summaryrefslogtreecommitdiff
path: root/gnu/packages/bioinformatics.scm
AgeCommit message (Collapse)Author
2024-05-05gnu: python-liana-py: Update to 1.1.0.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (python-liana-py): Update to 1.1.0. [arguments]: Adjust tests; add phase 'relax-requirements. [propagated-inputs]: Remove python-mofax; add python-numpy. [native-inputs]: Remove python-numpy; add python-poetry-core. Change-Id: I279be08ac3ac73d9a724f59652f2f0d333607696
2024-05-05gnu: python-cooltools: Update to 0.7.0.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (python-cooltools): Update to 0.7.0. [build-system]: Use pyproject-build-system. [arguments]: Remove. Change-Id: I4112bf0cbc309df551087b8bb3cb1d37af7f751d
2024-05-05gnu: python-bioframe: Update to 0.6.4.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (python-bioframe): Update to 0.6.4. [build-system]: Use pyproject-build-system. [arguments]: Remove custom 'check phase; add 'pre-check phase. Use #:test-flags to disable tests that require internet access. [native-inputs]: Add python-hatchling. [propagated-inputs]: Add python-pyyaml. Change-Id: Iad1c8c6ef8f52886e398e9c4d2d384c5fce075c6
2024-05-05gnu: python-decoupler-py: Update to 1.6.0.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (python-decoupler-py): Update to 1.6.0. [arguments]: Do not disable test_plot_volcano test. Change-Id: I44a31d30e8a03d2d1ffd86383c8bc6db79628def
2024-05-05gnu: python-hicexplorer: Update to 3.7.4.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (python-hicexplorer): Update to 3.7.4. [source]: Remove obsolete snippet. [arguments]: Remove obsolete phase 'scipy-compatibility. [propagated-inputs]: Replace python-cleanlab-1 with python-cleanlab. Change-Id: Iac9a24cc4551b7d7e1d41d1f07a6db6d620b119e
2024-05-05gnu: tadbit: Add R to inputs.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (tadbit)[inputs]: Add r-minimal. Change-Id: I4929dd89ddd27b4fcbd8b3a00b8ab8f3586945d2
2024-05-05gnu: tadbit: Patch for compatibility with latest scipy.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (tadbit)[arguments]: Add phase 'scipy-compatibility. Change-Id: Ib25b9cde75f0505c347c4ff470e61f06fb162839
2024-05-05gnu: tadbit: Update to 1.0.1-2.2838129.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (tadbit): Update to 1.0.1-2.2838129. Change-Id: I2c220ae37cd196ca508d30aefc24938cce985527
2024-05-05gnu: python-cooler: Update to 0.9.3.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (python-cooler): Update to 0.9.3. Change-Id: I4b89d552a424e74f76cda0c527dc7b712b8c9f31
2024-05-05gnu: python-scikit-bio: Update to 0.6.0.Ricardo Wurmus
* gnu/packages/patches/python-scikit-bio-1887.patch: Delete file. * gnu/local.mk (dist_patch_DATA): Remove patch. * gnu/packages/bioinformatics.scm (python-scikit-bio): Update to 0.6.0. [source]: Remove patch. [arguments]: Disable skbio.diversity doctest; remove 'compatibility phase. [propagated-inputs]: Add python-biom-format; remove python-ipython and python-matplotlib. Change-Id: I9bd9e0fd72f5f1b80ef6ff61c52da5fd56a715ed
2024-05-05gnu: python-biom-format: Untangle from python-scikit-bio.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (python-biom-format)[arguments]: Add phase 'pandas-compatibility; disable tests that need sciki-bio. [propagated-inputs]: Remove python-scikit-bio. Change-Id: Ifd528d256a1c75962fb05aef5602edbf67a5af26
2024-05-05gnu: tadbit: Use G-expression.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (tadbit)[arguments]: Use G-expression. Change-Id: I4fe4afc41eb3442f243b0e415ddcb363be36ce7f
2024-05-05gnu: python-plastid: Replace nose with pytest.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (python-plastid)[native-inputs]: Replace python-nose with python-pytest. Change-Id: Ie0e5362d2304d3af0bcb1405fa0c1ad36fb2ace6
2024-05-05gnu: Add python-metacells.Marco Baggio
* gnu/packages/bioinformatics.scm (python-metacells): New variable. Co-authored-by: Ricardo Wurmus <rekado@elephly.net> Change-Id: I4fc760dc4317bde79c815f441ad0cc453248990a
2024-04-22gnu: Add r-saige.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-saige): New variable. Change-Id: Id5bda4d25ca61fe26d11bae0af19900fd0f0080e
2024-04-22gnu: Add savvy.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (savvy): New variable. Change-Id: I48dcfad2c6c769778bd79dffa084332da53991ad
