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* gnu: Add r-saige.Ricardo Wurmus2024-04-22
| | | | | | * gnu/packages/bioinformatics.scm (r-saige): New variable. Change-Id: Id5bda4d25ca61fe26d11bae0af19900fd0f0080e
* gnu: Add savvy.Ricardo Wurmus2024-04-22
| | | | | | * gnu/packages/bioinformatics.scm (savvy): New variable. Change-Id: I48dcfad2c6c769778bd79dffa084332da53991ad
* gnu: python-deeptools: Replace python-nose with python-pytest.Ricardo Wurmus2024-04-22
| | | | | | | * gnu/packages/bioinformatics.scm (python-deeptools)[native-inputs]: Replace python-nose with python-pytest. Change-Id: Icba4ed3a464bfa36616aabe2cbbb26bfabec40aa
* gnu: Add python-cyvcf2.Alexis Simon2024-04-22
| | | | | | | * gnu/packages/bioinformatics.scm (python-cyvcf2): New variable. Co-authored-by: Ricardo Wurmus <rekado@elephly.net> Change-Id: I0db07e7b5840f5c1f5c68512ffabb3d6b39ab95c
* gnu: java-guava: Update to 31.1.Julien Lepiller2024-04-20
| | | | | | | | | | | | | | * 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
* gnu: go-github-com-fatih-color: Move to golang-xyz.Sharlatan Hellseher2024-04-12
| | | | | | | | | * 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
* gnu: python-deeptools: Update to 3.5.5.Simon Tournier2024-04-09
| | | | | | | | | * 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>
* gnu: proteinortho: Remove dependency on lapack.Romain GARBAGE2024-04-04
| | | | | | * gnu/packages/bioinformatics.scm (proteinortho): Remove dependency on lapack. Signed-off-by: Ludovic Courtès <ludo@gnu.org>
* gnu: eigensoft: Remove dependency on lapack.Romain GARBAGE2024-04-04
| | | | | | | * gnu/packages/bioinformatics.scm (eigensoft): Remove dependency on lapack. Change-Id: I9d4adfd64a32333a0d605d4ce1aa998035decf2a Signed-off-by: Ludovic Courtès <ludo@gnu.org>
* gnu: plink-ng: Remove lapack dep.Romain GARBAGE2024-04-04
| | | | | | | * gnu/packages/bioinformatics.scm (plink-ng): Remove dependency to lapack. Change-Id: I4d14789c42dc216244872d70120efeeb97127a62 Signed-off-by: Ludovic Courtès <ludo@gnu.org>
* gnu: plink: Switch to openblas.Romain GARBAGE2024-04-04
| | | | | | | | * gnu/packages/bioinformatics.scm (plink): Switch input dependency from lapack to openblas. Change-Id: I8066a50c880b72a77ba00c2bc39403e212605b9d Signed-off-by: Ludovic Courtès <ludo@gnu.org>
* gnu: Add r-pairadise.Ricardo Wurmus2024-03-21
| | | | | | * gnu/packages/bioinformatics.scm (r-pairadise): New variable. Change-Id: I7314d43c75ed008942757feb878628d1ac855f31
* gnu: Add pairadise.Ricardo Wurmus2024-03-21
| | | | | | * gnu/packages/bioinformatics.scm (pairadise): New variable. Change-Id: I4ad543dea3ddcafd5cbf07623f1faaabb954ba40
* gnu: r-dyngen: Move to (gnu packages cran).Ricardo Wurmus2024-03-19
| | | | | | | * gnu/packages/bioinformatics.scm (r-dyngen): Move variable from here... * gnu/packages/cran.scm (r-dyngen): ...to here. Change-Id: Id181200fb4cbf268542d93e79e43fdeffa99410d
* gnu: r-tictoc: Update to 1.2.1.Ricardo Wurmus2024-03-19
| | | | | | | * 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
* gnu: Add morpheus.Ricardo Wurmus2024-03-14
| | | | | | | * gnu/packages/bioinformatics.scm (morpheus): New variable. Co-authored-by: Navid Afkhami <navid.afkhami@mdc-berlin.de> Change-Id: I4bf14414f497ff17690b1d26420d442d236fd6b5
* gnu: go-github.com-ulikunitz-xz: Adjust name.Sharlatan Hellseher2024-03-06
