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2025-03-07gnu: Add sickle.Navid Afkhami
* gnu/packages/bioinformatics.scm (sickle): New variable. Change-Id: Ib74974b0ee887753d6ead5b5b388e7163abb11f8
2025-03-06gnu: Add r-bayesprism.Navid Afkhami
* gnu/packages/bioinformatics.scm (r-bayesprism): New variable. Change-Id: I0eaefbaee0de6143fb892dda9c41459a5a5d30d6
2025-03-04gnu: r-voltron: Update to 0.2.0-5.21886d8.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-voltron): Update to 0.2.0-5.21886d8. [arguments]: Ensure that reference to Python is accessible by adding phase 'record-python-reference. Change-Id: Icc63ba931c7861f1e735671720106ec02f729bae
2025-02-25gnu: python-pygenometracks: Add missing native input.Sharlatan Hellseher
* gnu/packages/bioinformatics.scm (python-pygenometracks): [native-inputs]: Add python-wheel. Change-Id: I0294c84446603680498a4af5065a78f42129c476
2025-02-24gnu: ravanan: Patch shebang in executable.Arun Isaac
* gnu/packages/bioinformatics.scm (ravanan)[arguments]: Replace patch-source-shebangs phase with custom phase.
2025-02-22gnu: r-voltron: Update to 0.2.0-4.3817548.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-voltron): Update to 0.2.0-4.3817548. Change-Id: Ia7fbfb82a4b040008dc5d8830712c14b37a7ebd2
2025-02-21gnu: Add python-pygam.Navid Afkhami
* gnu/packages/bioinformatics.scm (python-pygam): New variable. Change-Id: I0bdd26546b17e3e0f96a32c6de9674d1731ba978 Signed-off-by: Ricardo Wurmus <[email protected]>
2025-02-21gnu: python-pdbfixer: Add missing inputs.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (python-pdbfixer)[native-inputs]: Add python-setuptools and python-wheel. Change-Id: If51cf62c3f88bf73290f7d29af0a6e8277ecddea
2025-02-20gnu: r-netid: Add Python inputs.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-netid)[propagated-inputs]: Add python-anndata, python-geosketch, python-scanpy, and scvelo. Change-Id: I67661d55769dcd23a1bc448c127d81c0e54065ae
2025-02-20gnu: Add mageck.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (mageck): New variable. Change-Id: I0d232473c983ac98aa01ef39a96e938da8628b7d
2025-02-20gnu: Add python-multicore-tsne.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (python-multicore-tsne): New variable. Change-Id: I156deff8a55890776105d9c8867bbf8dc968e2e2
2025-02-19gnu: Fix some misspellings.Efraim Flashner
Change-Id: I316652aff7418af4b8e83bea24638b1513f8aa97
2025-02-17gnu: Fix typos in bioinformatics packages.Vagrant Cascadian
* gnu/packages/bioinformatics.scm (python-scrublet)[synopsis]: Fix spelling of "identify". (maffilter)[description]: Fix spelling of "inference". (r-azimuth)[description]: Fix spelling of "accounts".
2025-02-13gnu: r-voltron: Update to 0.2.0-3.8f88699.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-voltron): Update to 0.2.0-3.8f88699. [propagated-inputs]: Add r-giotto, r-rhdf5, r-s4vectors, r-summarizedexperiment, and r-viridislite; remove r-hdf5r. Change-Id: Ib542f0471663992d5293aca4dc0552a411823112
2025-02-13gnu: r-giotto: Update to 1.1.2-1.3e6671a.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-giotto): Update to 1.1.2-1.3e6671a. Change-Id: I60d5d7af3df81f0785bcc5940c7012302dd28d5e
2025-02-11gnu: r-presto: Update to 1.0.0-1.7636b3d.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-presto): Update to 1.0.0-1.7636b3d. [properties]: Fix typo. [propagated-inputs]: Remove r-deseq2 and r-reshape2; add r-purrr and r-tibble. [native-inputs]: Add r-knitr. Change-Id: I1285062405bd42b7f3162a44ccf7b174492e5201
2025-02-07gnu: r-voltron: Add suggested packages.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-voltron):[propagated-inputs]: Add r-anndata, r-anndatar, r-arrow, r-bpcells, r-circlize, r-codetools, r-complexheatmap, r-delayedarray, r-deseq2, r-geojsonr, r-ggforce, r-ggnewscale, r-glmgampoi, r-hdf5array, r-hdf5dataframe, r-hdf5r, r-imagearray, r-music, r-rstudioapi, r-seurat, r-seuratobject, r-singlecellexperiment, r-spacexr, r-spatialexperiment, r-vitesscer, r-xml, and r-zarrdataframe. Change-Id: I4333de31d40e5760f15c5453b8cb974598c8aa5d
2025-02-07gnu: Add r-imagearray.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-imagearray): New variable. Change-Id: I432258e2e93e9161bedd95f50dcdd3c52d30457d
2025-02-07gnu: Add r-zarrdataframe.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-zarrdataframe): New variable. Change-Id: Iffe8a0fdad92e4443184642a85863b3b888fbfae
