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
Efraim Flashner
1970662004
gnu: wfmash: Disable tests when cross-compiling.
...
* gnu/packages/bioinformatics.scm (wfmash)[arguments]: Also disable the
tests when cross-compiling.
Change-Id: Ie7e22a84bfa9b49d4a4b7c1b51a6b01743941af4
2024-11-06 12:49:39 +02:00
Navid Afkhami
0c1a6db809
gnu: Add r-seuratextend.
...
* gnu/packages/bioinformatics.scm (r-seuratextend): New variable.
Change-Id: I9ce0d90a2f05d4e074459046c380849cf9f63978
Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
2024-11-06 11:41:05 +01:00
Navid Afkhami
f5ca62fcad
gnu: Add r-seuratextenddata.
...
* gnu/packages/bioinformatics.scm (r-seuratextenddata): New variable.
Change-Id: Ic07ca4e55387ac914f915f3688bda2f9352435cc
Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
2024-11-05 23:52:06 +01:00
Navid Afkhami
254f465b61
gnu: r-demultiplex2: Update to 1.0.1-1.92130a6.
...
* gnu/packages/bioinformatics.scm (r-demultiplex2): Update to 1.0.1-1.92130a6.
Change-Id: Ic08756e0347ab6997fec0129a06923aebb9c7836
Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
2024-11-05 10:58:08 +01:00
guix@mawumag.com
915f807ce6
gnu: kallisto: Update to 0.50.1
...
See discussion at <https://issues.guix.gnu.org/71146 > for reasons to not
unbundle htslib and libbifrost.
* gnu/packages/bioinformatics.scm (kallisto): Update to 0.50.1.
[source]: Do not remove bundled libraries.
[arguments]: Remove phase 'do-not-use-bundled-htslib.
[inputs]: Remove htslib-1.9.
Change-Id: I6d3263fd49c7b07ce50185b722863b51816ff054
Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
2024-11-04 15:51:56 +01:00
Ricardo Wurmus
a019e11ed2
gnu: Add python-hotspotsc.
...
* gnu/packages/bioinformatics.scm (python-hotspotsc): New variable.
Change-Id: Ib3550837659f95d5a43e77137005db8cc03e6c3f
2024-11-04 10:29:36 +01:00
Vagrant Cascadian
8f49545fed
gnu: Grammar fixes in various package descriptions.
...
* gnu/packages/bioinformatics.scm (vembrane)[description]: Fix
grammar.
* gnu/packages/cran.scm (r-memisc)[description]: Fix grammar.
* gnu/packages/emacs-xyz.scm
(emacs-consult-xdg-recent-files)[description]: Fix grammar.
(emacs-org-margin)[description]: Fix grammar.
* gnu/packages/haskell-xyz.scm (ghc-hslua-core)[description]: Fix
grammar.
* gnu/packages/tex.scm (texlive-autoaligne)[description]: Fix grammar.
(texlive-biblatex-realauthor)[description]: Fix grammar.
(texlive-citeall)[description]: Fix grammar.
(texlive-formal-grammar)[description]: Fix grammar.
(texlive-musikui)[description]: Fix grammar.
(texlive-stanli)[description]: Fix grammar.
(texlive-theatre)[description]: Fix grammar.
(texlive-unitn-bimrep)[description]: Fix grammar.
(texlive-yquant)[description]: Fix grammar.
(texlive-expkv-bundle)[description]: Fix grammar.
(texlive-ketcindy)[description]: Fix grammar.
(texlive-srcredact)[description]: Fix grammar.
(texlive-luamesh)[description]: Fix grammar.
(texlive-maker)[description]: Fix grammar.
(texlive-puyotikz)[description]: Fix grammar.
(texlive-scratch)[description]: Fix grammar.
(texlive-scratch3)[description]: Fix grammar.
(texlive-strands)[description]: Fix grammar.
(texlive-tikz-imagelabels)[description]: Fix grammar.
(texlive-twemojis)[description]: Fix grammar.
(texlive-unicode-bidi)[description]: Fix grammar.
(texlive-pst-contourplot)[description]: Fix grammar.
(texlive-pst-rputover)[description]: Fix grammar.
(texlive-pst-vehicle)[description]: Fix grammar.
(texlive-truthtable)[description]: Fix grammar.
(texlive-esk)[description]: Fix grammar.
(texlive-luaimageembed)[description]: Fix grammar.
(texlive-bibletext)[description]: Fix grammar.
