| Age | Commit message (Expand) | Author |
|---|
| 2024-03-14 | gnu: Add morpheus....* gnu/packages/bioinformatics.scm (morpheus): New variable.
Co-authored-by: Navid Afkhami <navid.afkhami@mdc-berlin.de>
Change-Id: I4bf14414f497ff17690b1d26420d442d236fd6b5
| Ricardo Wurmus |
| 2024-03-06 | gnu: go-github.com-ulikunitz-xz: Adjust name....* gnu/packages/golang-compression.scm (go-github.com-ulikunitz-xz):
Rename variable to go-github-com-ulikunitz-xz to follow golang naming
style.
* gnu/packages/admin.scm (fiano) [inputs]: Remove
go-github.com-ulikunitz-xz. Add go-github-com-ulikunitz-xz.
* gnu/packages/bioinformatics.scm (go-github-com-biogo-hts-cram)
[propagated-inputs]: Remove go-github.com-ulikunitz-xz. Add
go-github-com-ulikunitz-xz.
Change-Id: Id2f2556666c4f9a08e0203f5ca7eb8352c492051
| Sharlatan Hellseher |
| 2024-02-28 | gnu: bowtie1: Enable cross-compiling....* gnu/packages/bioinformatics.scm (bowtie1)[arguments]: Adjust
make-flags to enable cross-compiling.
Change-Id: I6f5696e5ad6a1ea5b3f79e8dbbd162f0fe8d4905
| Efraim Flashner |
| 2024-02-28 | gnu: bowtie1: Enable building on more systems....* gnu/packages/bioinformatics.scm (bowtie1)[arguments]: Add make-flag to
disable searching for cpu features on non-x86 systems.
[supported-systems]: Enable all 64-bit supported systems.
Change-Id: Ice30df945ba154e39cd58a91847329e81038a3af
| Efraim Flashner |
| 2024-02-28 | gnu: bowtie1: Update to 1.3.1....* gnu/packages/bioinformatics.scm (bowtie1): Update to 1.3.1.
[arguments]: Add test-target.
[inputs]: Use newer tbb.
Change-Id: I7af6aa248e5db9f91ce84fba9ba741621b110479
| Efraim Flashner |
| 2024-02-22 | gnu: cwltool: Update to 3.1.20240112164112....* 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>
| Arun Isaac |
| 2024-02-22 | gnu: Add python-cwl-utils....* gnu/packages/bioinformatics.scm (python-cwl-utils): New variable.
Change-Id: I9347c80c0e866b89a7d432091fbcf1bc009209a5
Signed-off-by: Arun Isaac <arunisaac@systemreboot.net>
| Arun Isaac |
| 2024-02-22 | gnu: Add python-cwl-upgrader....* gnu/packages/bioinformatics.scm (python-cwl-upgrader): New variable.
Change-Id: I2022239840e9fe9e745689ef8b8bf4279be2ff9e
Signed-off-by: Arun Isaac <arunisaac@systemreboot.net>
| Arun Isaac |
| 2024-02-22 | gnu: Add python-cwlformat....* gnu/packages/bioinformatics.scm (python-cwlformat): New variable.
Change-Id: Ib2d79e350ab100c61c7afe2d5d3eafc72146e493
Signed-off-by: Arun Isaac <arunisaac@systemreboot.net>
| Arun Isaac |
| 2024-02-22 | gnu: python-schema-salad: Update to 8.5.20240102191335....* 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>
| Arun Isaac |
| 2024-02-20 | gnu: python-pyega3: Define as deprecated alias for python-ega-download-client....* 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
| Ricardo Wurmus |
| 2024-02-20 | gnu: python-ega-download-client: Disable some tests....* gnu/packages/bioinformatics.scm (python-ega-download-client)[arguments]:
Disable tests that fail on big machines; use "--ignore" where appropriate.
Change-Id: I010c3a0e7cb69184b72e8b13bad04ff2fd364f5a
| nafkhamdc |
| 2024-02-19 | gnu: r-archr: Update to 1.0.2-1.c61b064....* gnu/packages/bioinformatics.scm (r-archr): Update to 1.0.2-1.c61b064.
Change-Id: I8967cedbfc3390c364f188d50f8ecb2b27cb1417
| Ricardo Wurmus |
| 2024-02-19 | gnu: python-ega-download-client: Add missing input....* gnu/packages/bioinformatics.scm (python-ega-download-client)
[native-inputs]: Add python-mock.
