| Age | Commit message (Expand) | Author |
|---|
| 2024-12-03 | gnu: r-singlet: Add test inputs....* gnu/packages/bioinformatics.scm (r-singlet)[native-inputs]: Add r-testthat.
Change-Id: I617f6bbb9e11ef00148571b94a4aaf2d445cfcb2
| Ricardo Wurmus |
| 2024-12-03 | 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
| Ricardo Wurmus |
| 2024-12-02 | 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
| Ricardo Wurmus |
| 2024-12-02 | 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
| Ricardo Wurmus |
| 2024-12-02 | Merge remote-tracking branch 'origin/rust-team'...Change-Id: I6d5c28252f060eeb69eb02fd281e7268bb885b29
| Efraim Flashner |
| 2024-12-02 | 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
| Ricardo Wurmus |
| 2024-12-02 | gnu: Add macs-3....* gnu/packages/bioinformatics.scm (macs-3): New variable.
Change-Id: I4bc417e90a1e9d6d28226ea4f66ddc035826c2c4
| Ricardo Wurmus |
| 2024-12-01 | 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
| Ricardo Wurmus |
| 2024-12-01 | 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
| Ricardo Wurmus |
| 2024-12-01 | 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
| Ricardo Wurmus |
| 2024-12-01 | 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
| Ricardo Wurmus |
| 2024-11-28 | gnu: circtools: Skip tests....* gnu/packages/bioinformatics.scm (circtools)[arguments]: Skip the
tests. Don't install the sources.
Change-Id: I722470316e08686fb179bcdf07db12d2f9541b60
| Efraim Flashner |
| 2024-11-20 | gnu: Add python-whatshap....* gnu/packages/bioinformatics.scm (python-whatshap): New variable.
Change-Id: I42281932acb981a7500ef90b5700e7480b41dffe
| Ricardo Wurmus |
| 2024-11-13 | gnu: Add python-pybio....* gnu/packages/bioinformatics.scm (python-pybio): New variable.
Change-Id: I8f5c9cb6c7bb03cbc95386e67d46b1bdd78e01f2
Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
| Navid Afkhami |
| 2024-11-11 | 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
| Ricardo Wurmus |
| 2024-11-11 | gnu: Add r-hdwgcna....* gnu/packages/bioinformatics.scm (r-hdwgcna): New variable.
Change-Id: I1e3c7663a777ee543c53ccee90b6e71f544d89aa
| Ricardo Wurmus |
| 2024-11-11 | gnu: Add python-harmonypy....* gnu/packages/bioinformatics.scm (python-harmonypy): New variable.
Change-Id: Iad8be627099858776163fccfeb27c08129e6fb75
Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
| Navid Afkhami |
| 2024-11-07 | 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>
| Navid Afkhami |
| 2024-11-06 | gnu: wfmash: Disable tests when cross-compiling....* gnu/packages/bioinformatics.scm (wfmash)[arguments]: Also disable the
tests when cross-compiling.
Change-Id: Ie7e22a84bfa9b49d4a4b7c1b51a6b01743941af4
| Efraim Flashner |
| 2024-11-06 | gnu: Add r-seuratextend....* gnu/packages/bioinformatics.scm (r-seuratextend): New variable.
Change-Id: I9ce0d90a2f05d4e074459046c380849cf9f63978
Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
| Navid Afkhami |
| 2024-11-05 | gnu: Add r-seuratextenddata....* gnu/packages/bioinformatics.scm (r-seuratextenddata): New variable.
Change-Id: Ic07ca4e55387ac914f915f3688bda2f9352435cc
Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
| Navid Afkhami |
| 2024-11-05 | 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>
| Navid Afkhami |
| 2024-11-04 | 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>
| guix@mawumag.com |
| 2024-11-04 | gnu: Add python-hotspotsc....* gnu/packages/bioinformatics.scm (python-hotspotsc): New variable.
Change-Id: Ib3550837659f95d5a43e77137005db8cc03e6c3f
| Ricardo Wurmus |
| 2024-11-03 | 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.
| Vagrant Cascadian |
| 2024-11-01 | gnu: Add r-netid....* gnu/packages/bioinformatics.scm (r-netid): New variable.
Change-Id: Icf8fd23c6f24252350c783faa7f34f35eb1fbce2
Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
| Navid Afkhami |
| 2024-11-01 | gnu: Add r-cellchat-2....* gnu/packages/bioinformatics.scm (r-cellchat-2): New variable.
Change-Id: Iae15f373aefa1c2a0899d5271cf8dddbbfdfa2bd
| Afkhami, Navid |
| 2024-11-01 | gnu: Add r-scdesign2....* gnu/packages/bioinformatics.scm (r-scdesign2): New variable.
Change-Id: I25599df1cb8493bc2d9cc1839b5232aee03bf848
| Afkhami, Navid |
| 2024-11-01 | gnu: Add r-spacexr....* gnu/packages/bioinformatics.scm (r-spacexr): New variable.
Change-Id: Icf2a7dd9d637d14d835c7a428093ba8daf25e25a
| Afkhami, Navid |
| 2024-10-23 | gnu: wfmash: Skip tests on riscv64-linux....* gnu/packages/bioinformatics.scm (wfmash)[arguments]: Skip the tests
when building on riscv64-linux.
Change-Id: I95c7849f445b866756fed17ca46b3d0bad088f21
| Efraim Flashner |
| 2024-10-22 | 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
| Arun Isaac |
| 2024-10-20 | gnu: mudskipper: Build with cmake-minimal....* gnu/packages/bioinformatics.scm (mudskipper)[native-inputs]: Replace
cmake with cmake-minimal.
