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Author SHA1 Message Date
Ricardo Wurmus
dead8b3a52
gnu: Update references to python3.10 directory. 
* gnu/packages/admin.scm (ansible)[native-search-paths]: Refer to python3.11
directory.
* gnu/packages/bioinformatics.scm (scvelo)[arguments]: Same.
* gnu/packages/ebook.scm (calibre)[arguments]: Same.
* gnu/packages/engineering.scm (cadabra2)[arguments]: Same.
* gnu/packages/gnuzilla.scm (make-l10n-package)[arguments]: Same.
* gnu/packages/machine-learning.scm (python-vosk)[arguments]: Same.
* gnu/packages/python-science.scm (python-pandas-2)[arguments]: Same.
* gnu/packages/version-control.scm (mercurial)[native-search-paths]: Same.
* gnu/packages/irc.scm (go-gopkg-in-irc-v3): Update comment.

Change-Id: If2ea1060b42b137474d5cfda6611df6e6fc85270
 2025-04-16 11:46:08 +02:00
Ricardo Wurmus
d437e509cf
gnu: r-gutils: Update to 0.2.0-2.fc24db6. 
* gnu/packages/bioinformatics.scm (r-gutils): Update to 0.2.0-2.fc24db6.

Change-Id: I7ce713934acf9321c688d03ca9c7fbfb13a1efb3
 2025-04-16 11:01:11 +02:00
Ricardo Wurmus
09f5a8015e
gnu: r-anpan: Disable tests. 
* gnu/packages/bioinformatics.scm (r-anpan)[arguments]: Disable tests.

Change-Id: Ia78599512549bc90a01011c18e91d4adaa16b168
 2025-04-16 11:01:11 +02:00
Ricardo Wurmus
65025b9445
gnu: r-ewastools: Disable done test. 
* gnu/packages/bioinformatics.scm (r-ewastools)[arguments]: Add phase
'disable-bad-tests.

Change-Id: I65f3e8e1104ed51578dc25797692dc8e8ef199b9
 2025-04-16 11:00:55 +02:00
Ricardo Wurmus
cd748b6ea4
gnu: r-liana: Update to 0.1.14-1.6cab46c. 
* gnu/packages/bioinformatics.scm (r-liana): Update to 0.1.14-1.6cab46c.
[properties]: Record updater-extra-native-inputs.
[arguments]: Add phase 'disable-bad-tests.
[native-inputs]: Add r-delayedmatrixstats, r-seurat, and r-sparsematrixstats.

Change-Id: I58185ffdcd4f166f9f438e8fc2c87a4d782ed228
 2025-04-16 11:00:54 +02:00
Ricardo Wurmus
f438c38dce
gnu: r-omnipathr/devel: Update to 3.15.3. 
* gnu/packages/bioinformatics.scm (r-omnipathr/devel): Update to 3.15.3.
[propagated-inputs]: Add r-fs, r-httr2, r-lubridate, r-r-utils, r-rmarkdown,
r-rsqlite, r-sessioninfo, r-stringi, r-vctrs, r-xml, and r-zip; remove r-httr.

Change-Id: I062eda0ab64edf696d89c4527e353a72dd6c2aa0
 2025-04-16 11:00:54 +02:00
Ricardo Wurmus
a4d69d5d8c
gnu: r-circus: Disable one test. 
* gnu/packages/bioinformatics.scm (r-circus)[arguments]: Disable one test.

Change-Id: Iee65106316c81135f123fbe5c7b229bce9784d6d
 2025-04-16 11:00:52 +02:00
Ricardo Wurmus
e21fff596e
gnu: r-presto: Add test input. 
* gnu/packages/bioinformatics.scm (r-presto)[properties]: Record
updater-extra-native-inputs.
[native-inputs]: Add r-broom.

Change-Id: I965cfecd19563d36fc5cfae35c478a58eb95f9e0
 2025-04-16 11:00:50 +02:00
Ricardo Wurmus
23a8d448c7
gnu: r-spectre: Update to 1.2.0. 
* gnu/packages/bioinformatics.scm (r-spectre): Update to 1.2.0.
[arguments]: Enable tests.
[propagated-inputs]: Add r-dendsort, r-patchwork, r-scattermore, and r-uwot;
remove r-rgeos.

