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2024-02-22gnu: cwltool: Update to 3.1.20240112164112.Arun Isaac
* gnu/packages/bioinformatics.scm (cwltool): Update to 3.1.20240112164112. [arguments]: Use G-expressions. Set version in setup.py. Do not attempt to substitute files cwltool/schemas/v1.1/tests/env-tool1.cwl, cwltool/schemas/v1.1/tests/env-tool2.cwl and cwltool/schemas/v1.1/tests/imported-hint.cwl that have been removed in this release. Do not remove "-n auto" from pytest flags. [inputs]: Add python-cwl-utils and python-spython. [native-inputs]: Add python-pytest-xdist. Change-Id: If1be7cdf39b767c5ef2a1dbddfdc95f59ea98cb6 Change-Id: I2ba81e8569abcf43cd0fad33daab1e4f8689e77f Signed-off-by: Arun Isaac <arunisaac@systemreboot.net>
2024-02-22gnu: Add python-cwl-utils.Arun Isaac
* gnu/packages/bioinformatics.scm (python-cwl-utils): New variable. Change-Id: I9347c80c0e866b89a7d432091fbcf1bc009209a5 Signed-off-by: Arun Isaac <arunisaac@systemreboot.net>
2024-02-22gnu: Add python-cwl-upgrader.Arun Isaac
* gnu/packages/bioinformatics.scm (python-cwl-upgrader): New variable. Change-Id: I2022239840e9fe9e745689ef8b8bf4279be2ff9e Signed-off-by: Arun Isaac <arunisaac@systemreboot.net>
2024-02-22gnu: Add python-cwlformat.Arun Isaac
* gnu/packages/bioinformatics.scm (python-cwlformat): New variable. Change-Id: Ib2d79e350ab100c61c7afe2d5d3eafc72146e493 Signed-off-by: Arun Isaac <arunisaac@systemreboot.net>
2024-02-22gnu: python-schema-salad: Update to 8.5.20240102191335.Arun Isaac
* gnu/packages/bioinformatics.scm (python-schema-salad): Update to 8.5.20240102191335. [native-inputs]: Add python-pytest-xdist. [propagated-inputs]: Add python-importlib-resources and python-mypy-extensions. Remove python-lockfile, python-rdflib-jsonld and python-typing-extensions. Replace python-mistune with python-mistune-next. [arguments]: Use G-expressions. Set exact version number. Skip more tests that require network access. Change-Id: I4de4704f58f40fdf9bf4c02e41c2c353beaa3eb2 Signed-off-by: Arun Isaac <arunisaac@systemreboot.net>
2024-02-20gnu: python-pyega3: Define as deprecated alias for python-ega-download-client.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (python-pyega3): Define as deprecated alias for python-ega-download-client. (python-ega-download-client)[description]: Merge with contents from python-pyega3. Change-Id: Ic7f4d0cf49cedaca78035dca95b48d317307084d
2024-02-20gnu: python-ega-download-client: Disable some tests.nafkhamdc
* gnu/packages/bioinformatics.scm (python-ega-download-client)[arguments]: Disable tests that fail on big machines; use "--ignore" where appropriate. Change-Id: I010c3a0e7cb69184b72e8b13bad04ff2fd364f5a
2024-02-19gnu: r-archr: Update to 1.0.2-1.c61b064.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-archr): Update to 1.0.2-1.c61b064. Change-Id: I8967cedbfc3390c364f188d50f8ecb2b27cb1417
2024-02-19gnu: python-ega-download-client: Add missing input.nafkhamdc
* gnu/packages/bioinformatics.scm (python-ega-download-client) [native-inputs]: Add python-mock. Change-Id: I3befca6de33f959f4d916caa839d7201c77e8209 Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
2024-02-15gnu: Add python-ega-download-client.nafkhamdc
* gnu/packages/bioinformatics.scm (python-ega-download-client): New variable. Change-Id: I3233774975989f912281ab2e6ec6ad3362cae18b Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
2024-02-13gnu: go-github.com-ulikunitz-xz: Move to golang-compression.Sharlatan Hellseher
* gnu/packages/golang.scm (go-github.com-ulikunitz-xz): Move from here ... * gnu/packages/golang-compression.scm: ... to here. * gnu/packages/admin.scm: Add (gnu packages golang-compression) module. * gnu/packages/bioinformatics.scm: As above. Change-Id: I1901e67ac4336efd356085332572b3f09de90f7a
2024-02-13gnu: go-golang-org-x-text: Move to golang-build.Sharlatan Hellseher
* gnu/packages/golang.scm (go-golang-org-x-text): Move from here ... * gnu/packages/golang-build.scm: ... to here. * gnu/packages/admin.scm: Add (gnu packages golang-build) module. * gnu/packages/bioinformatics.scm: As above. * gnu/packages/mail.scm: As above. Change-Id: Ifd15b35b460ae30c5c1d677551e95842b322b246
2024-02-10gnu: Add python-pdbfixer.nafkhamdc
* gnu/packages/bioinformatics.scm (python-pdbfixer): New variable. Change-Id: I2894a08ab3eed463f052b9df6372d4016b718d1a Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
2024-01-26gnu: ccwl: Update to 0.3.0.Arun Isaac
* gnu/packages/bioinformatics.scm (ccwl): Update to 0.3.0. [arguments]: Add patch-more-source-shebangs phase. Change-Id: Ic7926d04c28eeafd799deba5e817574663431db8
