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Author SHA1 Message Date
Efraim Flashner
51c711a328
gnu: bitmapperbs: Limit to x86_64-linux. 
* gnu/packages/bioinformatics.scm (bitmapperbs)[supported-systems]: New
field.

Change-Id: I03484413e5af8e779fe0e5199e456eaab124e8b7
 2024-05-07 01:31:20 +03:00
Efraim Flashner
0a5929033f
gnu: minimap2: Fix make-flags. 
* gnu/packages/bioinformatics.scm (minimap2)[arguments]: Adjust the
make-flags to contain actual build flags for all architectures.

Change-Id: I5b4077a25d6d46172ff566ceaa16629ebf066721
 2024-05-06 23:53:04 +03:00
Efraim Flashner
6571231f2d
gnu: minimap2: Update to 2.28. 
* gnu/packages/bioinformatics.scm (minimap2): Update to 2.28.
[arguments]: Adjust custom 'install phase to not delete non-existent
file.  Remove trailing #t from phase.

Change-Id: Ie6cc21f2b761532f08967efea54d3a12b944f213
 2024-05-06 23:42:22 +03:00
Efraim Flashner
a4c0a58594
gnu: proteinortho: Add tunable property. 
* gnu/packages/bioinformatics.scm (proteinortho)[properties]: Add
tunable? flag.

Change-Id: If59d5785c8c8e4aedb5b88479da6fba0e9754640
 2024-05-06 23:16:57 +03:00
Efraim Flashner
dd23efe020
gnu: proteinortho: Update to 6.3.2. 
* gnu/packages/bioinformatics.scm (proteinortho): Update to 6.3.2.
[source]: Adjust snippet to also delete lapack source tarball.
[arguments]: Rewrite using g-expressions.  Add flag to run tests
sequentially.  Adjust make-flags for cross-compiling and to set PREFIX.
Delete 'configure and custom 'configure phase.  Remove trailing #t from
phases.

Change-Id: I40249e5ac92c26223119b81b4677c08d5ab230e6
 2024-05-06 23:16:56 +03:00
Ricardo Wurmus
f736a784e1
gnu: trust4: Update to 1.1.0. 
* gnu/packages/bioinformatics.scm (trust4): Update to 1.1.0.

Change-Id: I4780038a5db110514e27f07a576166def4063da7
 2024-05-06 12:36:53 +02:00
Mădălin Ionel Patrașcu
709e87caff
gnu: Add trust4. 
gnu/packages/bioinformatics.scm (trust4): New variable.

Change-Id: I6a0fd339a0f761a473f50c7da74c26cfac7b1caf
 2024-05-06 11:47:05 +02:00
Mădălin Ionel Patrașcu
57769fb0b3
gnu: Add r-seraster. 
* gnu/packages/bioinformatics.scm (r-seraster): New variable.

Change-Id: I9f9fd24a9aa563f7c74154e613b85dee46bdcf79
 2024-05-06 11:38:17 +02:00
Mădălin Ionel Patrașcu
64fcc49dc5
gnu: Add r-metadeconfoundr. 
* gnu/packages/bioinformatics.scm (r-metadeconfoundr): New variable.

Change-Id: I733fb464d2a3c7fd1335826be9f23e2610e6fd60
 2024-05-06 11:26:54 +02:00
nafkhamdc
00aa6b5a3c
gnu: Add python-pyrodigal. 
* gnu/packages/bioinformatics.scm (python-pyrodigal): New variable.

Co-authored-by: Ricardo Wurmus <rekado@elephly.net>

Change-Id: Iaa0bdb4b918d93f990d5b904f1df3a3f910726b0
 2024-05-06 10:37:41 +02:00
nafkhamdc
e33bf0bbe6
gnu: Add python-pyahocorasick. 
* gnu/packages/bioinformatics.scm (python-pyahocorasick): New variable.

