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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 <rekado@elephly.net>
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 <rekado@elephly.net>
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 <rekado@elephly.net>
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 <rekado@elephly.net>
2024-11-05gnu: Add r-seuratextenddata.Navid Afkhami
* gnu/packages/bioinformatics.scm (r-seuratextenddata): New variable. Change-Id: Ic07ca4e55387ac914f915f3688bda2f9352435cc Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
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 <rekado@elephly.net>
2024-11-04gnu: kallisto: Update to 0.50.1guix@mawumag.com
See discussion at <https://issues.guix.gnu.org/71146> for reasons to not unbundle htslib and libbifrost. * gnu/packages/bioinformatics.scm (kallisto): Update to 0.50.1. [source]: Do not remove bundled libraries. [arguments]: Remove phase 'do-not-use-bundled-htslib. [inputs]: Remove htslib-1.9. Change-Id: I6d3263fd49c7b07ce50185b722863b51816ff054 Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
2024-11-04gnu: Add python-hotspotsc.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (python-hotspotsc): New variable. Change-Id: Ib3550837659f95d5a43e77137005db8cc03e6c3f
2024-11-03gnu: Grammar fixes in various package descriptions.Vagrant Cascadian
* gnu/packages/bioinformatics.scm (vembrane)[description]: Fix grammar. * gnu/packages/cran.scm (r-memisc)[description]: Fix grammar. * gnu/packages/emacs-xyz.scm (emacs-consult-xdg-recent-files)[description]: Fix grammar. (emacs-org-margin)[description]: Fix grammar. * gnu/packages/haskell-xyz.scm (ghc-hslua-core)[description]: Fix grammar. * gnu/packages/tex.scm (texlive-autoaligne)[description]: Fix grammar. (texlive-biblatex-realauthor)[description]: Fix grammar. (texlive-citeall)[description]: Fix grammar. (texlive-formal-grammar)[description]: Fix grammar. (texlive-musikui)[description]: Fix grammar. (texlive-stanli)[description]: Fix grammar. (texlive-theatre)[description]: Fix grammar. (texlive-unitn-bimrep)[description]: Fix grammar. (texlive-yquant)[description]: Fix grammar. (texlive-expkv-bundle)[description]: Fix grammar. (texlive-ketcindy)[description]: Fix grammar. (texlive-srcredact)[description]: Fix grammar. (texlive-luamesh)[description]: Fix grammar. (texlive-maker)[description]: Fix grammar. (texlive-puyotikz)[description]: Fix grammar. (texlive-scratch)[description]: Fix grammar. (texlive-scratch3)[description]: Fix grammar. (texlive-strands)[description]: Fix grammar. (texlive-tikz-imagelabels)[description]: Fix grammar. (texlive-twemojis)[description]: Fix grammar. (texlive-unicode-bidi)[description]: Fix grammar. (texlive-pst-contourplot)[description]: Fix grammar. (texlive-pst-rputover)[description]: Fix grammar. (texlive-pst-vehicle)[description]: Fix grammar. (texlive-truthtable)[description]: Fix grammar. (texlive-esk)[description]: Fix grammar. (texlive-luaimageembed)[description]: Fix grammar. (texlive-bibletext)[description]: Fix grammar. (texlive-easyfloats)[description]: Fix grammar. (texlive-ehhline)[description]: Fix grammar. (texlive-exercises)[description]: Fix grammar. (texlive-extract)[description]: Fix grammar. (texlive-graphpaper)[description]: Fix grammar. (texlive-hereapplies)[description]: Fix grammar. (texlive-hvextern)[description]: Fix grammar. (texlive-hvqrurl)[description]: Fix grammar. (texlive-intopdf)[description]: Fix grammar. (texlive-jobname-suffix)[description]: Fix grammar. (texlive-modernposter)[description]: Fix grammar. (texlive-multiaudience)[description]: Fix grammar. (texlive-overlays)[description]: Fix grammar. (texlive-pdfpc)[description]: Fix grammar. (texlive-pgfmath-xfp)[description]: Fix grammar. (texlive-phonenumbers)[description]: Fix grammar. (texlive-romanbarpagenumber)[description]: Fix grammar. (texlive-texments)[description]: Fix grammar. (texlive-xcntperchap)[description]: Fix grammar. * gnu/packages/web.scm (libjuice)[description]: Fix grammar.