2024-01-25gnu: Add music.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (music): New variable. Change-Id: Iba5c986a0d3143118d4640d3ee9d4dae8119163f
2024-01-23gnu: Add flash.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (flash): New variable. Change-Id: Id657ba7850031ad24b4333b6bc79401511e00a85
2024-01-23gnu: Add isolator.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (isolator): New variable. Change-Id: I950baca5b6898576f358b3364b1fe541b3333298
2024-01-23gnu: Add metal.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (metal): New variable. Change-Id: I70fd30c18303f61a9f6720e70d4b4e57140a7140
2024-01-23gnu: Add randfold.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (randfold): New variable. Change-Id: If2cea9c8d5323296015dc21ea7a3d1b677ae2798
2024-01-23gnu: Add python-pyfasta.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (python-pyfasta): New variable. Change-Id: Ib2ab0a6eb250309633d5be33c18409227bce84ba
2024-01-23gnu: Add python-fcsparser.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (python-fcsparser): New variable. Change-Id: I87ed7f10bbfdf7d689cb6289a5f5ad31872f9de0
2024-01-23gnu: Add lsgkm.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (lsgkm): New variable. Change-Id: I0ea35354c7856e7425567cd4ac27ab7fc2ab0d9e
2024-01-23gnu: Add eddylab-squid.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (eddylab-squid): New variable. Change-Id: Icb02f42fc95d2001a639e22608a01ef9074158bc
2024-01-23gnu: Add python-magic-impute.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (python-magic-impute): New variable. Change-Id: Iba5240e9920a1045078c736553cb1d56069963b5
2024-01-23gnu: Add r-scenic.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-scenic): New variable. Change-Id: Iff1f501a406ba1a12e49093a575e03facc98f303
2024-01-19gnu: wfmash: Update to 0.12.5.Arun Isaac
* gnu/packages/bioinformatics.scm (wfmash): Update to 0.12.5. (source): Use git-fetch. Update git repository URL. (arguments): In check phase, symlink to "../source/data" and change wfmash invocation arguments. (home-page): Update URL. Change-Id: I78f228f06a6a12e6904a58a12fd4201743e84d72
2024-01-17gnu: python-snaptools: Disable tests.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (python-snaptools)[arguments]: Disable tests. Change-Id: I4934bda3cfbaf42a87f57035ec12d084112dcc24
2024-01-16gnu: Add samtools-1.14.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (samtools-1.14): New variable. Change-Id: I0bd35b3865d7a417f55f1f768f7eb0c78a795e0f
2024-01-16gnu: samtools: Update to 1.19.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (samtools): Update to 1.19. [source]: Simplify snippet. Change-Id: If0e02bbbc8e0443eb418c078dc47525f432d7ebe
2024-01-16gnu: htslib: Update to 1.19.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (htslib): Update to 1.19. Change-Id: I4d66d8ce37bfd335411a2acc6060f9a8c20c9e4a
2024-01-16gnu: htscodecs: Update to 1.6.0.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (htscodecs): Update to 1.6.0. Change-Id: Ibd5be30e8fbe7fe5d0ef494c1b1e0cd9ec3333cc
2024-01-16gnu: python-readpaf: Explicitly disable tests.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (python-readpaf)[arguments]: Disable tests. Change-Id: I28ddfa46675b74bd5073c12e5d33bcbf9dee8252
2024-01-16gnu: python-bbknn: Update to 1.6.0.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (python-bbknn): Update to 1.6.0. [arguments]: Remove phase 'do-not-fail-to-find-sklearn. [propagated-inputs]: Add python-pynndescent. [native-inputs]: Add python-flit-core. Change-Id: I5fca2d6ca52e54eb7650b3bb24a34a0aa47b1782
2024-01-16gnu: python-telomerecat: Disable tests.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (python-telomerecat)[arguments]: Disable tests. Change-Id: I0422ae1e563374a8cc408fc9584cfb7b0e880e95
2024-01-16gnu: python-scikit-bio: Update to 0.5.9.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (python-scikit-bio): Update to 0.5.9. [source]: Add patch. [arguments]: Disable one test via #:test-flags; adjust 'compatibility phase; update 'check phase. [propagated-inputs]: Remove python-cachecontrol, python-lockfile, and python-scikit-learn; add python-requests. * gnu/packages/patches/python-scikit-bio-1887.patch: New file. * gnu/local.mk (dist_patch_DATA): Add it. Change-Id: Ie57b0256cf695e5ea088545cd2102335303a93e7
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
generated by cgit-pink 1.4.1 (git 2.36.1) at 2024-12-18 10:18:58 +0000