e89a4a25232003d410f98c304ff021
2024-12-03gnu: r-streamgraph: Add missing input.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-streamgraph)[native-inputs]: Add r-testthat. Change-Id: I1209a467c5a966c916f0d0416c6c1e283ae9226d
2024-12-03gnu: r-signac: Add missing input.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-signac)[native-inputs]: Add r-testthat. Change-Id: I0aacabf77171903cca2bc0f443f77e479b6331b2
2024-12-03gnu: r-psupertime: Add missing input.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-psupertime)[native-inputs]: Add r-testthat. Change-Id: I9993547e2e757b4218c2229495a7eaa0c8fecbe2
2024-12-03gnu: r-demuxmix: Add missing input.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-demuxmix)[native-inputs]: Add r-testthat. Change-Id: Ia09b929b4d5bb521d58fb74f17f1ac91a4d44a60
2024-12-03gnu: r-cmdstanr: Add missing input.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-cmdstanr)[native-inputs]: Add r-testthat. Change-Id: Idd81b903e9e9a8308703c9ee8dc5583a04854678
2024-12-03gnu: r-gutils: Add missing input.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-gutils)[native-inputs]: Add r-testthat. Change-Id: I1b5e34441b48bc92bff6538378d2e2bbc7111631
2024-12-03gnu: r-rnacrosslinkoo: Add missing inputs.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-rnacrosslinkoo)[native-inputs]: Add r-testthat. Change-Id: Iedd2dee7a32dcd19a99d25d92b6f453dd197f5b4
2024-12-03gnu: r-bedtorch: Disable tests.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-bedtorch)[arguments]: Disable tests. [native-inputs]: Add r-testthat. Change-Id: Ia06aca330528eb2b9eea569d5d12db0f12d6511e
2024-12-03gnu: r-presto: Add missing inputs.Ricardo Wurmus
* gnu/packages/bioconductor.scm (r-presto)[native-inputs]: Add r-testthat. Change-Id: I3fe5ec83478e384fe34701b0672b6f216255b1d6
2024-12-03gnu: r-psiplot: Add missing inputs.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-psiplot)[native-inputs]: Add r-testthat. Change-Id: I19ad7216f86968c87abad64313bf09d03e3ad612
2024-12-03gnu: r-omnipathr/devel: Add missing inputs.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-omnipathr/devel)[native-inputs]: Add r-testthat. Change-Id: I7e339871d65ed0ff263db14ff9fb0aa1bb3ed0bb
2024-12-03gnu: r-millefy: Add missing inputs.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-millefy)[native-inputs]: Add r-testthat. Change-Id: Id5d1f74074f05f1af2e3726e9a9e49f2d63f13c9
2024-12-03gnu: r-singlet: Add test inputs.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-singlet)[native-inputs]: Add r-testthat. Change-Id: I617f6bbb9e11ef00148571b94a4aaf2d445cfcb2
2024-12-03gnu: r-anndatar: Add test inputs.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-anndatar)[native-inputs]: Add r-rhdf5, r-seuratobject, r-singlecellexperiment, and r-testthat. Change-Id: I233a1f7216241b5d9d8301e07acdf811edb24a28
2024-12-02gnu: homer: Install config.txt.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (homer)[native-inputs]: Add config.txt. [arguments]: Update 'configure phase to place config.txt in expected location; patch configuration code to optionally load a user's configuration file. Change-Id: Ib05c828e751c6568524bbef45997a42fade4545a
2024-12-02gnu: homer: Install homer executable.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (homer)[arguments]: Update 'install phase to also install "homer" to the bin directory. Change-Id: Ia2d23fce493f9c10cc43ac126cd83956b4b9bb05
2024-12-02Merge remote-tracking branch 'origin/rust-team'Efraim Flashner
Change-Id: I6d5c28252f060eeb69eb02fd281e7268bb885b29
2024-12-02gnu: python-pairtools: Update to 1.1.0-fix.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (python-pairtools): Update to 1.1.0-fix. [build-system]: Use pyproject-build-system. [arguments]: Add phase 'patch-setup.py. [native-inputs]: Add python-pytest-cov, python-setuptools, and python-wheel. Change-Id: Ifa3c12de228420d8fdd7b0053bb9da80b9b3efe4