2024-11-01gnu: Add r-netid.Navid Afkhami
* gnu/packages/bioinformatics.scm (r-netid): New variable. Change-Id: Icf8fd23c6f24252350c783faa7f34f35eb1fbce2 Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
2024-11-01gnu: Add r-cellchat-2.Afkhami, Navid
* gnu/packages/bioinformatics.scm (r-cellchat-2): New variable. Change-Id: Iae15f373aefa1c2a0899d5271cf8dddbbfdfa2bd
2024-11-01gnu: Add r-scdesign2.Afkhami, Navid
* gnu/packages/bioinformatics.scm (r-scdesign2): New variable. Change-Id: I25599df1cb8493bc2d9cc1839b5232aee03bf848
2024-11-01gnu: Add r-spacexr.Afkhami, Navid
* gnu/packages/bioinformatics.scm (r-spacexr): New variable. Change-Id: Icf2a7dd9d637d14d835c7a428093ba8daf25e25a
2024-10-23gnu: wfmash: Skip tests on riscv64-linux.Efraim Flashner
* gnu/packages/bioinformatics.scm (wfmash)[arguments]: Skip the tests when building on riscv64-linux. Change-Id: I95c7849f445b866756fed17ca46b3d0bad088f21
2024-10-22gnu: wfmash: Update to 0.21.0.Arun Isaac
* gnu/packages/bioinformatics.scm (wfmash): Update to 0.21.0. [source]: Use url-fetch. [arguments]: Do not replace standard check phase. Add fix-cmakelists and build-check-prerequisites phases. [inputs]: Remove jemalloc. Add libdeflate. Change-Id: I664178e9fac7320b9d6e3190e8a3779b2bce2c6b
2024-10-20gnu: mudskipper: Build with cmake-minimal.Efraim Flashner
* gnu/packages/bioinformatics.scm (mudskipper)[native-inputs]: Replace cmake with cmake-minimal. Change-Id: I3af7ced7a0547900aa3f452d0b56ceac2e8d0a0c
2024-10-20gnu: circtools: Build with cmake-minimal.Efraim Flashner
* gnu/packages/bioinformatics.scm (circtools)[native-inputs]: Replace cmake with cmake-minimal. Change-Id: I4a7c49e88c3e820bfcaaea9c7bf2cff4b018a853
2024-09-30gnu: Update python-rdflib to 7.0.0.Roel Janssen
* gnu/packages/rdf.scm: Add updated recipe for python-rdflib; Keep python-rdflib-6 for compatibility. * gnu/packages/python-xyz.scm: Build python-prov with python-rdflib-6 because rdflib-7 is not supported. * gnu/packages/bioinformatics.scm: Build cwltool with python-rdflib-6 because it fails to build with rdflib-7. Change-Id: Ibc40c16ede20e69e702915488d6b2f0a7e70b868
2024-09-25gnu: python-pyfaidx: Add dependency on UTF-8 locales for tests.Ludovic Courtès
Fixes a regression introduced in 92727f4af5d410b0a521d57d5ecef6b35779bdc2 whereby the “en_US.utf8” locale would no longer be available in the build environment. * gnu/packages/bioinformatics.scm (python-pyfaidx)[native-inputs]: Add ‘libc-utf8-locales-for-target’. Change-Id: I4f868edb82ef08bb56e5d7e3d2ea861bd23c03bf
2024-09-21gnu: Add r-pairwiseadonis.Mădălin Ionel Patrașcu
* gnu/packages/bioinformatics.scm (r-pairwiseadonis): New variable. Change-Id: Idf7ad9efa3625bb60663f421ec79d0a69170e4dd Signed-off-by: Andreas Enge <andreas@enge.fr>
2024-08-31gnu: bandage: Do not yet use the 'imagemagick/stable' variant.Maxime Devos
Once <https://issues.guix.gnu.org/47475> (‘Closure of bandage is way too large’) has been fixed, the variant will probably be usable. * gnu/packages/bioinformatics.scm (bandage): [arguments]<#:disallowed-references>: Once the issue has been fixed, prevent the imagemagick/stable package from ending up in the closure. [native-inputs]: Note that 'imagemagick/stable' cannot be used yet. Signed-off-by: Maxim Cournoyer <maxim.cournoyer@gmail.com> Modified-by: Maxim Cournoyer <maxim.cournoyer@gmail.com> Change-Id: Ie13100eb424b14971055ff91db49bc7029cb6168
2024-08-31gnu: flair: Add bash-minimal to inputs.Maxim Cournoyer
* gnu/packages/bioinformatics.scm (flair) [inputs]: Add bash-minimal. Change-Id: I66fd550c617430ebbede36e140ee48df1c6149ca
2024-08-31gnu: ccwl: Remove input labels.Maxim Cournoyer
* gnu/packages/bioinformatics.scm (ccwl) [inputs]: Remove input labels. Change-Id: Ie00325f7472524a0c8431b98ca6172a2f7f7096a
2024-08-31gnu: arriba: Add bash-minimal to inputs.Maxim Cournoyer
