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3719 Commits

Author SHA1 Message Date
Ricardo Wurmus
02df0a8a7d
gnu: Add r-saige. 
* gnu/packages/bioinformatics.scm (r-saige): New variable.

Change-Id: Id5bda4d25ca61fe26d11bae0af19900fd0f0080e
 2024-04-22 16:35:31 +02:00
Ricardo Wurmus
4a5a23aceb
gnu: Add savvy. 
* gnu/packages/bioinformatics.scm (savvy): New variable.

Change-Id: I48dcfad2c6c769778bd79dffa084332da53991ad
 2024-04-22 16:35:31 +02:00
Ricardo Wurmus
a78de8f792
gnu: python-deeptools: Replace python-nose with python-pytest. 
* gnu/packages/bioinformatics.scm (python-deeptools)[native-inputs]: Replace
python-nose with python-pytest.

Change-Id: Icba4ed3a464bfa36616aabe2cbbb26bfabec40aa
 2024-04-22 11:29:31 +02:00
Alexis Simon
78d24b78d3
gnu: Add python-cyvcf2. 
* gnu/packages/bioinformatics.scm (python-cyvcf2): New variable.

Co-authored-by: Ricardo Wurmus <rekado@elephly.net>
Change-Id: I0db07e7b5840f5c1f5c68512ffabb3d6b39ab95c
 2024-04-22 11:29:29 +02:00
Julien Lepiller
7ce7464934
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
 2024-04-20 18:31:34 +02:00
Sharlatan Hellseher
b8558c740e
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
 2024-04-12 16:35:20 +01:00
Simon Tournier
cf29c427e9
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>
 2024-04-09 17:04:02 +01:00
Romain GARBAGE
fc3bc4ecb9
gnu: proteinortho: Remove dependency on lapack. 
* gnu/packages/bioinformatics.scm (proteinortho): Remove dependency on lapack.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2024-04-04 16:19:00 +02:00
Romain GARBAGE
9c29648a32
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>
 2024-04-04 16:18:56 +02:00
Romain GARBAGE
63b073d787
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>
 2024-04-04 16:18:03 +02:00
Romain GARBAGE
034b16453e
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>
 2024-04-04 16:17:55 +02:00
Ricardo Wurmus
9b84b36296
gnu: Add r-pairadise. 
* gnu/packages/bioinformatics.scm (r-pairadise): New variable.

Change-Id: I7314d43c75ed008942757feb878628d1ac855f31
 2024-03-21 14:39:38 +01:00
Ricardo Wurmus
0944c5b028
gnu: Add pairadise. 
* gnu/packages/bioinformatics.scm (pairadise): New variable.

Change-Id: I4ad543dea3ddcafd5cbf07623f1faaabb954ba40
 2024-03-21 14:33:47 +01:00
Ricardo Wurmus
5bef5f4c7c
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
 2024-03-19 14:33:24 +01:00
Ricardo Wurmus
16855a1c9e
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
 2024-03-19 14:30:40 +01:00
Ricardo Wurmus
efe62c5ed3
gnu: Add morpheus. 
* gnu/packages/bioinformatics.scm (morpheus): New variable.

Co-authored-by: Navid Afkhami <navid.afkhami@mdc-berlin.de>
Change-Id: I4bf14414f497ff17690b1d26420d442d236fd6b5
 2024-03-14 21:01:37 +01:00
Sharlatan Hellseher
b75db99600
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
 2024-03-06 23:28:29 +00:00
Efraim Flashner
c034088e37
gnu: bowtie1: Enable cross-compiling. 
* gnu/packages/bioinformatics.scm (bowtie1)[arguments]: Adjust
make-flags to enable cross-compiling.

Change-Id: I6f5696e5ad6a1ea5b3f79e8dbbd162f0fe8d4905
 2024-02-28 11:50:05 +02:00
Efraim Flashner
9d882d2ef5
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
 2024-02-28 11:46:14 +02:00
Efraim Flashner
aa1d419586
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
 2024-02-28 11:35:27 +02:00
Arun Isaac
58233e6c21
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>
 2024-02-22 13:02:43 +00:00
Arun Isaac
1de86105ab
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>
 2024-02-22 13:02:43 +00:00
Arun Isaac
4e6b7f4c45
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>
 2024-02-22 13:02:42 +00:00
Arun Isaac
0728b45295
gnu: Add python-cwlformat. 
* gnu/packages/bioinformatics.scm (python-cwlformat): New variable.

Change-Id: Ib2d79e350ab100c61c7afe2d5d3eafc72146e493
Signed-off-by: Arun Isaac <arunisaac@systemreboot.net>
 2024-02-22 13:02:42 +00:00
Arun Isaac
65584b9ba8
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>
 2024-02-22 13:02:42 +00:00
Ricardo Wurmus
2e656d674c
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
 2024-02-20 09:41:01 +01:00
nafkhamdc
312a479f8f
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
 2024-02-20 08:45:39 +01:00
Ricardo Wurmus
391b612d0a
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
 2024-02-19 13:37:14 +01:00
nafkhamdc
07ecdb99b6
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>
 2024-02-19 10:13:41 +01:00
nafkhamdc
fb79e58995
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>
 2024-02-15 11:53:29 +01:00
Sharlatan Hellseher
c185c51e14
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
 2024-02-13 14:33:17 +00:00
Sharlatan Hellseher
de36ec1480
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
 2024-02-13 14:33:16 +00:00
nafkhamdc
ca4c9062c4
gnu: Add python-pdbfixer. 
* gnu/packages/bioinformatics.scm (python-pdbfixer): New variable.