2024-12-02gnu: Add macs-3.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (macs-3): New variable. Change-Id: I4bc417e90a1e9d6d28226ea4f66ddc035826c2c4
2024-12-01gnu: r-voltron: Add Python inputs.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-voltron)[inputs]: Add python, python-numpy, python-pandas, python-anndata, python-h5py, python-natsort, python-numcodecs, python-packaging, python-scipy, python-tifffile, and python-zarr. Change-Id: Iab137936550b51d6839d9beaa47f6102a8f3c355
2024-12-01gnu: r-voltron: Update to 0.2.0-1.9f9415c.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-voltron): Update to 0.2.0-1.9f9415c. [inputs]: Remove tbb. [propagated-inputs]: Remove r-anndata, r-fastdummies, r-fnn, r-ggforce, r-hdf5r, r-htmltools, r-interp, r-morpho, r-raster, r-s4vectors, r-scales, r-terra, r-umap, and r-xml; add r-basilisk, r-ids, r-rann, r-rcdt, r-rcppannoy, r-rcpparmadillo, r-reticulate, r-s4arrays, and r-sp. [native-inputs]: Add r-testthat. [description]: Update. Change-Id: I8051ade560e03f8e3760560ec7b78d9941c00e08
2024-12-01gnu: pigx-scrnaseq: Update to 1.1.10.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (pigx-scrnaseq): Update to 1.1.10. [arguments]: Remove quasiquote. Change-Id: I6cab358addfb376a878929bfb5041edc00cd336a
2024-12-01gnu: pigx-bsseq: Update to 0.1.10.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (pigx-bsseq): Update to 0.1.10. [native-inputs]: Use tzdata-for-tests instead of tzdata. [arguments]: Remove quasiquote. Change-Id: I680b08cda788fc03a8bedb87f241116a051798d6
2024-11-28gnu: circtools: Skip tests.Efraim Flashner
* gnu/packages/bioinformatics.scm (circtools)[arguments]: Skip the tests. Don't install the sources. Change-Id: I722470316e08686fb179bcdf07db12d2f9541b60
2024-11-20gnu: Add python-whatshap.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (python-whatshap): New variable. Change-Id: I42281932acb981a7500ef90b5700e7480b41dffe
2024-11-13gnu: Add python-pybio.Navid Afkhami
* gnu/packages/bioinformatics.scm (python-pybio): New variable. Change-Id: I8f5c9cb6c7bb03cbc95386e67d46b1bdd78e01f2 Signed-off-by: Ricardo Wurmus <[email protected]>
2024-11-11gnu: r-hdwgcna: Use R build system phases.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-hdwgcna)[arguments]: Explicitly select %STANDARD-PHASES from r-build-system module. Change-Id: I8f6593ab1243884827698cf84d34d9f7aef5c28c
2024-11-11gnu: Add r-hdwgcna.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-hdwgcna): New variable. Change-Id: I1e3c7663a777ee543c53ccee90b6e71f544d89aa
2024-11-11gnu: Add python-harmonypy.Navid Afkhami
* gnu/packages/bioinformatics.scm (python-harmonypy): New variable. Change-Id: Iad8be627099858776163fccfeb27c08129e6fb75 Signed-off-by: Ricardo Wurmus <[email protected]>
2024-11-07gnu: r-demultiplex2: Update to 1.0.2-2.c1ce09e.Navid Afkhami
* gnu/packages/bioinformatics.scm (r-demultiplex2): Update to 1.0.2-2.c1ce09e. Change-Id: I42038c8f4a003ae5c274fe635ddb8c2a027ddce4 Signed-off-by: Ricardo Wurmus <[email protected]>
2024-11-06gnu: wfmash: Disable tests when cross-compiling.Efraim Flashner
* gnu/packages/bioinformatics.scm (wfmash)[arguments]: Also disable the tests when cross-compiling. Change-Id: Ie7e22a84bfa9b49d4a4b7c1b51a6b01743941af4
2024-11-06gnu: Add r-seuratextend.Navid Afkhami
* gnu/packages/bioinformatics.scm (r-seuratextend): New variable. Change-Id: I9ce0d90a2f05d4e074459046c380849cf9f63978 Signed-off-by: Ricardo Wurmus <[email protected]>
2024-11-05gnu: Add r-seuratextenddata.Navid Afkhami
* gnu/packages/bioinformatics.scm (r-seuratextenddata): New variable. Change-Id: Ic07ca4e55387ac914f915f3688bda2f9352435cc Signed-off-by: Ricardo Wurmus <[email protected]>
2024-11-05gnu: r-demultiplex2: Update to 1.0.1-1.92130a6.Navid Afkhami
* gnu/packages/bioinformatics.scm (r-demultiplex2): Update to 1.0.1-1.92130a6. Change-Id: Ic08756e0347ab6997fec0129a06923aebb9c7836 Signed-off-by: Ricardo Wurmus <[email protected]>
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