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Author SHA1 Message Date
Ricardo Wurmus
61c16f3e55
gnu: r-skitools: Add missing input. 
* gnu/packages/bioinformatics.scm (r-skitools)[native-inputs]: Add
r-bsgenome-hsapiens-ucsc-hg19.

Change-Id: I8331e0df21bda001d6e3ec944f02791c0a9301b6
 2024-12-03 16:59:58 +01:00
Ricardo Wurmus
bd109162b3
gnu: r-scseqcomm: Remove commented inputs. 
* gnu/packages/bioinformatics.scm (r-scseqcomm): Remove comments.

Change-Id: I537f6377da44637674a0413a30ddd6b70a620ad3
 2024-12-03 16:59:58 +01:00
Ricardo Wurmus
0b3aa43797
gnu: r-chromunity: Add missing input. 
* gnu/packages/bioinformatics.scm (r-chromunity)[native-inputs]: Add
r-testthat.

Change-Id: I5d208a5ab0cb63567ab49783d0fbe0733b08161a
 2024-12-03 16:59:58 +01:00
Ricardo Wurmus
64e941ef7a
gnu: r-liana: Add missing input. 
* gnu/packages/bioinformatics.scm (r-liana)[native-inputs]: Add r-testthat.

Change-Id: I04c9c5f60842e1ed0a0415e51c25b46b64a60104
 2024-12-03 16:59:57 +01:00
Ricardo Wurmus
f6b6eb26b9
gnu: r-circus: Add missing input. 
* gnu/packages/bioinformatics.scm (r-circus)[native-inputs]: Add r-testthat.

Change-Id: I7178baece0a8134923fd550e2f1cc303f32aaaea
 2024-12-03 16:59:56 +01:00
Ricardo Wurmus
e3bbf678e3
gnu: Remove r-numbat. 
This is a duplicate of a package in (gnu packages bioconductor).

* gnu/packages/bioinformatics.scm (r-numbat): Delete variable.

Change-Id: Ic1f5d9779a594432a0dd8bd0be9059423a2f5b34
 2024-12-03 16:59:56 +01:00
Ricardo Wurmus
dff6f58688
gnu: r-spectre: Disable tests. 
* gnu/packages/bioinformatics.scm (r-spectre)[arguments]: Disable tests.

Change-Id: I7978b05d0c1c2de3ada6b1b490ae36b28171f17c
 2024-12-03 16:59:56 +01:00
Ricardo Wurmus
e2561d2ec8
gnu: r-gchain: Add missing inputs. 
* gnu/packages/bioinformatics.scm (r-gchain)[native-inputs]: Add
r-pwalign and r-testthat.
[arguments]: Add phase 'skip-bad-tests.

Change-Id: Ia11c6e50e0d2886762ec551df3e5d73ef98547f8
 2024-12-03 16:59:56 +01:00
Ricardo Wurmus
5d6561a87d
gnu: r-seraster: Add missing input. 
* gnu/packages/bioinformatics.scm (r-seraster)[native-inputs]: Add r-testthat.

Change-Id: I88fb4a51831aff1b08437ef08adb62e344185a07
 2024-12-03 16:59:55 +01:00
Ricardo Wurmus
88ce625adb
gnu: r-gtrack: Add missing input. 
* gnu/packages/bioinformatics.scm (r-gtrack)[native-inputs]: Add r-testthat.

Change-Id: I7b0cad1b8fd27d88ff766c5a46bd01dae2933422
 2024-12-03 16:59:54 +01:00
Ricardo Wurmus
10296b8cae
gnu: r-doubletcollection: Add missing input and disable tests. 
* gnu/packages/bioinformatics.scm (r-doubletcollection)[native-inputs]: Add
r-testthat.
[arguments]: Disable tests.

Change-Id: I8802f703ecfd8d69e6e457cffb28e34d3f4f2b06
 2024-12-03 16:59:53 +01:00
Ricardo Wurmus
bb939442b0
gnu: r-pando: Add missing inputs and disable tests. 
* gnu/packages/bioinformatics.scm (r-pando)[native-inputs]: Add
r-bsgenome-hsapiens-ucsc-hg38, r-devtools, r-doparallel, and
r-ensdb-hsapiens-v86.
[arguments]: Disable tests.

Change-Id: Ic66679e2b8c4cdb9835ce08dc4dbb0a42e35e291
 2024-12-03 16:59:53 +01:00
Ricardo Wurmus
066b53965c
gnu: r-anpan: Add missing input. 
* gnu/packages/bioinformatics.scm (r-anpan)[native-inputs]: Add r-testthat.