Change-Id: If5f3c4dfee6ef4f2817fa36531ef49fba745e03e
 2025-04-16 11:00:32 +02:00
Ricardo Wurmus
c798c89495
gnu: r-pizzarr: Disable tests. 
* gnu/packages/bioinformatics.scm (r-pizzarr)[arguments]: Disable tests.

Change-Id: Ibda4eb0435435659b393b3aa415c6855a7b50158
 2025-04-16 10:59:54 +02:00
Ricardo Wurmus
df78b82672
gnu: r-anndatar: Add test input. 
* gnu/packages/bioinformatics.scm (r-anndatar)[properties]: Record
updater-extra-native-inputs.
[native-inputs]: Add r-vctrs.

Change-Id: I8512c7357cb55006bb65da326fab9d9dcc06606a
 2025-04-16 10:59:54 +02:00
Ricardo Wurmus
32e9a1298b
gnu: Add chromap. 
* gnu/packages/bioinformatics.scm (chromap): New variable.

Change-Id: I3b477cf793591b5f9f4583cc47c09854bffd9f6d
 2025-04-09 15:19:56 +02:00
Ricardo Wurmus
efaa20d2d8
gnu: freebayes: Update to 1.3.9. 
* gnu/packages/bioinformatics.scm (freebayes): Update to 1.3.9.
[inputs]: Add bzip2 and xz.
[native-inputs]: Drop labels; remove bash-tap and test-simple-bash-src; add
perl6-tap-harness.
[arguments]: Remove phase 'unpack-submodule-sources; adjust other phases.

Change-Id: I7448a95882ae3a900e697f23824abe40444d039c
 2025-04-03 21:33:46 +02:00
Ricardo Wurmus
e0c92dd647
gnu: vcflib: Update to 1.0.12. 
* gnu/packages/bioinformatics.scm (vcflib): Update to 1.0.12.
[arguments]: Adjust patches.
[native-inputs]: Remove multichoose sources.

Change-Id: I9e5158e04dd695e90565994be4356201518bedc5
 2025-04-03 21:33:45 +02:00
Andreas Enge
309e23567e
gnu: hdf5: Make hdf5@1.14 the default version. 
This replaces all inputs hdf5@1.10 by hdf5@1.14 unless explicitly
specified otherwise.

* gnu/packages/maths.scm (hdf5-1.14): Rename to...
(hdf5): ...this, which was previously defined as hdf5-1.10.
(hdf-eos5, hdf5-parallel-openmpi, scilab): Adapt variable names.
* gnu/packages/bioinformatics.scm (fast5, ncbi-vdb),
gnu/packages/cran.scm (r-h5), gnu/packages/image.scm (vigra)[inputs]:
Keep hdf5-1.10.

Change-Id: Ie43a13ecbb4da597ec1d3f7c0428102b45881485
 2025-03-31 10:29:57 +02:00
Navid Afkhami
b44031fa87
gnu: Add sickle. 
* gnu/packages/bioinformatics.scm (sickle): New variable.

Change-Id: Ib74974b0ee887753d6ead5b5b388e7163abb11f8
 2025-03-07 12:35:23 +01:00
Navid Afkhami
c10ca0d37a
gnu: Add r-bayesprism. 
* gnu/packages/bioinformatics.scm (r-bayesprism): New variable.

Change-Id: I0eaefbaee0de6143fb892dda9c41459a5a5d30d6
 2025-03-06 22:05:09 +01:00
Ricardo Wurmus
1bdf8a450f
gnu: r-voltron: Update to 0.2.0-5.21886d8. 
* gnu/packages/bioinformatics.scm (r-voltron): Update to 0.2.0-5.21886d8.
[arguments]: Ensure that reference to Python is accessible by adding phase
'record-python-reference.

Change-Id: Icc63ba931c7861f1e735671720106ec02f729bae
 2025-03-04 20:59:22 +01:00
Sharlatan Hellseher
03b0ca9e93
gnu: python-pygenometracks: Add missing native input. 
* gnu/packages/bioinformatics.scm (python-pygenometracks):
[native-inputs]: Add python-wheel.

