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Author SHA1 Message Date
Zheng Junjie 4e92ed625f
gnu: bwa,bwa-pssm: Improve package style. 
* gnu/packages/bioinformatics.scm (bwa)[arguments]: Use G-expression.
(bwa-pssm)[arguments]: Use G-expression.

Change-Id: I63dd0f13f337fbf84967f1ef1b6332ce3391ae97
 2024-07-30 15:57:44 +08:00
Zheng Junjie 18a69ddbf3
gnu: bwa: Fix cross-compiling. 
* gnu/packages/bioinformatics.scm (bwa)[arguments]<#:make-flags>: Use
CC-FOR-TARGET.

Change-Id: I63dd0f13f337fbf84967f1ef1b6332ce3391ae97
 2024-07-30 15:53:58 +08:00
Spencer King 471c4322df
gnu: bwa: Update to 0.7.18. 
* gnu/packages/bioinformatics.scm (bwa): Update to 0.7.18.
[source]: Switch to git-fetch.
[supported-systems]: Add aarch64-linux.

Change-Id: I63dd0f13f337fbf84967f1ef1b6332ce3391ae97
 2024-07-30 15:44:36 +08:00
guix@mawumag.com ddce6b2303
gnu: Add python-muon. 
* gnu/packages/bioinformatics.scm (python-muon): New variable.

Change-Id: I21431b089d1f404828b78d79124d96e7d36d5a2d
Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
 2024-07-01 16:18:34 +02:00
guix@mawumag.com 58ead4baf9
gnu: Add python-mofapy2. 
* gnu/packages/bioinformatics.scm (python-mofapy2): New variable.

Change-Id: Ide92878258511b3daf4e56d5faa94d190fdee62f
Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
 2024-07-01 15:55:33 +02:00
Afkhami, Navid b77491909b
gnu: Add r-anpan. 
* gnu/packages/bioinformatics.scm (r-anpan): New variable.

Change-Id: Ia01ba3be7424306674b9c9b2904f1f0cfa66d818
Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
 2024-07-01 15:43:56 +02:00
Afkhami, Navid 1731b45c51
gnu: Add r-cmdstanr. 
* gnu/packages/bioinformatics.scm (r-cmdstanr): New variable.

Change-Id: Ic9e83486f7ab7f0e7075343af630c4dcecf597b5
Signed-off-by: Andreas Enge <andreas@enge.fr>
 2024-06-30 10:48:50 +02:00
Efraim Flashner 4b67b38a79
gnu: jellyfish: Enable building on all 64bit platforms. 
* gnu/packages/bioinformatics.scm (jellyfish)[supported-systems]: Mark
all 64bit platforms as supported.

Change-Id: Ia79d8052bf6ff347422e4b1ce38dc379d45a9be6
 2024-06-30 10:15:03 +03:00
Afkhami, Navid 385fb14f64
gnu: Add r-rphyloxml. 
* gnu/packages/bioinformatics.scm (r-rphyloxml): New variable.

Co-authored-by: Ricardo Wurmus <rekado@elephly.net>
Change-Id: I5b799986064f2af5fe74454f2e78fea7d9947260
 2024-06-28 22:37:36 +02:00
Afkhami, Navid 6a7d5cda17
gnu: Add r-rnacrosslinkoo. 
* gnu/packages/bioinformatics.scm (r-rnacrosslinkoo): New variable.

Change-Id: I1ca6dcef9c093627c3743d1176e587cf40053ba0
 2024-06-28 11:53:19 +02:00
Afkhami, Navid 30dbc8e7b0
gnu: Add r-scent. 
* gnu/packages/bioinformatics.scm (r-scent): New variable.

Change-Id: Ie517c0619683590f630013982e831fad528c1dea
 2024-06-18 09:24:53 +02:00
Ricardo Wurmus 01de17143c
gnu: Add python-celltypist. 
* gnu/packages/bioinformatics.scm (python-celltypist): New variable.

Change-Id: I196b7a07955224fe4c641d79729f0facb6367adb
 2024-05-31 07:43:12 +02:00
Ricardo Wurmus 9f9127e80a
gnu: ensembl-vep: Update to 112. 
* gnu/packages/bioinformatics.scm (ensembl-vep): Update to 112.
[propagated-inputs]: Add perl-list-moreutils.
[native-inputs]: Add perl-test-deep and perl-test-warnings.

Change-Id: I8c7de9f3dbc8c6fe4d1383f9dc215aeba018af0d
 2024-05-22 17:44:49 +02:00
Efraim Flashner 58614c9b4b
gnu: samtools: Fix build on i686-linux. 
* gnu/packages/bioinformatics.scm (samtools)[arguments]: When building
for i686-linux adjust the make-flags to specifically use the sse math
libraries.

Change-Id: I322d521cbe87e10db7c23db8e68bb377db966aa7
 2024-05-19 16:10:47 +03:00
Ricardo Wurmus 2b161f6130
gnu: pigx-rnaseq: Update to 0.1.1. 
* gnu/packages/bioinformatics.scm (pigx-rnaseq): Update to 0.1.1.

Change-Id: I16db332e3559bed5b302f08bd85f31c6c40e9619
 2024-05-15 09:37:29 +02:00
Ricardo Wurmus be235a3092
gnu: Add r-anndatar. 
* gnu/packages/bioinformatics.scm (r-anndatar): New variable.

Change-Id: I6060c5c15a46c064aa03ec2431a72ea88f925706
 2024-05-13 16:12:12 +02:00
Efraim Flashner 39059b9390
gnu: minimap2: Remove included file from gcc. 
* gnu/packages/bioinformatics.scm (minimap2)[arguments]: Adjust custom
'install phase to remove included emmintrin.h header.

Change-Id: Id994dd2bd4a98e8d1c162c4e011fc77b9d5565d2
 2024-05-12 09:59:55 +03:00
Ricardo Wurmus 6745d692d4
gnu: rcas-web: Update to latest commit. 
The latest commit fixes a problem in configure.ac.

* gnu/packages/bioinformatics.scm (rcas-web)[source]: Fetch from git.
[arguments]: Remove 'find-RCAS phase; use G-expression.
[inputs]: Drop labels.  Use Guile 3.0.
[native-inputs]: Add autoconf and automake.

Change-Id: I6f1d300df589a99b9493b2857f58d49e468b210e
 2024-05-08 12:53:43 +02:00
Ricardo Wurmus babafe251c
gnu: r-icellnet: Update to 2.2.1-1.e10ee4a. 
* gnu/packages/bioinformatics.scm (r-icellnet): Update to 2.2.1-1.e10ee4a.
[propagated-inputs]: Add r-complexheatmap and r-circlize.

Change-Id: Ib844f83cb1ca4f88259593153d9e66289307dccc
 2024-05-08 12:53:43 +02:00
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