Change-Id: I69be3fa82db5f9c4e1302c9a3bd2d4f5253bde13
 2024-12-03 16:59:53 +01:00
Ricardo Wurmus
5a2ba07676
gnu: r-hdwgcna: Add missing inputs. 
* gnu/packages/bioinformatics.scm (r-hdwgcna)[native-inputs]: Add r-devtools
and r-testthat.

Change-Id: I553d4fc2f1a682e5d552862c5e50a31140528073
 2024-12-03 16:59:52 +01:00
Ricardo Wurmus
4b78a0dde4
gnu: r-ewastools: Add missing inputs. 
* gnu/packages/bioinformatics.scm (r-ewastools)[native-inputs]: Add r-enmix,
r-illuminahumanmethylationepicanno-ilm10b4-hg19, r-minfi, r-stringi, and
r-testthat.

Change-Id: I8ba2b1c46a4898b27874a7dc8648bb142f4b5a70
 2024-12-03 16:59:52 +01:00
Ricardo Wurmus
387ca84d52
gnu: r-bamutils: Add test inputs and disable tests. 
* gnu/packages/bioinformatics.scm (r-bamutils)[arguments]: Disable tests.
[native-inputs]: Add r-testthat and samtools.

Change-Id: I781c38fb59355a51f2cd27a833d7ed5dbe5277ab
 2024-12-03 16:59:52 +01:00
Ricardo Wurmus
bf20a8fb15
gnu: r-bamutils: Update to 0.0.0.9000-2.0a7d2d9. 
* gnu/packages/bioinformatics.scm (r-bamutils): Update to
0.0.0.9000-2.0a7d2d9.

Change-Id: I04e86c2ff1059f23a34615ac6067926cdd9cb355
 2024-12-03 16:59:52 +01:00
Ricardo Wurmus
d352e2ac18
gnu: r-dropbead: Disable tests. 
* gnu/packages/bioinformatics.scm (r-dropbead)[native-inputs]: Add
r-data-table.
[arguments]: Disable tests.

Change-Id: I48c74a7b4253695ab5c877f6f1cebdca6ed42cb7
 2024-12-03 16:59:49 +01:00
Ricardo Wurmus
f8d38c785d
gnu: r-sleuth: Disable tests. 
* gnu/packages/bioinformatics.scm (r-sleuth)[native-inputs]: Add r-testthat.
[arguments]: Disable tests.

Change-Id: Ib060eb18f8964212eb38b7025a35c16f0aca97b9
 2024-12-03 16:59:49 +01:00
Ricardo Wurmus
cc3d2e78ed
gnu: r-ggsankey: Add missing inputs. 
* gnu/packages/bioinformatics.scm (r-ggsankey)[native-inputs]: Add r-testthat.

Change-Id: Iaafb75cc47e89a4a25232003d410f98c304ff021
 2024-12-03 16:59:48 +01:00
Ricardo Wurmus
c777e6ba75
gnu: r-streamgraph: Add missing input. 
* gnu/packages/bioinformatics.scm (r-streamgraph)[native-inputs]: Add
r-testthat.

Change-Id: I1209a467c5a966c916f0d0416c6c1e283ae9226d
 2024-12-03 16:59:48 +01:00
Ricardo Wurmus
dd561e0cf7
gnu: r-signac: Add missing input. 
* gnu/packages/bioinformatics.scm (r-signac)[native-inputs]: Add r-testthat.

Change-Id: I0aacabf77171903cca2bc0f443f77e479b6331b2
 2024-12-03 16:59:48 +01:00
Ricardo Wurmus
32657c03bc
gnu: r-psupertime: Add missing input. 
* gnu/packages/bioinformatics.scm (r-psupertime)[native-inputs]: Add
r-testthat.

Change-Id: I9993547e2e757b4218c2229495a7eaa0c8fecbe2
 2024-12-03 16:59:46 +01:00
Ricardo Wurmus
92301c7a27
gnu: r-demuxmix: Add missing input. 
* gnu/packages/bioinformatics.scm (r-demuxmix)[native-inputs]: Add r-testthat.

Change-Id: Ia09b929b4d5bb521d58fb74f17f1ac91a4d44a60
 2024-12-03 16:59:46 +01:00
Ricardo Wurmus
6ec643fd9d
gnu: r-cmdstanr: Add missing input. 
* gnu/packages/bioinformatics.scm (r-cmdstanr)[native-inputs]: Add
r-testthat.

Change-Id: Idd81b903e9e9a8308703c9ee8dc5583a04854678
 2024-12-03 16:59:46 +01:00
Ricardo Wurmus
0dcdeea3e5
gnu: r-gutils: Add missing input. 
* gnu/packages/bioinformatics.scm (r-gutils)[native-inputs]: Add r-testthat.