Change-Id: I0294c84446603680498a4af5065a78f42129c476
 2025-02-25 00:02:46 +00:00
Arun Isaac
61428ccf41
gnu: ravanan: Patch shebang in executable. 
* gnu/packages/bioinformatics.scm (ravanan)[arguments]: Replace
patch-source-shebangs phase with custom phase.
 2025-02-24 19:11:29 +00:00
Ricardo Wurmus
1fbc2625d2
gnu: r-voltron: Update to 0.2.0-4.3817548. 
* gnu/packages/bioinformatics.scm (r-voltron): Update to 0.2.0-4.3817548.

Change-Id: Ia7fbfb82a4b040008dc5d8830712c14b37a7ebd2
 2025-02-22 09:12:41 +01:00
Navid Afkhami
dfabaa8a6f
gnu: Add python-pygam. 
* gnu/packages/bioinformatics.scm (python-pygam): New variable.

Change-Id: I0bdd26546b17e3e0f96a32c6de9674d1731ba978
Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
 2025-02-21 17:40:49 +01:00
Ricardo Wurmus
a036a455da
gnu: python-pdbfixer: Add missing inputs. 
* gnu/packages/bioinformatics.scm (python-pdbfixer)[native-inputs]: Add
python-setuptools and python-wheel.

Change-Id: If51cf62c3f88bf73290f7d29af0a6e8277ecddea
 2025-02-21 12:10:19 +01:00
Ricardo Wurmus
2f6e5bc507
gnu: r-netid: Add Python inputs. 
* gnu/packages/bioinformatics.scm (r-netid)[propagated-inputs]: Add
python-anndata, python-geosketch, python-scanpy, and scvelo.

Change-Id: I67661d55769dcd23a1bc448c127d81c0e54065ae
 2025-02-20 15:33:48 +01:00
Ricardo Wurmus
a614aaecce
gnu: Add mageck. 
* gnu/packages/bioinformatics.scm (mageck): New variable.

Change-Id: I0d232473c983ac98aa01ef39a96e938da8628b7d
 2025-02-20 14:37:44 +01:00
Ricardo Wurmus
5ece584e07
gnu: Add python-multicore-tsne. 
* gnu/packages/bioinformatics.scm (python-multicore-tsne): New variable.

Change-Id: I156deff8a55890776105d9c8867bbf8dc968e2e2
 2025-02-20 14:32:21 +01:00
Efraim Flashner
66daf46b41
gnu: Fix some misspellings. 
Change-Id: I316652aff7418af4b8e83bea24638b1513f8aa97
 2025-02-19 11:21:47 +02:00
Vagrant Cascadian
d91f76219b
gnu: Fix typos in bioinformatics packages. 
* gnu/packages/bioinformatics.scm (python-scrublet)[synopsis]: Fix spelling of
"identify".  (maffilter)[description]: Fix spelling of "inference".
(r-azimuth)[description]: Fix spelling of "accounts".
 2025-02-17 02:25:07 -08:00
Ricardo Wurmus
ff5a9f32db
gnu: r-voltron: Update to 0.2.0-3.8f88699. 
* gnu/packages/bioinformatics.scm (r-voltron): Update to 0.2.0-3.8f88699.
[propagated-inputs]: Add r-giotto, r-rhdf5, r-s4vectors,
r-summarizedexperiment, and r-viridislite; remove r-hdf5r.

Change-Id: Ib542f0471663992d5293aca4dc0552a411823112
 2025-02-13 18:32:36 +01:00
Ricardo Wurmus
d7453a7a94
gnu: r-giotto: Update to 1.1.2-1.3e6671a. 
* gnu/packages/bioinformatics.scm (r-giotto): Update to 1.1.2-1.3e6671a.

Change-Id: I60d5d7af3df81f0785bcc5940c7012302dd28d5e
 2025-02-13 18:32:36 +01:00
Ricardo Wurmus
e72b988cfb
gnu: r-presto: Update to 1.0.0-1.7636b3d. 
* gnu/packages/bioinformatics.scm (r-presto): Update to 1.0.0-1.7636b3d.
[properties]: Fix typo.
[propagated-inputs]: Remove r-deseq2 and r-reshape2; add r-purrr and r-tibble.
[native-inputs]: Add r-knitr.