Change-Id: I468bed450351b49cf81344a328841cd77f67cb4e
Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
 2024-05-06 00:07:40 +02:00
Ricardo Wurmus
99bf1b1002
gnu: python-liana-py: Update to 1.1.0. 
* 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
 2024-05-05 22:38:18 +02:00
Ricardo Wurmus
1ea0e3e6dd
gnu: python-cooltools: Update to 0.7.0. 
* gnu/packages/bioinformatics.scm (python-cooltools): Update to 0.7.0.
[build-system]: Use pyproject-build-system.
[arguments]: Remove.

Change-Id: I4112bf0cbc309df551087b8bb3cb1d37af7f751d
 2024-05-05 22:38:18 +02:00
Ricardo Wurmus
d14d5147b1
gnu: python-bioframe: Update to 0.6.4. 
* 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
 2024-05-05 22:38:18 +02:00
Ricardo Wurmus
cb9ec4c5c5
gnu: python-decoupler-py: Update to 1.6.0. 
* gnu/packages/bioinformatics.scm (python-decoupler-py): Update to 1.6.0.
[arguments]: Do not disable test_plot_volcano test.

Change-Id: I44a31d30e8a03d2d1ffd86383c8bc6db79628def
 2024-05-05 22:38:18 +02:00
Ricardo Wurmus
31f57ae7df
gnu: python-hicexplorer: Update to 3.7.4. 
* 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
 2024-05-05 22:38:17 +02:00
Ricardo Wurmus
2d8c81a8d7
gnu: tadbit: Add R to inputs. 
* gnu/packages/bioinformatics.scm (tadbit)[inputs]: Add r-minimal.

Change-Id: I4929dd89ddd27b4fcbd8b3a00b8ab8f3586945d2
 2024-05-05 22:38:17 +02:00
Ricardo Wurmus
93a397f8b7
gnu: tadbit: Patch for compatibility with latest scipy. 
* gnu/packages/bioinformatics.scm (tadbit)[arguments]: Add phase
'scipy-compatibility.

Change-Id: Ib25b9cde75f0505c347c4ff470e61f06fb162839
 2024-05-05 22:38:17 +02:00
Ricardo Wurmus
453b7a267b
gnu: tadbit: Update to 1.0.1-2.2838129. 
* gnu/packages/bioinformatics.scm (tadbit): Update to 1.0.1-2.2838129.

Change-Id: I2c220ae37cd196ca508d30aefc24938cce985527
 2024-05-05 22:38:17 +02:00
Ricardo Wurmus
332a8fa4bc
gnu: python-cooler: Update to 0.9.3. 
* gnu/packages/bioinformatics.scm (python-cooler): Update to 0.9.3.

Change-Id: I4b89d552a424e74f76cda0c527dc7b712b8c9f31
 2024-05-05 22:38:17 +02:00
Ricardo Wurmus
53b2fe2973
gnu: python-scikit-bio: Update to 0.6.0. 
* 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
 2024-05-05 22:38:16 +02:00
Ricardo Wurmus
e9d70b85eb
gnu: python-biom-format: Untangle from python-scikit-bio. 
* 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
 2024-05-05 22:38:16 +02:00
Ricardo Wurmus
5def84031f
gnu: tadbit: Use G-expression. 
* gnu/packages/bioinformatics.scm (tadbit)[arguments]: Use G-expression.

Change-Id: I4fe4afc41eb3442f243b0e415ddcb363be36ce7f
 2024-05-05 22:38:16 +02:00
Ricardo Wurmus
da4006d474
gnu: python-plastid: Replace nose with pytest. 
* gnu/packages/bioinformatics.scm (python-plastid)[native-inputs]: Replace
python-nose with python-pytest.

Change-Id: Ie0e5362d2304d3af0bcb1405fa0c1ad36fb2ace6
 2024-05-05 22:38:15 +02:00
Marco Baggio
854c42e30c
gnu: Add python-metacells. 
* gnu/packages/bioinformatics.scm (python-metacells): New variable.

Co-authored-by: Ricardo Wurmus <rekado@elephly.net>
Change-Id: I4fc760dc4317bde79c815f441ad0cc453248990a
 2024-05-05 22:38:15 +02:00
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