Change-Id: I3af7ced7a0547900aa3f452d0b56ceac2e8d0a0c
| Efraim Flashner |
| 2024-10-20 | gnu: circtools: Build with cmake-minimal....* gnu/packages/bioinformatics.scm (circtools)[native-inputs]: Replace
cmake with cmake-minimal.
Change-Id: I4a7c49e88c3e820bfcaaea9c7bf2cff4b018a853
| Efraim Flashner |
| 2024-09-30 | 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
| Roel Janssen |
| 2024-09-25 | gnu: python-pyfaidx: Add dependency on UTF-8 locales for tests....Fixes a regression introduced in
92727f4af5d410b0a521d57d5ecef6b35779bdc2 whereby the “en_US.utf8” locale
would no longer be available in the build environment.
* gnu/packages/bioinformatics.scm (python-pyfaidx)[native-inputs]: Add
‘libc-utf8-locales-for-target’.
Change-Id: I4f868edb82ef08bb56e5d7e3d2ea861bd23c03bf
| Ludovic Courtès |
| 2024-09-21 | gnu: Add r-pairwiseadonis....* gnu/packages/bioinformatics.scm (r-pairwiseadonis): New variable.
Change-Id: Idf7ad9efa3625bb60663f421ec79d0a69170e4dd
Signed-off-by: Andreas Enge <andreas@enge.fr>
| Mădălin Ionel Patrașcu |
| 2024-08-31 | 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
| Maxime Devos |
| 2024-08-31 | gnu: flair: Add bash-minimal to inputs....* gnu/packages/bioinformatics.scm (flair)
[inputs]: Add bash-minimal.
Change-Id: I66fd550c617430ebbede36e140ee48df1c6149ca
| Maxim Cournoyer |
| 2024-08-31 | gnu: ccwl: Remove input labels....* gnu/packages/bioinformatics.scm (ccwl)
[inputs]: Remove input labels.
Change-Id: Ie00325f7472524a0c8431b98ca6172a2f7f7096a
| Maxim Cournoyer |
| 2024-08-31 | gnu: arriba: Add bash-minimal to inputs....* gnu/packages/bioinformatics.scm (arriba)
[inputs]: Add bash-minimal.
Change-Id: Ib30f9e0872dc24ca24e498eba51560c750e75d22
| Maxim Cournoyer |
| 2024-08-31 | gnu: nanopolish: Add bash-minimal to inputs....* gnu/packages/bioinformatics.scm (nanopolish)
[inputs]: Add bash-minimal.
Change-Id: Ie9cbe808e1ae678fb56db03537721f43da3c2b4c
| Maxim Cournoyer |
| 2024-08-31 | gnu: filtlong: Add bash-minimal to inputs....* gnu/packages/bioinformatics.scm (filtlong)
[inputs]: Add bash-minimal.
Change-Id: I8a4b402d66a06a27c9cc8abacdefecd251c2095c
| Maxim Cournoyer |
| 2024-08-31 | gnu: ngless: Add bash-minimal to inputs....* gnu/packages/bioinformatics.scm (ngless)
[inputs]: Add bash-minimal.
Change-Id: I3560d4f10261f87c819bd12cf0956a6cf77324cb
| Maxim Cournoyer |
| 2024-08-31 | gnu: rcas-web: Add bash-minimal to inputs....* gnu/packages/bioinformatics.scm (rcas-web)[inputs]: Add bash-minimal.
Change-Id: I71f0e435e969e0a689caea90d9f442929c7d9431
| Maxim Cournoyer |
| 2024-08-31 | gnu: shorah: Add bash-minimal to inputs....* gnu/packages/bioinformatics.scm (shorah)
[inputs]: Add bash-minimal.
Change-Id: Ibe428a0ec32a5acf7e70269376aaf16e97507d51
| Maxim Cournoyer |
| 2024-08-31 | gnu: rsem: Add bash-minimal to inputs....* gnu/packages/bioinformatics.scm (rsem)
[inputs]: Add bash-minimal.
Change-Id: Idd9fbf729e9bcdd009cf517ec23064544bdf6f43
| Maxim Cournoyer |
| 2024-08-31 | gnu: roary: Add bash-minimal to inputs....* gnu/packages/bioinformatics.scm (roary): Delete trailing #t.
[inputs]: Add bash-minimal. Remove labels.
Change-Id: Id5ea1b12e2fa641d96a762f5f3b89edbd43a4ffa
| Maxim Cournoyer |
| 2024-08-31 | gnu: proteinortho: Add bash-minimal to inputs....* gnu/packages/bioinformatics.scm (proteinortho)[inputs]: Add bash-minimal.
Remove labels.
Change-Id: I74e243d598a544a9a58ea77a229b6a2b2f56c5b2
| Maxim Cournoyer |
| 2024-08-31 | gnu: mafft: Add bash-minimal to inputs....* gnu/packages/bioinformatics.scm (mafft): Delete trailing #t.
[inputs]: Add bash-minimal.
Change-Id: Id30d22dc37ee57591f17dc116de81500b09adf3c
| Maxim Cournoyer |
| 2024-08-31 | gnu: edirect: Add bash-minimal to inputs....* gnu/packages/bioinformatics.scm (edirect): Delete trailing #t.
[inputs]: Add bash-minimal.
Change-Id: I28474c3ec5866b5e9f824d5d71e6cc8be5791f58
| Maxim Cournoyer |