| | | | | | | | | | | | | | | * 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
* gnu: bowtie1: Enable cross-compiling.Efraim Flashner2024-02-28
| | | | | | | * gnu/packages/bioinformatics.scm (bowtie1)[arguments]: Adjust make-flags to enable cross-compiling. Change-Id: I6f5696e5ad6a1ea5b3f79e8dbbd162f0fe8d4905
* gnu: bowtie1: Enable building on more systems.Efraim Flashner2024-02-28
| | | | | | | | * 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
* gnu: bowtie1: Update to 1.3.1.Efraim Flashner2024-02-28
| | | | | | | | * gnu/packages/bioinformatics.scm (bowtie1): Update to 1.3.1. [arguments]: Add test-target. [inputs]: Use newer tbb. Change-Id: I7af6aa248e5db9f91ce84fba9ba741621b110479
* gnu: cwltool: Update to 3.1.20240112164112.Arun Isaac2024-02-22
| | | | | | | | | | | | | | | | * 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>
* gnu: Add python-cwl-utils.Arun Isaac2024-02-22
| | | | | | | * gnu/packages/bioinformatics.scm (python-cwl-utils): New variable. Change-Id: I9347c80c0e866b89a7d432091fbcf1bc009209a5 Signed-off-by: Arun Isaac <arunisaac@systemreboot.net>
* gnu: Add python-cwl-upgrader.Arun Isaac2024-02-22
| | | | | | | * gnu/packages/bioinformatics.scm (python-cwl-upgrader): New variable. Change-Id: I2022239840e9fe9e745689ef8b8bf4279be2ff9e Signed-off-by: Arun Isaac <arunisaac@systemreboot.net>
* gnu: Add python-cwlformat.Arun Isaac2024-02-22
| | | | | | | * gnu/packages/bioinformatics.scm (python-cwlformat): New variable. Change-Id: Ib2d79e350ab100c61c7afe2d5d3eafc72146e493 Signed-off-by: Arun Isaac <arunisaac@systemreboot.net>
* gnu: python-schema-salad: Update to 8.5.20240102191335.Arun Isaac2024-02-22
| | | | | | | | | | | | | | * 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>
* gnu: python-pyega3: Define as deprecated alias for python-ega-download-client.Ricardo Wurmus2024-02-20
| | | | | | | | | * 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
* gnu: python-ega-download-client: Disable some tests.nafkhamdc2024-02-20
| | | | | | | * gnu/packages/bioinformatics.scm (python-ega-download-client)[arguments]: Disable tests that fail on big machines; use "--ignore" where appropriate. Change-Id: I010c3a0e7cb69184b72e8b13bad04ff2fd364f5a
* gnu: r-archr: Update to 1.0.2-1.c61b064.Ricardo Wurmus2024-02-19
| | | | | | * gnu/packages/bioinformatics.scm (r-archr): Update to 1.0.2-1.c61b064. Change-Id: I8967cedbfc3390c364f188d50f8ecb2b27cb1417
* gnu: python-ega-download-client: Add missing input.nafkhamdc2024-02-19
| | | | | | | | * gnu/packages/bioinformatics.scm (python-ega-download-client) [native-inputs]: Add python-mock. Change-Id: I3befca6de33f959f4d916caa839d7201c77e8209 Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
* gnu: Add python-ega-download-client.nafkhamdc2024-02-15
| | | | | | | * gnu/packages/bioinformatics.scm (python-ega-download-client): New variable. Change-Id: I3233774975989f912281ab2e6ec6ad3362cae18b Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
* gnu: go-github.com-ulikunitz-xz: Move to golang-compression.Sharlatan Hellseher2024-02-13
| | | | | | | | | | * 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
* gnu: go-golang-org-x-text: Move to golang-build.Sharlatan Hellseher2024-02-13
| | | | | | | | | | | * 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