2025-02-07gnu: Add r-zarrarray.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-zarrarray): New variable. Change-Id: Ibc66e12966071551b0bc977f67c867303ca958d9
2025-02-07gnu: Add r-hdf5dataframe.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-hdf5dataframe): New variable. Change-Id: I0faa57f4d82ef71ad37f7c4cfa97fcc5aef5d67a
2025-02-07gnu: r-bpcells: Update to 0.3.0.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-bpcells): Update to 0.3.0. [arguments]: Remove phase 'do-not-tune; add phase 'chdir. [propagated-inputs]: Add r-lifecycle, r-readr, r-genomicranges, r-igraph, r-iranges, and r-matrixstats. [license]: Update to dual licensed ASL2.0 or Expat/MIT. Change-Id: I972c18e896372e3b44cd5c0ad2f669242568443f
2025-02-07gnu: Add r-music.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-music): New variable. Change-Id: I3cf73fcb58f9a407d2795a4525038ab00d1b523f
2025-02-06gnu: imp: Use an older version of boost.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (imp):[inputs]: Replace boost with boost-for-mysql. Change-Id: I3d3bec8589972f15770c264f4b2445f4798b7901
2025-02-06gnu: imp: Drop input labels.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (imp)[native-inputs]: Drop labels. Change-Id: I3182a4608a88c59ba0de2fa00d74b8d72b72d8bb
2025-02-05gnu: Add python-cnmf.Navid Afkhami
* gnu/packages/bioinformatics.scm (python-cnmf): New variable. Change-Id: I8a4f2293bde59b10e7b673025bbb4c5a8420738b Co-authored-by: Sharlatan Hellseher <[email protected]> Signed-off-by: Sharlatan Hellseher <[email protected]>
2025-02-05gnu: python-harmonypy: Patch invalid field in pyproject.toml.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (python-harmonypy)[arguments]: Add phase 'patch-pyproject. Change-Id: I0d80b96458c7bb5ddb571ad640babf6b95fb051f
2025-02-03gnu: Add ravanan.Arun Isaac
* gnu/packages/bioinformatics.scm (ravanan): New variable. Change-Id: Ib93ea64a3a0313be167dd1cd2f036c72f1c0f138 Signed-off-by: jgart <[email protected]>
2025-01-29gnu: python-scanpy: Disable one more test.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (python-scanpy)[arguments]: Disable one failing test. Change-Id: If262b33a3e2c6789c0ce4b8a91f26a8a48054632
2025-01-28gnu: ccwl: Update to 0.4.0.Arun Isaac
* gnu/packages/bioinformatics.scm (ccwl): Update to 0.4.0. Change-Id: I6726438f3a2ec9bb01971f14a22e4123abc01793
2025-01-26Merge remote-tracking branch 'origin/go-team'Sharlatan Hellseher
Change-Id: I3672a7dc248a41b1a83e4c488523f62cf1806710
2025-01-23gnu: Add r-vitesscer.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-vitesscer): New variable. Change-Id: I3e0426abd2ed1346efb833ab21c2524d28b41a99
2025-01-22gnu: Add go-github-com-biogo-store.Sharlatan Hellseher
This change merges all extracted subdirs under the same variable as it's distributed in single module according to project's go.mod. * gnu/packages/bioinformatics.scm (go-github-com-biogo-store-kdtree, go-github-com-biogo-store-llrb, go-github-com-biogo-store-step): Delete variables. (go-github-com-biogo-store): New variable. [arguments] <skip-build?>: No go files in project's root. <import-path>: Set as seen in go.mod. (go-github-com-biogo-biogo) [propagated-inputs]: Remove go-github-com-biogo-store-kdtree, go-github-com-biogo-store-llrb, and go-github-com-biogo-store-step. Add go-github-com-biogo-store. Change-Id: I1db4efea31fc7f1f5e96b21e874a523cf631f370
2025-01-22gnu: Add go-github-com-biogo-hts.Sharlatan Hellseher
This change merges all extracted subdirs under the same variable as it's distributed in single module according to project's go.mod. * gnu/packages/bioinformatics.scm (go-github-com-biogo-hts-bam, go-github-com-biogo-hts-bgzf, go-github-com-biogo-hts-cram, go-github-com-biogo-hts-csi, go-github-com-biogo-hts-fai, go-github-com-biogo-hts-sam, go-github-com-biogo-hts-tabix): Delete variables. (go-github-com-biogo-hts): New variable. [arguments] <skip-build?>: No go files in project's root. <import-path>: Set as seen in go.mod. <test-flags>: Skip 2 tests requiring network access. (go-github-com-biogo-biogo) [propagated-inputs]: Remove go-github-com-biogo-hts-bam, add go-github-com-biogo-hts. Change-Id: I2cace7a0c732e7590b3b34865323bc38b41b0d86
2025-01-22gnu: Add r-sigfit.Alexis Simon