(texlive-easyfloats)[description]: Fix grammar.
(texlive-ehhline)[description]: Fix grammar.
(texlive-exercises)[description]: Fix grammar.
(texlive-extract)[description]: Fix grammar.
(texlive-graphpaper)[description]: Fix grammar.
(texlive-hereapplies)[description]: Fix grammar.
(texlive-hvextern)[description]: Fix grammar.
(texlive-hvqrurl)[description]: Fix grammar.
(texlive-intopdf)[description]: Fix grammar.
(texlive-jobname-suffix)[description]: Fix grammar.
(texlive-modernposter)[description]: Fix grammar.
(texlive-multiaudience)[description]: Fix grammar.
(texlive-overlays)[description]: Fix grammar.
(texlive-pdfpc)[description]: Fix grammar.
(texlive-pgfmath-xfp)[description]: Fix grammar.
(texlive-phonenumbers)[description]: Fix grammar.
(texlive-romanbarpagenumber)[description]: Fix grammar.
(texlive-texments)[description]: Fix grammar.
(texlive-xcntperchap)[description]: Fix grammar.
* gnu/packages/web.scm (libjuice)[description]: Fix grammar.
2024-11-03 23:00:16 -08:00
Navid Afkhami
a007045b7c
gnu: Add r-netid.
...
* gnu/packages/bioinformatics.scm (r-netid): New variable.
Change-Id: Icf8fd23c6f24252350c783faa7f34f35eb1fbce2
Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
2024-11-01 12:16:22 +01:00
Afkhami, Navid
e96af11f2b
gnu: Add r-cellchat-2.
...
* gnu/packages/bioinformatics.scm (r-cellchat-2): New variable.
Change-Id: Iae15f373aefa1c2a0899d5271cf8dddbbfdfa2bd
2024-11-01 12:10:30 +01:00
Afkhami, Navid
aa7511eeb4
gnu: Add r-scdesign2.
...
* gnu/packages/bioinformatics.scm (r-scdesign2): New variable.
Change-Id: I25599df1cb8493bc2d9cc1839b5232aee03bf848
2024-11-01 12:09:01 +01:00
Afkhami, Navid
3d7b1a2768
gnu: Add r-spacexr.
...
* gnu/packages/bioinformatics.scm (r-spacexr): New variable.
Change-Id: Icf2a7dd9d637d14d835c7a428093ba8daf25e25a
2024-11-01 12:08:18 +01:00
Efraim Flashner
ac19ae37b5
gnu: wfmash: Skip tests on riscv64-linux.
...
* gnu/packages/bioinformatics.scm (wfmash)[arguments]: Skip the tests
when building on riscv64-linux.
Change-Id: I95c7849f445b866756fed17ca46b3d0bad088f21
2024-10-23 14:39:59 +03:00
Arun Isaac
789300000c
gnu: wfmash: Update to 0.21.0.
...
* gnu/packages/bioinformatics.scm (wfmash): Update to 0.21.0.
[source]: Use url-fetch.
[arguments]: Do not replace standard check phase. Add fix-cmakelists and
build-check-prerequisites phases.
[inputs]: Remove jemalloc. Add libdeflate.
Change-Id: I664178e9fac7320b9d6e3190e8a3779b2bce2c6b
2024-10-22 17:32:39 +01:00
Efraim Flashner
5703914e93
gnu: mudskipper: Build with cmake-minimal.
...
* gnu/packages/bioinformatics.scm (mudskipper)[native-inputs]: Replace
cmake with cmake-minimal.
Change-Id: I3af7ced7a0547900aa3f452d0b56ceac2e8d0a0c
2024-10-20 20:25:53 +03:00
Efraim Flashner
cd7fb8ce91
gnu: circtools: Build with cmake-minimal.
...
* gnu/packages/bioinformatics.scm (circtools)[native-inputs]: Replace
cmake with cmake-minimal.
Change-Id: I4a7c49e88c3e820bfcaaea9c7bf2cff4b018a853
2024-10-20 20:25:17 +03:00
Roel Janssen
d057d59170
gnu: Update python-rdflib to 7.0.0.
...
* gnu/packages/rdf.scm: Add updated recipe for python-rdflib; Keep
python-rdflib-6 for compatibility.
* gnu/packages/python-xyz.scm: Build python-prov with python-rdflib-6 because
rdflib-7 is not supported.
* gnu/packages/bioinformatics.scm: Build cwltool with python-rdflib-6 because
it fails to build with rdflib-7.