Change-Id: I1285062405bd42b7f3162a44ccf7b174492e5201
 2025-02-11 16:40:05 +01:00
Ricardo Wurmus
696b99dac6
gnu: r-voltron: Add suggested packages. 
* gnu/packages/bioinformatics.scm (r-voltron):[propagated-inputs]: Add
r-anndata, r-anndatar, r-arrow, r-bpcells, r-circlize, r-codetools,
r-complexheatmap, r-delayedarray, r-deseq2, r-geojsonr, r-ggforce,
r-ggnewscale, r-glmgampoi, r-hdf5array, r-hdf5dataframe, r-hdf5r,
r-imagearray, r-music, r-rstudioapi, r-seurat, r-seuratobject,
r-singlecellexperiment, r-spacexr, r-spatialexperiment, r-vitesscer, r-xml,
and r-zarrdataframe.

Change-Id: I4333de31d40e5760f15c5453b8cb974598c8aa5d
 2025-02-07 13:47:34 +01:00
Ricardo Wurmus
c2e2ed8b1a
gnu: Add r-imagearray. 
* gnu/packages/bioinformatics.scm (r-imagearray): New variable.

Change-Id: I432258e2e93e9161bedd95f50dcdd3c52d30457d
 2025-02-07 10:28:44 +01:00
Ricardo Wurmus
ef10714386
gnu: Add r-zarrdataframe. 
* gnu/packages/bioinformatics.scm (r-zarrdataframe): New variable.

Change-Id: Iffe8a0fdad92e4443184642a85863b3b888fbfae
 2025-02-07 10:28:44 +01:00
Ricardo Wurmus
6a4c04531b
gnu: Add r-zarrarray. 
* gnu/packages/bioinformatics.scm (r-zarrarray): New variable.

Change-Id: Ibc66e12966071551b0bc977f67c867303ca958d9
 2025-02-07 10:28:44 +01:00
Ricardo Wurmus
65fb705c27
gnu: Add r-hdf5dataframe. 
* gnu/packages/bioinformatics.scm (r-hdf5dataframe): New variable.

Change-Id: I0faa57f4d82ef71ad37f7c4cfa97fcc5aef5d67a
 2025-02-07 10:28:43 +01:00
Ricardo Wurmus
84794fee72
gnu: r-bpcells: Update to 0.3.0. 
* gnu/packages/bioinformatics.scm (r-bpcells): Update to 0.3.0.
[arguments]: Remove phase 'do-not-tune; add phase 'chdir.
[propagated-inputs]: Add r-lifecycle, r-readr, r-genomicranges, r-igraph,
r-iranges, and r-matrixstats.
[license]: Update to dual licensed ASL2.0 or Expat/MIT.

Change-Id: I972c18e896372e3b44cd5c0ad2f669242568443f
 2025-02-07 10:28:43 +01:00
Ricardo Wurmus
abfd703c4e
gnu: Add r-music. 
* gnu/packages/bioinformatics.scm (r-music): New variable.

Change-Id: I3cf73fcb58f9a407d2795a4525038ab00d1b523f
 2025-02-07 10:28:43 +01:00
Ricardo Wurmus
7786b4e477
gnu: imp: Use an older version of boost. 
* gnu/packages/bioinformatics.scm (imp):[inputs]: Replace boost with
boost-for-mysql.

Change-Id: I3d3bec8589972f15770c264f4b2445f4798b7901
 2025-02-06 11:29:23 +01:00
Ricardo Wurmus
475248bfaa
gnu: imp: Drop input labels. 
* gnu/packages/bioinformatics.scm (imp)[native-inputs]: Drop labels.

Change-Id: I3182a4608a88c59ba0de2fa00d74b8d72b72d8bb
 2025-02-06 11:27:17 +01:00
Navid Afkhami
985c0fd63c
gnu: Add python-cnmf. 
* gnu/packages/bioinformatics.scm (python-cnmf): New variable.