Change-Id: I1b5e34441b48bc92bff6538378d2e2bbc7111631
 2024-12-03 16:59:45 +01:00
Ricardo Wurmus
0afafd8b21
gnu: r-rnacrosslinkoo: Add missing inputs. 
* gnu/packages/bioinformatics.scm (r-rnacrosslinkoo)[native-inputs]: Add
r-testthat.

Change-Id: Iedd2dee7a32dcd19a99d25d92b6f453dd197f5b4
 2024-12-03 16:59:42 +01:00
Ricardo Wurmus
d344c8dd7a
gnu: r-bedtorch: Disable tests. 
* gnu/packages/bioinformatics.scm (r-bedtorch)[arguments]: Disable tests.
[native-inputs]: Add r-testthat.

Change-Id: Ia06aca330528eb2b9eea569d5d12db0f12d6511e
 2024-12-03 16:59:42 +01:00
Ricardo Wurmus
ddad87926c
gnu: r-presto: Add missing inputs. 
* gnu/packages/bioconductor.scm (r-presto)[native-inputs]: Add r-testthat.

Change-Id: I3fe5ec83478e384fe34701b0672b6f216255b1d6
 2024-12-03 16:59:41 +01:00
Ricardo Wurmus
0b191fda81
gnu: r-psiplot: Add missing inputs. 
* gnu/packages/bioinformatics.scm (r-psiplot)[native-inputs]: Add r-testthat.

Change-Id: I19ad7216f86968c87abad64313bf09d03e3ad612
 2024-12-03 16:59:41 +01:00
Ricardo Wurmus
132a8451a1
gnu: r-omnipathr/devel: Add missing inputs. 
* gnu/packages/bioinformatics.scm (r-omnipathr/devel)[native-inputs]: Add
r-testthat.

Change-Id: I7e339871d65ed0ff263db14ff9fb0aa1bb3ed0bb
 2024-12-03 16:59:40 +01:00
Ricardo Wurmus
6b2dda4068
gnu: r-millefy: Add missing inputs. 
* gnu/packages/bioinformatics.scm (r-millefy)[native-inputs]: Add r-testthat.

Change-Id: Id5d1f74074f05f1af2e3726e9a9e49f2d63f13c9
 2024-12-03 16:59:39 +01:00
Ricardo Wurmus
65ea023a14
gnu: r-singlet: Add test inputs. 
* gnu/packages/bioinformatics.scm (r-singlet)[native-inputs]: Add r-testthat.

Change-Id: I617f6bbb9e11ef00148571b94a4aaf2d445cfcb2
 2024-12-03 16:59:38 +01:00
Ricardo Wurmus
7b5b76c18c
gnu: r-anndatar: Add test inputs. 
* gnu/packages/bioinformatics.scm (r-anndatar)[native-inputs]: Add r-rhdf5,
r-seuratobject, r-singlecellexperiment, and r-testthat.

Change-Id: I233a1f7216241b5d9d8301e07acdf811edb24a28
 2024-12-03 16:59:36 +01:00
Ricardo Wurmus
d97a67d41d
gnu: homer: Install config.txt. 
* gnu/packages/bioinformatics.scm (homer)[native-inputs]: Add config.txt.
[arguments]: Update 'configure phase to place config.txt in expected location;
patch configuration code to optionally load a user's configuration file.

Change-Id: Ib05c828e751c6568524bbef45997a42fade4545a
 2024-12-02 13:41:08 +01:00
Ricardo Wurmus
af774e2780
gnu: homer: Install homer executable. 
* gnu/packages/bioinformatics.scm (homer)[arguments]: Update 'install phase to
also install "homer" to the bin directory.

Change-Id: Ia2d23fce493f9c10cc43ac126cd83956b4b9bb05
 2024-12-02 13:41:08 +01:00
Efraim Flashner
541abedc0a
Merge remote-tracking branch 'origin/rust-team' 
Change-Id: I6d5c28252f060eeb69eb02fd281e7268bb885b29
 2024-12-02 14:13:39 +02:00
Ricardo Wurmus
2756c660fb
gnu: python-pairtools: Update to 1.1.0-fix. 
* gnu/packages/bioinformatics.scm (python-pairtools): Update to 1.1.0-fix.
[build-system]: Use pyproject-build-system.
[arguments]: Add phase 'patch-setup.py.
[native-inputs]: Add python-pytest-cov, python-setuptools, and python-wheel.

Change-Id: Ifa3c12de228420d8fdd7b0053bb9da80b9b3efe4
 2024-12-02 10:49:06 +01:00
Ricardo Wurmus
207c69e40d
gnu: Add macs-3. 
* gnu/packages/bioinformatics.scm (macs-3): New variable.