* gnu/packages/bioinformatics.scm (arriba) [inputs]: Add bash-minimal. Change-Id: Ib30f9e0872dc24ca24e498eba51560c750e75d22
2024-08-31gnu: nanopolish: Add bash-minimal to inputs.Maxim Cournoyer
* gnu/packages/bioinformatics.scm (nanopolish) [inputs]: Add bash-minimal. Change-Id: Ie9cbe808e1ae678fb56db03537721f43da3c2b4c
2024-08-31gnu: filtlong: Add bash-minimal to inputs.Maxim Cournoyer
* gnu/packages/bioinformatics.scm (filtlong) [inputs]: Add bash-minimal. Change-Id: I8a4b402d66a06a27c9cc8abacdefecd251c2095c
2024-08-31gnu: ngless: Add bash-minimal to inputs.Maxim Cournoyer
* gnu/packages/bioinformatics.scm (ngless) [inputs]: Add bash-minimal. Change-Id: I3560d4f10261f87c819bd12cf0956a6cf77324cb
2024-08-31gnu: rcas-web: Add bash-minimal to inputs.Maxim Cournoyer
* gnu/packages/bioinformatics.scm (rcas-web)[inputs]: Add bash-minimal. Change-Id: I71f0e435e969e0a689caea90d9f442929c7d9431
2024-08-31gnu: shorah: Add bash-minimal to inputs.Maxim Cournoyer
* gnu/packages/bioinformatics.scm (shorah) [inputs]: Add bash-minimal. Change-Id: Ibe428a0ec32a5acf7e70269376aaf16e97507d51
2024-08-31gnu: rsem: Add bash-minimal to inputs.Maxim Cournoyer
* gnu/packages/bioinformatics.scm (rsem) [inputs]: Add bash-minimal. Change-Id: Idd9fbf729e9bcdd009cf517ec23064544bdf6f43
2024-08-31gnu: roary: Add bash-minimal to inputs.Maxim Cournoyer
* gnu/packages/bioinformatics.scm (roary): Delete trailing #t. [inputs]: Add bash-minimal. Remove labels. Change-Id: Id5ea1b12e2fa641d96a762f5f3b89edbd43a4ffa
2024-08-31gnu: proteinortho: Add bash-minimal to inputs.Maxim Cournoyer
* gnu/packages/bioinformatics.scm (proteinortho)[inputs]: Add bash-minimal. Remove labels. Change-Id: I74e243d598a544a9a58ea77a229b6a2b2f56c5b2
2024-08-31gnu: mafft: Add bash-minimal to inputs.Maxim Cournoyer
* gnu/packages/bioinformatics.scm (mafft): Delete trailing #t. [inputs]: Add bash-minimal. Change-Id: Id30d22dc37ee57591f17dc116de81500b09adf3c
2024-08-31gnu: edirect: Add bash-minimal to inputs.Maxim Cournoyer
* gnu/packages/bioinformatics.scm (edirect): Delete trailing #t. [inputs]: Add bash-minimal. Change-Id: I28474c3ec5866b5e9f824d5d71e6cc8be5791f58
2024-08-31gnu: repeat-masker: Add bash-minimal to inputs.Maxim Cournoyer
* gnu/packages/bioinformatics.scm (repeat-masker) [inputs]: Add bash-minimal. Change-Id: I81d4806cc65eed8040824cb72d6c462c8762294e
2024-08-31gnu: bioperl-minimal: Add bash-minimal to inputs.Maxim Cournoyer
* gnu/packages/bioinformatics.scm (bioperl-minimal) [inputs]: Add bash-minimal. Change-Id: I274572a2e87f63afcca2e433454a71f078291a06
2024-08-31gnu: ribotaper: Add bash-minimal to inputs.Maxim Cournoyer
* gnu/packages/bioinformatics.scm (ribotaper) [inputs]: Add bash-minimal. Change-Id: I5adc841c15c054101d32f30579a89aa7290c6f3c
2024-08-31gnu: ccwl: Import the correct set of modules.Maxim Cournoyer
* gnu/packages/bioinformatics.scm (ccwl) [arguments] <modules>: Replace %default-gnu-imported-modules with %default-gnu-modules. Change-Id: I9c96e847de537b11bc8396d6c0e7968a1a9f3e98
2024-08-31build-systems: gnu: Export %default-gnu-imported-modules and ↵Maxim Cournoyer
%default-gnu-modules. Until now users would have to cargo cult or inspect the private %default-modules variable of (guix build-systems gnu) to discover which modules to include when extending the used modules via the #:modules argument. The renaming was automated via the command: $ git grep -l %gnu-build-system-modules | xargs sed 's/%gnu-build-system-modules/%default-gnu-imported-modules/' -i * guix/build-system/gnu.scm (%gnu-build-system-modules): Rename to... (%default-gnu-imported-modules): ... this. (%default-modules): Rename to... (%default-gnu-modules): ... this. Export. (dist-package, gnu-build, gnu-cross-build): Adjust accordingly. Change-Id: Idef307fff13cb76f3182d782b26e1cd3a5c757ee
generated by cgit v1.2.3 (git 2.45.2) at 2025-04-16 05:08:44 +0000