Change-Id: I3befca6de33f959f4d916caa839d7201c77e8209
Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
| nafkhamdc |
| 2024-02-15 | gnu: Add python-ega-download-client....* gnu/packages/bioinformatics.scm (python-ega-download-client): New variable.
Change-Id: I3233774975989f912281ab2e6ec6ad3362cae18b
Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
| nafkhamdc |
| 2024-02-13 | gnu: go-github.com-ulikunitz-xz: Move to golang-compression....* 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
| Sharlatan Hellseher |
| 2024-02-13 | gnu: go-golang-org-x-text: Move to golang-build....* 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
| Sharlatan Hellseher |
| 2024-02-10 | gnu: Add python-pdbfixer....* gnu/packages/bioinformatics.scm (python-pdbfixer): New variable.
Change-Id: I2894a08ab3eed463f052b9df6372d4016b718d1a
Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
| nafkhamdc |
| 2024-01-26 | gnu: ccwl: Update to 0.3.0....* gnu/packages/bioinformatics.scm (ccwl): Update to 0.3.0.
[arguments]: Add patch-more-source-shebangs phase.
Change-Id: Ic7926d04c28eeafd799deba5e817574663431db8
| Arun Isaac |
| 2024-01-25 | gnu: Add music....* gnu/packages/bioinformatics.scm (music): New variable.
Change-Id: Iba5c986a0d3143118d4640d3ee9d4dae8119163f
| Ricardo Wurmus |
| 2024-01-23 | gnu: Add flash....* gnu/packages/bioinformatics.scm (flash): New variable.
Change-Id: Id657ba7850031ad24b4333b6bc79401511e00a85
| Ricardo Wurmus |
| 2024-01-23 | gnu: Add isolator....* gnu/packages/bioinformatics.scm (isolator): New variable.
Change-Id: I950baca5b6898576f358b3364b1fe541b3333298
| Ricardo Wurmus |
| 2024-01-23 | gnu: Add metal....* gnu/packages/bioinformatics.scm (metal): New variable.
Change-Id: I70fd30c18303f61a9f6720e70d4b4e57140a7140
| Ricardo Wurmus |
| 2024-01-23 | gnu: Add randfold....* gnu/packages/bioinformatics.scm (randfold): New variable.
Change-Id: If2cea9c8d5323296015dc21ea7a3d1b677ae2798
| Ricardo Wurmus |
| 2024-01-23 | gnu: Add python-pyfasta....* gnu/packages/bioinformatics.scm (python-pyfasta): New variable.
Change-Id: Ib2ab0a6eb250309633d5be33c18409227bce84ba
| Ricardo Wurmus |
| 2024-01-23 | gnu: Add python-fcsparser....* gnu/packages/bioinformatics.scm (python-fcsparser): New variable.
Change-Id: I87ed7f10bbfdf7d689cb6289a5f5ad31872f9de0
| Ricardo Wurmus |
| 2024-01-23 | gnu: Add lsgkm....* gnu/packages/bioinformatics.scm (lsgkm): New variable.
Change-Id: I0ea35354c7856e7425567cd4ac27ab7fc2ab0d9e
| Ricardo Wurmus |
| 2024-01-23 | gnu: Add eddylab-squid....* gnu/packages/bioinformatics.scm (eddylab-squid): New variable.
Change-Id: Icb02f42fc95d2001a639e22608a01ef9074158bc
| Ricardo Wurmus |
| 2024-01-23 | gnu: Add python-magic-impute....* gnu/packages/bioinformatics.scm (python-magic-impute): New variable.
Change-Id: Iba5240e9920a1045078c736553cb1d56069963b5
| Ricardo Wurmus |
| 2024-01-23 | gnu: Add r-scenic....* gnu/packages/bioinformatics.scm (r-scenic): New variable.
Change-Id: Iff1f501a406ba1a12e49093a575e03facc98f303
| Ricardo Wurmus |
| 2024-01-19 | gnu: wfmash: Update to 0.12.5....* 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
| Arun Isaac |
| 2024-01-17 | gnu: python-snaptools: Disable tests....* gnu/packages/bioinformatics.scm (python-snaptools)[arguments]: Disable
tests.
Change-Id: I4934bda3cfbaf42a87f57035ec12d084112dcc24
| Ricardo Wurmus |
| 2024-01-16 | gnu: Add samtools-1.14....* gnu/packages/bioinformatics.scm (samtools-1.14): New variable.
Change-Id: I0bd35b3865d7a417f55f1f768f7eb0c78a795e0f
| Ricardo Wurmus |
| 2024-01-16 | gnu: samtools: Update to 1.19....* gnu/packages/bioinformatics.scm (samtools): Update to 1.19.