* gnu/packages/bioinformatics.scm (r-sigfit): New variable. Change-Id: I9d63975d3512cf8583e7ec22f450bb4963c9ff2f Signed-off-by: Ricardo Wurmus <[email protected]>
2025-01-22gnu: r-voltron: Update to 0.2.0-2.bbd7abb.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-voltron): Update to 0.2.0-2.bbd7abb. [arguments]: Add phase 'do-not-use-conda. [propagated-inputs]: Remove r-basilisk; add r-pizzarr and r-rhdf5. Change-Id: I4c57c154c8bac41d056fadb936a109ca6310d8d6
2025-01-22gnu: Add r-pizzarr.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-pizzarr): New variable. Change-Id: Ia922dfb4ef418ecd4317ce6127b88ecf91bd2cc7
2025-01-22gnu: python-biom-format: Add missing input.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (python-biom-format)[native-inputs]: Add python-wheel. Change-Id: I7d462a05a73335bd1be72ab615d2550ed48a0383
2025-01-20gnu: Move python-pysnptools to (gnu packages bioinformatics).Ricardo Wurmus
* gnu/packages/python-xyz.scm (python-pysnptools): Move from here... * gnu/packages/bioinformatics.scm (python-pysnptools): ...to here. Change-Id: I4dbd9cbe3f2d9a6dd4906be79b78862b39a57c28
2025-01-20gnu: Add python-bed-reader.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (python-bed-reader): New variable. Change-Id: Iad3f1d1c05abe706d8cd52a4d046247a5a9738e2
2025-01-20gnu: python-fanc: Update to 0.9.28.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (python-fanc): Update to 0.9.28. [arguments]: Remove custom 'check phase; disable tests that seemingly freeze. [propagated-inputs]: Add python-imageio, python-pywavelets, and python-tifffile; remove python-pytest. [native-inputs]: Add python-pytest, python-setuptools, and python-wheel. Change-Id: Ia83f5fe1d0cbbf56840061feb9561e439380e965
2025-01-20gnu: Deprecate fanc.Ricardo Wurmus
fanc is a duplicate of python-fanc. * gnu/packages/bioinformatics.scm (fanc): Define as deprecated name for python-fanc. Change-Id: I28e330d9bfe64fd59b49001ecc56e2c6fd191b55
2025-01-20gnu: python-screed: Update to 1.1.3.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (python-screed): Update to 1.1.3. [native-inputs]: Add python-importlib-resources, python-pycodestyle, python-pytest, python-setuptools-scm, and python-setuptools-scm-git-archive; removve python-pytest-runner. Change-Id: I3ce12acedbbc97d58f2266e042872494556afd3b
2025-01-20gnu: python-mofax: Update to 0.3.7-1.e4821fe.Ricardo Wurmus
This looks like a downgrade, but it is in fact a more recent commit. * gnu/packages/bioinformatics.scm (python-mofax): Update to 0.3.7-1.e4821fe. [source]: Remove obsolete snippet. [arguments]: Remove test flags. [propagated-inputs]: Move python-poetry-core from here... [native-inputs]: ...to here. Change-Id: I6093d282887135f6b99d34a853cd9371cffe98f1
2025-01-20gnu: python-pybio: Fix build.宋文武
* gnu/packages/bioinformatics.scm (python-pybio)[native-inputs]: Add python-setuptools and python-wheel. Change-Id: I1eca46c4a8dc5aa6eb090e20de387129c4590529
2025-01-20gnu: python-whatshap: Add missing input.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (python-whatshap)[native-inputs]: Add python-wheel. Change-Id: I51f9bb3791434befb61ecc6225060d6a4eb92dab
2025-01-20gnu: python-pyrodigal: Add missing input.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (python-pyrodigal)[native-inputs]: Add python-wheel. Change-Id: Ide41099084a50748f32a9ba11cbbe9dd4514094f
2025-01-20gnu: instrain: Update to 1.9.0.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (instrain): Update to 1.9.0. [source]: Fetch git repository. [build-system]: Use pyproject-build-system. [arguments]: Disable tests. [inputs]: Move all from here... [propagated-inputs]: ...to here; remove python-boto3, python-numba, python-scikit-learn, and python-drep. [native-inputs]: Add python-boto3, python-setuptools, and python-wheel. Change-Id: Ied1e909a6b22518908b95a43b8db5f35bd6c6ac6
2025-01-20gnu: scregseg: Patch for numpy compatibility.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (scregseg)[arguments]: Add phase 'compatibility. Change-Id: I738d675c10acdbae7d40b3f806703ba8f7936a19
2025-01-20gnu: python-episcanpy: Add missing input.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (python-episcanpy)[native-inputs]: Add python-wheel. Change-Id: Iba4ac520faf00e3db64df3532752b1de3eec1bc6
generated by cgit v1.2.3 (git 2.45.2) at 2025-04-04 13:09:30 +0000