Change-Id: I2894a08ab3eed463f052b9df6372d4016b718d1a
Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
 2024-02-10 11:21:21 +01:00
Arun Isaac
4671925528
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
 2024-01-26 15:31:56 +00:00
Ricardo Wurmus
6623a8151a
gnu: Add music. 
* gnu/packages/bioinformatics.scm (music): New variable.

Change-Id: Iba5c986a0d3143118d4640d3ee9d4dae8119163f
 2024-01-25 15:13:51 +01:00
Ricardo Wurmus
c376298c7c
gnu: Add flash. 
* gnu/packages/bioinformatics.scm (flash): New variable.

Change-Id: Id657ba7850031ad24b4333b6bc79401511e00a85
 2024-01-23 23:47:31 +01:00
Ricardo Wurmus
825b3ca763
gnu: Add isolator. 
* gnu/packages/bioinformatics.scm (isolator): New variable.

Change-Id: I950baca5b6898576f358b3364b1fe541b3333298
 2024-01-23 23:43:19 +01:00
Ricardo Wurmus
b9a5c50d8c
gnu: Add metal. 
* gnu/packages/bioinformatics.scm (metal): New variable.

Change-Id: I70fd30c18303f61a9f6720e70d4b4e57140a7140
 2024-01-23 21:41:58 +01:00
Ricardo Wurmus
25f0964c3e
gnu: Add randfold. 
* gnu/packages/bioinformatics.scm (randfold): New variable.

Change-Id: If2cea9c8d5323296015dc21ea7a3d1b677ae2798
 2024-01-23 21:31:51 +01:00
Ricardo Wurmus
ebad9d6c0e
gnu: Add python-pyfasta. 
* gnu/packages/bioinformatics.scm (python-pyfasta): New variable.

Change-Id: Ib2ab0a6eb250309633d5be33c18409227bce84ba
 2024-01-23 21:26:50 +01:00
Ricardo Wurmus
f7373261e9
gnu: Add python-fcsparser. 
* gnu/packages/bioinformatics.scm (python-fcsparser): New variable.

Change-Id: I87ed7f10bbfdf7d689cb6289a5f5ad31872f9de0
 2024-01-23 21:22:45 +01:00
Ricardo Wurmus
469405375c
gnu: Add lsgkm. 
* gnu/packages/bioinformatics.scm (lsgkm): New variable.

Change-Id: I0ea35354c7856e7425567cd4ac27ab7fc2ab0d9e
 2024-01-23 21:18:07 +01:00
Ricardo Wurmus
d3129b3f1e
gnu: Add eddylab-squid. 
* gnu/packages/bioinformatics.scm (eddylab-squid): New variable.

Change-Id: Icb02f42fc95d2001a639e22608a01ef9074158bc
 2024-01-23 13:52:36 +01:00
Ricardo Wurmus
6a82745746
gnu: Add python-magic-impute. 
* gnu/packages/bioinformatics.scm (python-magic-impute): New variable.

Change-Id: Iba5240e9920a1045078c736553cb1d56069963b5
 2024-01-23 13:42:55 +01:00
Ricardo Wurmus
6e835cd380
gnu: Add r-scenic. 
* gnu/packages/bioinformatics.scm (r-scenic): New variable.

Change-Id: Iff1f501a406ba1a12e49093a575e03facc98f303
 2024-01-23 13:36:47 +01:00
Arun Isaac
4987618368
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
 2024-01-19 18:04:39 +00:00
Ricardo Wurmus
270570f090
gnu: python-snaptools: Disable tests. 
* gnu/packages/bioinformatics.scm (python-snaptools)[arguments]: Disable
tests.

Change-Id: I4934bda3cfbaf42a87f57035ec12d084112dcc24
 2024-01-17 21:41:45 +01:00
Ricardo Wurmus
9a9f05f1f2
gnu: Add samtools-1.14. 
* gnu/packages/bioinformatics.scm (samtools-1.14): New variable.

Change-Id: I0bd35b3865d7a417f55f1f768f7eb0c78a795e0f
 2024-01-16 19:35:37 +01:00
Ricardo Wurmus
e0369ba57d
gnu: samtools: Update to 1.19. 
* gnu/packages/bioinformatics.scm (samtools): Update to 1.19.
[source]: Simplify snippet.

Change-Id: If0e02bbbc8e0443eb418c078dc47525f432d7ebe
 2024-01-16 19:31:35 +01:00
Ricardo Wurmus
eda31ffaab
gnu: htslib: Update to 1.19. 
* gnu/packages/bioinformatics.scm (htslib): Update to 1.19.

Change-Id: I4d66d8ce37bfd335411a2acc6060f9a8c20c9e4a
 2024-01-16 19:22:03 +01:00