Change-Id: Ibc40c16ede20e69e702915488d6b2f0a7e70b868
2024-09-30 22:48:09 +02:00
Ludovic Courtès
bd67531b82
gnu: python-pyfaidx: Add dependency on UTF-8 locales for tests.
...
Fixes a regression introduced in
92727f4af5
2024-09-25 16:02:18 +02:00
Mădălin Ionel Patrașcu
2fb4ce5110
gnu: Add r-pairwiseadonis.
...
* gnu/packages/bioinformatics.scm (r-pairwiseadonis): New variable.
Change-Id: Idf7ad9efa3625bb60663f421ec79d0a69170e4dd
Signed-off-by: Andreas Enge <andreas@enge.fr>
2024-09-21 09:25:33 +02:00
Maxime Devos
dbb5650682
gnu: bandage: Do not yet use the 'imagemagick/stable' variant.
...
Once <https://issues.guix.gnu.org/47475 > (‘Closure of bandage is way too
large’) has been fixed, the variant will probably be usable.
* gnu/packages/bioinformatics.scm (bandage):
[arguments]<#:disallowed-references>: Once the issue
has been fixed, prevent the imagemagick/stable package from ending up in the
closure.
[native-inputs]: Note that 'imagemagick/stable' cannot be used yet.
Signed-off-by: Maxim Cournoyer <maxim.cournoyer@gmail.com>
Modified-by: Maxim Cournoyer <maxim.cournoyer@gmail.com>
Change-Id: Ie13100eb424b14971055ff91db49bc7029cb6168
2024-08-31 10:44:41 +02:00
Maxim Cournoyer
08ee4ea24b
gnu: flair: Add bash-minimal to inputs.
...
* gnu/packages/bioinformatics.scm (flair)
[inputs]: Add bash-minimal.
Change-Id: I66fd550c617430ebbede36e140ee48df1c6149ca
2024-08-31 10:42:31 +02:00
Maxim Cournoyer
5ce08ad5b4
gnu: ccwl: Remove input labels.
...
* gnu/packages/bioinformatics.scm (ccwl)
[inputs]: Remove input labels.
Change-Id: Ie00325f7472524a0c8431b98ca6172a2f7f7096a
2024-08-31 10:42:31 +02:00
Maxim Cournoyer
200bd2ebad
gnu: arriba: Add bash-minimal to inputs.
...
* gnu/packages/bioinformatics.scm (arriba)
[inputs]: Add bash-minimal.
Change-Id: Ib30f9e0872dc24ca24e498eba51560c750e75d22
2024-08-31 10:42:31 +02:00
Maxim Cournoyer
aecc957a56
gnu: nanopolish: Add bash-minimal to inputs.
...
* gnu/packages/bioinformatics.scm (nanopolish)
[inputs]: Add bash-minimal.
Change-Id: Ie9cbe808e1ae678fb56db03537721f43da3c2b4c
2024-08-31 10:42:30 +02:00
Maxim Cournoyer
92364dfb41
gnu: filtlong: Add bash-minimal to inputs.
...
* gnu/packages/bioinformatics.scm (filtlong)
[inputs]: Add bash-minimal.
Change-Id: I8a4b402d66a06a27c9cc8abacdefecd251c2095c
2024-08-31 10:42:30 +02:00
Maxim Cournoyer
0e219544f1
gnu: ngless: Add bash-minimal to inputs.
...
* gnu/packages/bioinformatics.scm (ngless)
[inputs]: Add bash-minimal.
Change-Id: I3560d4f10261f87c819bd12cf0956a6cf77324cb
2024-08-31 10:42:30 +02:00
Maxim Cournoyer
cf04172b3f
gnu: rcas-web: Add bash-minimal to inputs.
...
* gnu/packages/bioinformatics.scm (rcas-web)[inputs]: Add bash-minimal.
Change-Id: I71f0e435e969e0a689caea90d9f442929c7d9431
2024-08-31 10:42:30 +02:00
Maxim Cournoyer
59fdb6c3d5
gnu: shorah: Add bash-minimal to inputs.
...
* gnu/packages/bioinformatics.scm (shorah)
[inputs]: Add bash-minimal.
Change-Id: Ibe428a0ec32a5acf7e70269376aaf16e97507d51
2024-08-31 10:42:30 +02:00
Maxim Cournoyer
87c29e0542
gnu: rsem: Add bash-minimal to inputs.
...