2024-04-22gnu: python-deeptools: Replace python-nose with python-pytest.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (python-deeptools)[native-inputs]: Replace python-nose with python-pytest. Change-Id: Icba4ed3a464bfa36616aabe2cbbb26bfabec40aa
2024-04-22gnu: Add python-cyvcf2.Alexis Simon
* gnu/packages/bioinformatics.scm (python-cyvcf2): New variable. Co-authored-by: Ricardo Wurmus <rekado@elephly.net> Change-Id: I0db07e7b5840f5c1f5c68512ffabb3d6b39ab95c
2024-04-20gnu: java-guava: Update to 31.1.Julien Lepiller
* gnu/packages/patches/java-guava-remove-annotation-deps.patch: New file. * gnu/local.mk (dist_patch_DATA): Add it. * gnu/packages/java.scm (java-guava): Update to 31.1. [source]: Use patch. (java-guava-futures-failureaccess): New variable. * gnu/packages/bioinformatics.scm (java-picard, java-picard-2.10.3): Fix for newer guava. * gnu/packages/maven.scm (maven): Add java-guava-futures-failureaccess. Change-Id: Id2553c48e11c6001fb45a0589720cef1551804d9
2024-04-12gnu: go-github-com-fatih-color: Move to golang-xyz.Sharlatan Hellseher
* gnu/packages/golang.scm (go-github-com-fatih-color): Move from here ... * gnu/packages/golang-xyz.scm: ... to here. * gnu/packages/bioinformatics.scm: Add (gnu packages golang-xyz) module. Change-Id: I302327d3426100d7984e6086726396e9fe7f7468
2024-04-09gnu: python-deeptools: Update to 3.5.5.Simon Tournier
* gnu/packages/bioinformatics.scm (python-deeptools): Update to 3.5.5. [build-system]: Replace by pyproject-build-system. [arguments]: Add phase that fixes 'test/test_tools.py'. Change-Id: Ibb51939275c96df2c4a1e248a03d683f2f4904ac Signed-off-by: Christopher Baines <mail@cbaines.net>
2024-04-04gnu: proteinortho: Remove dependency on lapack.Romain GARBAGE
* gnu/packages/bioinformatics.scm (proteinortho): Remove dependency on lapack. Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2024-04-04gnu: eigensoft: Remove dependency on lapack.Romain GARBAGE
* gnu/packages/bioinformatics.scm (eigensoft): Remove dependency on lapack. Change-Id: I9d4adfd64a32333a0d605d4ce1aa998035decf2a Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2024-04-04gnu: plink-ng: Remove lapack dep.Romain GARBAGE
* gnu/packages/bioinformatics.scm (plink-ng): Remove dependency to lapack. Change-Id: I4d14789c42dc216244872d70120efeeb97127a62 Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2024-04-04gnu: plink: Switch to openblas.Romain GARBAGE
* gnu/packages/bioinformatics.scm (plink): Switch input dependency from lapack to openblas. Change-Id: I8066a50c880b72a77ba00c2bc39403e212605b9d Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2024-03-21gnu: Add r-pairadise.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-pairadise): New variable. Change-Id: I7314d43c75ed008942757feb878628d1ac855f31
2024-03-21gnu: Add pairadise.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (pairadise): New variable. Change-Id: I4ad543dea3ddcafd5cbf07623f1faaabb954ba40
2024-03-19gnu: r-dyngen: Move to (gnu packages cran).Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-dyngen): Move variable from here... * gnu/packages/cran.scm (r-dyngen): ...to here. Change-Id: Id181200fb4cbf268542d93e79e43fdeffa99410d
2024-03-19gnu: r-tictoc: Update to 1.2.1.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-tictoc): Move variable from here... * gnu/packages/cran.scm (r-tictoc): ...to here; update to 1.2.1. Change-Id: I3fc9dde3928a6c5cbe0e25eba8ec001c16e2b66f
2024-03-14gnu: Add morpheus.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (morpheus): New variable. Co-authored-by: Navid Afkhami <navid.afkhami@mdc-berlin.de> Change-Id: I4bf14414f497ff17690b1d26420d442d236fd6b5
2024-03-06gnu: go-github.com-ulikunitz-xz: Adjust name.Sharlatan Hellseher
* 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
2024-02-28gnu: bowtie1: Enable cross-compiling.Efraim Flashner
* gnu/packages/bioinformatics.scm (bowtie1)[arguments]: Adjust make-flags to enable cross-compiling. Change-Id: I6f5696e5ad6a1ea5b3f79e8dbbd162f0fe8d4905
2024-02-28gnu: bowtie1: Enable building on more systems.Efraim Flashner
* 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
2024-02-28gnu: bowtie1: Update to 1.3.1.Efraim Flashner
* gnu/packages/bioinformatics.scm (bowtie1): Update to 1.3.1. [arguments]: Add test-target. [inputs]: Use newer tbb. Change-Id: I7af6aa248e5db9f91ce84fba9ba741621b110479
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
generated by cgit v1.2.3 (git 2.46.0) at 2024-08-21 17:34:34 +0000