Change-Id: I8a4f2293bde59b10e7b673025bbb4c5a8420738b
Co-authored-by: Sharlatan Hellseher <sharlatanus@gmail.com>
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
 2025-02-05 17:47:00 +00:00
Ricardo Wurmus
216a37ba50
gnu: python-harmonypy: Patch invalid field in pyproject.toml. 
* gnu/packages/bioinformatics.scm (python-harmonypy)[arguments]: Add phase
'patch-pyproject.

Change-Id: I0d80b96458c7bb5ddb571ad640babf6b95fb051f
 2025-02-05 15:08:30 +01:00
Arun Isaac
c4d1b41493
gnu: Add ravanan. 
* gnu/packages/bioinformatics.scm (ravanan): New variable.

Change-Id: Ib93ea64a3a0313be167dd1cd2f036c72f1c0f138
Signed-off-by: jgart <jgart@dismail.de>
 2025-02-03 14:26:22 -05:00
Ricardo Wurmus
a6a4f773f3
gnu: python-scanpy: Disable one more test. 
* gnu/packages/bioinformatics.scm (python-scanpy)[arguments]: Disable one
failing test.

Change-Id: If262b33a3e2c6789c0ce4b8a91f26a8a48054632
 2025-01-29 09:51:19 +01:00
Arun Isaac
49a113e3fc
gnu: ccwl: Update to 0.4.0. 
* gnu/packages/bioinformatics.scm (ccwl): Update to 0.4.0.

Change-Id: I6726438f3a2ec9bb01971f14a22e4123abc01793
 2025-01-28 13:26:51 +00:00
Sharlatan Hellseher
75437dbb76
Merge remote-tracking branch 'origin/go-team' 
Change-Id: I3672a7dc248a41b1a83e4c488523f62cf1806710
 2025-01-26 20:55:06 +00:00
Ricardo Wurmus
e3f3095895
gnu: Add r-vitesscer. 
* gnu/packages/bioinformatics.scm (r-vitesscer): New variable.

Change-Id: I3e0426abd2ed1346efb833ab21c2524d28b41a99
 2025-01-23 15:59:20 +01:00
Sharlatan Hellseher
1b83198655
gnu: Add go-github-com-biogo-store. 
This change merges all extracted subdirs under the same variable as it's
distributed in single module according to project's go.mod.

* gnu/packages/bioinformatics.scm (go-github-com-biogo-store-kdtree,
go-github-com-biogo-store-llrb, go-github-com-biogo-store-step):
Delete variables.

(go-github-com-biogo-store): New variable.
[arguments] <skip-build?>: No go files in project's root.
<import-path>: Set as seen in go.mod.

(go-github-com-biogo-biogo) [propagated-inputs]: Remove
go-github-com-biogo-store-kdtree, go-github-com-biogo-store-llrb, and
go-github-com-biogo-store-step. Add go-github-com-biogo-store.

Change-Id: I1db4efea31fc7f1f5e96b21e874a523cf631f370
 2025-01-22 21:06:22 +00:00
Sharlatan Hellseher
acbff09fe5
gnu: Add go-github-com-biogo-hts. 
This change merges all extracted subdirs under the same variable as it's
distributed in single module according to project's go.mod.

* gnu/packages/bioinformatics.scm (go-github-com-biogo-hts-bam,
go-github-com-biogo-hts-bgzf, go-github-com-biogo-hts-cram,
go-github-com-biogo-hts-csi, go-github-com-biogo-hts-fai,
go-github-com-biogo-hts-sam, go-github-com-biogo-hts-tabix): Delete
variables.

(go-github-com-biogo-hts): New variable.
[arguments] <skip-build?>: No go files in project's root.
<import-path>: Set as seen in go.mod.
<test-flags>: Skip 2 tests requiring network access.

(go-github-com-biogo-biogo) [propagated-inputs]: Remove
go-github-com-biogo-hts-bam, add go-github-com-biogo-hts.

Change-Id: I2cace7a0c732e7590b3b34865323bc38b41b0d86
 2025-01-22 21:02:28 +00:00
Alexis Simon
cc678d0e4d
gnu: Add r-sigfit. 
* gnu/packages/bioinformatics.scm (r-sigfit): New variable.

Change-Id: I9d63975d3512cf8583e7ec22f450bb4963c9ff2f
Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
 2025-01-22 22:01:18 +01:00