* gnu/packages/bioinformatics.scm (rsem)
[inputs]: Add bash-minimal.
Change-Id: Idd9fbf729e9bcdd009cf517ec23064544bdf6f43
2024-08-31 10:42:30 +02:00
Maxim Cournoyer
f1aa06f0b7
gnu: roary: Add bash-minimal to inputs.
...
* gnu/packages/bioinformatics.scm (roary): Delete trailing #t.
[inputs]: Add bash-minimal. Remove labels.
Change-Id: Id5ea1b12e2fa641d96a762f5f3b89edbd43a4ffa
2024-08-31 10:42:30 +02:00
Maxim Cournoyer
3fbd948450
gnu: proteinortho: Add bash-minimal to inputs.
...
* gnu/packages/bioinformatics.scm (proteinortho)[inputs]: Add bash-minimal.
Remove labels.
Change-Id: I74e243d598a544a9a58ea77a229b6a2b2f56c5b2
2024-08-31 10:42:30 +02:00
Maxim Cournoyer
6bcc2f6571
gnu: mafft: Add bash-minimal to inputs.
...
* gnu/packages/bioinformatics.scm (mafft): Delete trailing #t.
[inputs]: Add bash-minimal.
Change-Id: Id30d22dc37ee57591f17dc116de81500b09adf3c
2024-08-31 10:42:29 +02:00
Maxim Cournoyer
bff03561c4
gnu: edirect: Add bash-minimal to inputs.
...
* gnu/packages/bioinformatics.scm (edirect): Delete trailing #t.
[inputs]: Add bash-minimal.
Change-Id: I28474c3ec5866b5e9f824d5d71e6cc8be5791f58
2024-08-31 10:42:29 +02:00
Maxim Cournoyer
2efe24adc0
gnu: repeat-masker: Add bash-minimal to inputs.
...
* gnu/packages/bioinformatics.scm (repeat-masker)
[inputs]: Add bash-minimal.
Change-Id: I81d4806cc65eed8040824cb72d6c462c8762294e
2024-08-31 10:42:29 +02:00
Maxim Cournoyer
385a47d51a
gnu: bioperl-minimal: Add bash-minimal to inputs.
...
* gnu/packages/bioinformatics.scm (bioperl-minimal)
[inputs]: Add bash-minimal.
Change-Id: I274572a2e87f63afcca2e433454a71f078291a06
2024-08-31 10:42:29 +02:00
Maxim Cournoyer
c872260148
gnu: ribotaper: Add bash-minimal to inputs.
...
* gnu/packages/bioinformatics.scm (ribotaper)
[inputs]: Add bash-minimal.
Change-Id: I5adc841c15c054101d32f30579a89aa7290c6f3c
2024-08-31 10:42:29 +02:00
Maxim Cournoyer
f7b46e4fa2
gnu: ccwl: Import the correct set of modules.
...
* gnu/packages/bioinformatics.scm (ccwl) [arguments] <modules>: Replace
%default-gnu-imported-modules with %default-gnu-modules.
Change-Id: I9c96e847de537b11bc8396d6c0e7968a1a9f3e98
2024-08-31 10:42:17 +02:00
Maxim Cournoyer
f59df1aa3c
build-systems: gnu: Export %default-gnu-imported-modules and %default-gnu-modules.
...
Until now users would have to cargo cult or inspect the private
%default-modules variable of (guix build-systems gnu) to discover which
modules to include when extending the used modules via the #:modules argument.
The renaming was automated via the command:
$ git grep -l %gnu-build-system-modules
| xargs sed 's/%gnu-build-system-modules/%default-gnu-imported-modules/' -i
* guix/build-system/gnu.scm (%gnu-build-system-modules): Rename to...
(%default-gnu-imported-modules): ... this.
(%default-modules): Rename to...
(%default-gnu-modules): ... this. Export.
(dist-package, gnu-build, gnu-cross-build): Adjust accordingly.
Change-Id: Idef307fff13cb76f3182d782b26e1cd3a5c757ee
2024-08-31 10:42:16 +02:00
Bruno Victal
ee33cb893e
gnu: gdcm: Build manpages.
...
* gnu/packages/bioinformatics.scm (gdcm)[arguments]<#:configure-flags>:
Re-enable manpages.
[native-inputs]: Add libxslt.
Signed-off-by: Maxim Cournoyer <maxim.cournoyer@gmail.com>
2024-08-31 10:42:13 +02:00
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
