| Commit message (Expand) | Author | Age | Files | Lines |
|---|
| * | gnu: java-guava: Update to 31.1.•••* 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
| Julien Lepiller | 2024-04-20 | 1 | -0/+8 |
| * | gnu: go-github-com-fatih-color: Move to golang-xyz.•••* 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
| Sharlatan Hellseher | 2024-04-12 | 1 | -0/+1 |
| * | gnu: python-deeptools: Update to 3.5.5.•••* 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>
| Simon Tournier | 2024-04-09 | 1 | -4/+19 |
| * | gnu: proteinortho: Remove dependency on lapack.•••* gnu/packages/bioinformatics.scm (proteinortho): Remove dependency on lapack.
Signed-off-by: Ludovic Courtès <ludo@gnu.org>
| Romain GARBAGE | 2024-04-04 | 1 | -2/+3 |
| * | gnu: eigensoft: Remove dependency on lapack.•••* gnu/packages/bioinformatics.scm (eigensoft): Remove dependency on lapack.
Change-Id: I9d4adfd64a32333a0d605d4ce1aa998035decf2a
Signed-off-by: Ludovic Courtès <ludo@gnu.org>
| Romain GARBAGE | 2024-04-04 | 1 | -1/+1 |
| * | gnu: plink-ng: Remove lapack dep.•••* gnu/packages/bioinformatics.scm (plink-ng): Remove dependency to lapack.
Change-Id: I4d14789c42dc216244872d70120efeeb97127a62
Signed-off-by: Ludovic Courtès <ludo@gnu.org>
| Romain GARBAGE | 2024-04-04 | 1 | -2/+2 |
| * | gnu: plink: Switch to openblas.•••* gnu/packages/bioinformatics.scm (plink): Switch input dependency from
lapack to openblas.
Change-Id: I8066a50c880b72a77ba00c2bc39403e212605b9d
Signed-off-by: Ludovic Courtès <ludo@gnu.org>
| Romain GARBAGE | 2024-04-04 | 1 | -3/+3 |
| * | gnu: Add r-pairadise.•••* gnu/packages/bioinformatics.scm (r-pairadise): New variable.
Change-Id: I7314d43c75ed008942757feb878628d1ac855f31
| Ricardo Wurmus | 2024-03-21 | 1 | -0/+15 |
| * | gnu: Add pairadise.•••* gnu/packages/bioinformatics.scm (pairadise): New variable.
Change-Id: I4ad543dea3ddcafd5cbf07623f1faaabb954ba40
| Ricardo Wurmus | 2024-03-21 | 1 | -0/+38 |
| * | gnu: r-dyngen: Move to (gnu packages cran).•••* gnu/packages/bioinformatics.scm (r-dyngen): Move variable from here...
* gnu/packages/cran.scm (r-dyngen): ...to here.
Change-Id: Id181200fb4cbf268542d93e79e43fdeffa99410d
| Ricardo Wurmus | 2024-03-19 | 1 | -39/+0 |
| * | gnu: r-tictoc: Update to 1.2.1.•••* 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
| Ricardo Wurmus | 2024-03-19 | 1 | -24/+0 |
| * | 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 | 2024-03-14 | 1 | -0/+63 |
| * | 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 | 2024-03-06 | 1 | -1/+1 |
| * | 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 | 1 | -1/+3 |
| * | 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 | 1 | -3/+6 |
| * | 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 | 2024-02-28 | 1 | -5/+6 |
| * | 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 | 1 | -46/+43 |
| * | 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 | 1 | -0/+43 |
| * | 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 | 1 | -0/+24 |
| * | 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 | 1 | -0/+27 |
| * | 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 | 2024-02-22 | 1 | -23/+38 |
| * | 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 | 1 | -36/+16 |
| * | 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 | 2024-02-20 | 1 | -5/+18 |
| * | 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 | 1 | -3/+3 |
| * | 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 | 2024-02-19 | 1 | -1/+1 |
| * | 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 | 2024-02-15 | 1 | -0/+39 |
| * | 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 | 1 | -0/+1 |
| * | 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 | 2024-02-13 | 1 | -0/+1 |
| * | gnu: Add python-pdbfixer.•••* gnu/packages/bioinformatics.scm (python-pdbfixer): New variable.
Change-Id: I2894a08ab3eed463f052b9df6372d4016b718d1a
Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
| nafkhamdc | 2024-02-10 | 1 | -0/+32 |
| * | 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 | 2024-01-26 | 1 | -2/+8 |
| * | gnu: Add music.•••* gnu/packages/bioinformatics.scm (music): New variable.