[source]: Simplify snippet.
Change-Id: If0e02bbbc8e0443eb418c078dc47525f432d7ebe
| Ricardo Wurmus |
| 2024-01-16 | gnu: htslib: Update to 1.19....* gnu/packages/bioinformatics.scm (htslib): Update to 1.19.
Change-Id: I4d66d8ce37bfd335411a2acc6060f9a8c20c9e4a
| Ricardo Wurmus |
| 2024-01-16 | gnu: htscodecs: Update to 1.6.0....* gnu/packages/bioinformatics.scm (htscodecs): Update to 1.6.0.
Change-Id: Ibd5be30e8fbe7fe5d0ef494c1b1e0cd9ec3333cc
| Ricardo Wurmus |
| 2024-01-16 | gnu: python-readpaf: Explicitly disable tests....* gnu/packages/bioinformatics.scm (python-readpaf)[arguments]: Disable tests.
Change-Id: I28ddfa46675b74bd5073c12e5d33bcbf9dee8252
| Ricardo Wurmus |
| 2024-01-16 | gnu: python-bbknn: Update to 1.6.0....* 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
| Ricardo Wurmus |
| 2024-01-16 | gnu: python-telomerecat: Disable tests....* gnu/packages/bioinformatics.scm (python-telomerecat)[arguments]: Disable tests.
Change-Id: I0422ae1e563374a8cc408fc9584cfb7b0e880e95
| Ricardo Wurmus |
| 2024-01-16 | gnu: python-scikit-bio: Update to 0.5.9....* 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
| Ricardo Wurmus |
| 2024-01-16 | gnu: python-hicexplorer: Make compatible with latest scipy....* gnu/packages/bioinformatics.scm (python-hicexplorer)[arguments]: Add
'scipy-compatibility phase.
Change-Id: I31e9058b7fd4ff9245837d5f1cd145b569ec35ad
| Ricardo Wurmus |
| 2024-01-16 | gnu: python-hicmatrix: Update to 17.1....* gnu/packages/bioinformatics.scm (python-hicmatrix): Update to 17.1.
[arguments]: Remove.
Change-Id: I6b1230d703d0dc1a88ee61a84cc6cd95f7eeb6f9
| Ricardo Wurmus |
| 2024-01-16 | gnu: scvelo: Make compatible with latest matplotlib....* gnu/packages/bioinformatics.scm (scvelo)[arguments]: Add phase
'matplotlib-compatibility.
Change-Id: Ia761821c8aa1e516525cff7c680db471a5908e5f
| Ricardo Wurmus |
| 2024-01-16 | gnu: python-demuxem: Disable tests....* gnu/packages/bioinformatics.scm (python-demuxem)[arguments]: Disable tests,
because there aren't any.
Change-Id: I50364ca6744cf9d2704d4b75a8c79c4fdc4ada6e
| Ricardo Wurmus |
| 2024-01-16 | gnu: python-cooler: Update to 0.9.1....* 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
| Ricardo Wurmus |
| 2024-01-16 | gnu: python-plastid: Update to 0.6.1....* gnu/packages/bioinformatics.scm (python-plastid): Update to 0.6.1.
[arguments]: Disable four tests.
Change-Id: If0225f226e702e89d451e2955d0f76691a8816c0
| Ricardo Wurmus |
| 2024-01-16 | gnu: cnvkit: Update to 0.9.10....* gnu/packages/bioinformatics.scm (cnvkit): Update to 0.9.10.
[arguments]: Remove.
[inputs]: Add r-minimal.
Change-Id: Iaa27fd3dddc507c7a955441f066d4b0e3b8f1757
| Ricardo Wurmus |
| 2024-01-16 | gnu: python-pegasusio: Disable tests....* gnu/packages/bioinformatics.scm (python-pegasusio)[arguments]: Disable
tests.
Change-Id: I6b32ed416b562b47088dbc34eb7bcb0b8e2cc414
| Ricardo Wurmus |
| 2024-01-16 | gnu: python-pyani: Disable tests....There are none.
* gnu/packages/bioinformatics.scm (python-pyani)[arguments]: Disable tests.
Change-Id: I6862082c8335e5d487da6d1705ed094922f14e47
| Ricardo Wurmus |
| 2024-01-16 | gnu: tadbit: Add missing input....* gnu/packages/bioinformatics.scm (tadbit)[native-inputs]: Add glib.
Change-Id: Ia1f79e2a30f5b57616cf3d1f7b6438f07451fbbf
| Ricardo Wurmus |