Change-Id: I4bc417e90a1e9d6d28226ea4f66ddc035826c2c4
 2024-12-02 10:28:59 +01:00
Ricardo Wurmus
c5b16964bb
gnu: r-voltron: Add Python inputs. 
* gnu/packages/bioinformatics.scm (r-voltron)[inputs]: Add python,
python-numpy, python-pandas, python-anndata, python-h5py, python-natsort,
python-numcodecs, python-packaging, python-scipy, python-tifffile, and
python-zarr.

Change-Id: Iab137936550b51d6839d9beaa47f6102a8f3c355
 2024-12-01 10:41:35 +01:00
Ricardo Wurmus
c7e412e775
gnu: r-voltron: Update to 0.2.0-1.9f9415c. 
* gnu/packages/bioinformatics.scm (r-voltron): Update to 0.2.0-1.9f9415c.
[inputs]: Remove tbb.
[propagated-inputs]: Remove r-anndata, r-fastdummies, r-fnn, r-ggforce,
r-hdf5r, r-htmltools, r-interp, r-morpho, r-raster, r-s4vectors, r-scales,
r-terra, r-umap, and r-xml; add r-basilisk, r-ids, r-rann, r-rcdt,
r-rcppannoy, r-rcpparmadillo, r-reticulate, r-s4arrays, and r-sp.
[native-inputs]: Add r-testthat.
[description]: Update.

Change-Id: I8051ade560e03f8e3760560ec7b78d9941c00e08
 2024-12-01 10:26:38 +01:00
Ricardo Wurmus
adfda4a075
gnu: pigx-scrnaseq: Update to 1.1.10. 
* gnu/packages/bioinformatics.scm (pigx-scrnaseq): Update to 1.1.10.
[arguments]: Remove quasiquote.

Change-Id: I6cab358addfb376a878929bfb5041edc00cd336a
 2024-12-01 08:52:51 +01:00
Ricardo Wurmus
b21b8e909d
gnu: pigx-bsseq: Update to 0.1.10. 
* gnu/packages/bioinformatics.scm (pigx-bsseq): Update to 0.1.10.
[native-inputs]: Use tzdata-for-tests instead of tzdata.
[arguments]: Remove quasiquote.

Change-Id: I680b08cda788fc03a8bedb87f241116a051798d6
 2024-12-01 08:52:51 +01:00
Efraim Flashner
b7eb50ddca
gnu: circtools: Skip tests. 
* gnu/packages/bioinformatics.scm (circtools)[arguments]: Skip the
tests.  Don't install the sources.

Change-Id: I722470316e08686fb179bcdf07db12d2f9541b60
 2024-11-28 11:05:03 +02:00
Ricardo Wurmus
d5eab53a72
gnu: Add python-whatshap. 
* gnu/packages/bioinformatics.scm (python-whatshap): New variable.

Change-Id: I42281932acb981a7500ef90b5700e7480b41dffe
 2024-11-20 21:57:48 +01:00
Navid Afkhami
bf96496f17
gnu: Add python-pybio. 
* gnu/packages/bioinformatics.scm (python-pybio): New variable.

Change-Id: I8f5c9cb6c7bb03cbc95386e67d46b1bdd78e01f2
Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
 2024-11-13 19:08:39 +01:00
Ricardo Wurmus
b790db7589
gnu: r-hdwgcna: Use R build system phases. 
* gnu/packages/bioinformatics.scm (r-hdwgcna)[arguments]: Explicitly select
%STANDARD-PHASES from r-build-system module.

Change-Id: I8f6593ab1243884827698cf84d34d9f7aef5c28c
 2024-11-11 20:45:16 +01:00
Ricardo Wurmus
c0260cafe5
gnu: Add r-hdwgcna. 
* gnu/packages/bioinformatics.scm (r-hdwgcna): New variable.

Change-Id: I1e3c7663a777ee543c53ccee90b6e71f544d89aa
 2024-11-11 18:47:58 +01:00
Navid Afkhami
6e19a94d5a
gnu: Add python-harmonypy. 
* gnu/packages/bioinformatics.scm (python-harmonypy): New variable.

Change-Id: Iad8be627099858776163fccfeb27c08129e6fb75
Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
 2024-11-11 10:43:58 +01:00
Navid Afkhami
2a6d96425e
gnu: r-demultiplex2: Update to 1.0.2-2.c1ce09e. 
* gnu/packages/bioinformatics.scm (r-demultiplex2): Update to 1.0.2-2.c1ce09e.

Change-Id: I42038c8f4a003ae5c274fe635ddb8c2a027ddce4
Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
 2024-11-07 11:30:39 +01:00