* gnu: Add python-pdbfixer.nafkhamdc2024-02-10
| | | | | | | * gnu/packages/bioinformatics.scm (python-pdbfixer): New variable. Change-Id: I2894a08ab3eed463f052b9df6372d4016b718d1a Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
* gnu: ccwl: Update to 0.3.0.Arun Isaac2024-01-26
| | | | | | | * gnu/packages/bioinformatics.scm (ccwl): Update to 0.3.0. [arguments]: Add patch-more-source-shebangs phase. Change-Id: Ic7926d04c28eeafd799deba5e817574663431db8
* gnu: Add music.Ricardo Wurmus2024-01-25
| | | | | | * gnu/packages/bioinformatics.scm (music): New variable. Change-Id: Iba5c986a0d3143118d4640d3ee9d4dae8119163f
* gnu: Add flash.Ricardo Wurmus2024-01-23
| | | | | | * gnu/packages/bioinformatics.scm (flash): New variable. Change-Id: Id657ba7850031ad24b4333b6bc79401511e00a85
* gnu: Add isolator.Ricardo Wurmus2024-01-23
| | | | | | * gnu/packages/bioinformatics.scm (isolator): New variable. Change-Id: I950baca5b6898576f358b3364b1fe541b3333298
* gnu: Add metal.Ricardo Wurmus2024-01-23
| | | | | | * gnu/packages/bioinformatics.scm (metal): New variable. Change-Id: I70fd30c18303f61a9f6720e70d4b4e57140a7140
* gnu: Add randfold.Ricardo Wurmus2024-01-23
| | | | | | * gnu/packages/bioinformatics.scm (randfold): New variable. Change-Id: If2cea9c8d5323296015dc21ea7a3d1b677ae2798
* gnu: Add python-pyfasta.Ricardo Wurmus2024-01-23
| | | | | | * gnu/packages/bioinformatics.scm (python-pyfasta): New variable. Change-Id: Ib2ab0a6eb250309633d5be33c18409227bce84ba
* gnu: Add python-fcsparser.Ricardo Wurmus2024-01-23
| | | | | | * gnu/packages/bioinformatics.scm (python-fcsparser): New variable. Change-Id: I87ed7f10bbfdf7d689cb6289a5f5ad31872f9de0
* gnu: Add lsgkm.Ricardo Wurmus2024-01-23
| | | | | | * gnu/packages/bioinformatics.scm (lsgkm): New variable. Change-Id: I0ea35354c7856e7425567cd4ac27ab7fc2ab0d9e
* gnu: Add eddylab-squid.Ricardo Wurmus2024-01-23
| | | | | | * gnu/packages/bioinformatics.scm (eddylab-squid): New variable. Change-Id: Icb02f42fc95d2001a639e22608a01ef9074158bc
* gnu: Add python-magic-impute.Ricardo Wurmus2024-01-23
| | | | | | * gnu/packages/bioinformatics.scm (python-magic-impute): New variable. Change-Id: Iba5240e9920a1045078c736553cb1d56069963b5
* gnu: Add r-scenic.Ricardo Wurmus2024-01-23
| | | | | | * gnu/packages/bioinformatics.scm (r-scenic): New variable. Change-Id: Iff1f501a406ba1a12e49093a575e03facc98f303
* gnu: wfmash: Update to 0.12.5.Arun Isaac2024-01-19
| | | | | | | | | | * 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
* gnu: python-snaptools: Disable tests.Ricardo Wurmus2024-01-17
| | | | | | | * gnu/packages/bioinformatics.scm (python-snaptools)[arguments]: Disable tests. Change-Id: I4934bda3cfbaf42a87f57035ec12d084112dcc24
* gnu: Add samtools-1.14.Ricardo Wurmus2024-01-16
| | | | | | * gnu/packages/bioinformatics.scm (samtools-1.14): New variable. Change-Id: I0bd35b3865d7a417f55f1f768f7eb0c78a795e0f
* gnu: samtools: Update to 1.19.Ricardo Wurmus2024-01-16
| | | | | | | * gnu/packages/bioinformatics.scm (samtools): Update to 1.19. [source]: Simplify snippet. Change-Id: If0e02bbbc8e0443eb418c078dc47525f432d7ebe
* gnu: htslib: Update to 1.19.Ricardo Wurmus2024-01-16
| | | | | | * gnu/packages/bioinformatics.scm (htslib): Update to 1.19. Change-Id: I4d66d8ce37bfd335411a2acc6060f9a8c20c9e4a
generated by cgit v1.2.3 (git 2.25.4) at 2024-10-04 13:49:13 +0000