Change-Id: Iba5c986a0d3143118d4640d3ee9d4dae8119163f
| Ricardo Wurmus | 2024-01-25 | 1 | -0/+35 |
| * | gnu: Add flash.•••* gnu/packages/bioinformatics.scm (flash): New variable.
Change-Id: Id657ba7850031ad24b4333b6bc79401511e00a85
| Ricardo Wurmus | 2024-01-23 | 1 | -0/+37 |
| * | gnu: Add isolator.•••* gnu/packages/bioinformatics.scm (isolator): New variable.
Change-Id: I950baca5b6898576f358b3364b1fe541b3333298
| Ricardo Wurmus | 2024-01-23 | 1 | -0/+43 |
| * | gnu: Add metal.•••* gnu/packages/bioinformatics.scm (metal): New variable.
Change-Id: I70fd30c18303f61a9f6720e70d4b4e57140a7140
| Ricardo Wurmus | 2024-01-23 | 1 | -0/+39 |
| * | gnu: Add randfold.•••* gnu/packages/bioinformatics.scm (randfold): New variable.
Change-Id: If2cea9c8d5323296015dc21ea7a3d1b677ae2798
| Ricardo Wurmus | 2024-01-23 | 1 | -0/+33 |
| * | gnu: Add python-pyfasta.•••* gnu/packages/bioinformatics.scm (python-pyfasta): New variable.
Change-Id: Ib2ab0a6eb250309633d5be33c18409227bce84ba
| Ricardo Wurmus | 2024-01-23 | 1 | -6/+78 |
| * | gnu: Add python-fcsparser.•••* gnu/packages/bioinformatics.scm (python-fcsparser): New variable.
Change-Id: I87ed7f10bbfdf7d689cb6289a5f5ad31872f9de0
| Ricardo Wurmus | 2024-01-23 | 1 | -0/+19 |
| * | gnu: Add lsgkm.•••* gnu/packages/bioinformatics.scm (lsgkm): New variable.
Change-Id: I0ea35354c7856e7425567cd4ac27ab7fc2ab0d9e
| Ricardo Wurmus | 2024-01-23 | 1 | -0/+39 |
| * | gnu: Add eddylab-squid.•••* gnu/packages/bioinformatics.scm (eddylab-squid): New variable.
Change-Id: Icb02f42fc95d2001a639e22608a01ef9074158bc
| Ricardo Wurmus | 2024-01-23 | 1 | -0/+29 |
| * | gnu: Add python-magic-impute.•••* gnu/packages/bioinformatics.scm (python-magic-impute): New variable.
Change-Id: Iba5240e9920a1045078c736553cb1d56069963b5
| Ricardo Wurmus | 2024-01-23 | 1 | -0/+39 |
| * | gnu: Add r-scenic.•••* gnu/packages/bioinformatics.scm (r-scenic): New variable.
Change-Id: Iff1f501a406ba1a12e49093a575e03facc98f303
| Ricardo Wurmus | 2024-01-23 | 1 | -0/+37 |
| * | 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 | 2024-01-19 | 1 | -11/+12 |
| * | gnu: python-snaptools: Disable tests.•••* gnu/packages/bioinformatics.scm (python-snaptools)[arguments]: Disable
tests.
Change-Id: I4934bda3cfbaf42a87f57035ec12d084112dcc24
| Ricardo Wurmus | 2024-01-17 | 1 | -0/+1 |
| * | gnu: Add samtools-1.14.•••* gnu/packages/bioinformatics.scm (samtools-1.14): New variable.
Change-Id: I0bd35b3865d7a417f55f1f768f7eb0c78a795e0f
| Ricardo Wurmus | 2024-01-16 | 1 | -0/+20 |
| * | 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 | 1 | -7/+7 |
| * | gnu: htslib: Update to 1.19.•••* gnu/packages/bioinformatics.scm (htslib): Update to 1.19.
Change-Id: I4d66d8ce37bfd335411a2acc6060f9a8c20c9e4a
| Ricardo Wurmus | 2024-01-16 | 1 | -2/+2 |
| * | 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 | 1 | -2/+2 |
| * | gnu: python-readpaf: Explicitly disable tests.•••* gnu/packages/bioinformatics.scm (python-readpaf)[arguments]: Disable tests.
Change-Id: I28ddfa46675b74bd5073c12e5d33bcbf9dee8252
| Ricardo Wurmus | 2024-01-16 | 1 | -0/+1 |
| * | 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 | 1 | -12/+10 |
| * | gnu: python-telomerecat: Disable tests.•••* gnu/packages/bioinformatics.scm (python-telomerecat)[arguments]: Disable tests.
Change-Id: I0422ae1e563374a8cc408fc9584cfb7b0e880e95
| Ricardo Wurmus | 2024-01-16 | 1 | -0/+1 |
