| Age | Commit message (Expand) | Author |
|---|
| 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 |
| 2024-08-31 | gnu: repeat-masker: Add bash-minimal to inputs....* gnu/packages/bioinformatics.scm (repeat-masker)
[inputs]: Add bash-minimal.
Change-Id: I81d4806cc65eed8040824cb72d6c462c8762294e
| Maxim Cournoyer |
| 2024-08-31 | gnu: bioperl-minimal: Add bash-minimal to inputs....* gnu/packages/bioinformatics.scm (bioperl-minimal)
[inputs]: Add bash-minimal.
Change-Id: I274572a2e87f63afcca2e433454a71f078291a06
| Maxim Cournoyer |
| 2024-08-31 | gnu: ribotaper: Add bash-minimal to inputs....* gnu/packages/bioinformatics.scm (ribotaper)
[inputs]: Add bash-minimal.
Change-Id: I5adc841c15c054101d32f30579a89aa7290c6f3c
| Maxim Cournoyer |
| 2024-08-31 | 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
| Maxim Cournoyer |
| 2024-08-31 | build-systems: gnu: Export %default-gnu-imported-modules and %default-gnu-mod......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
| Maxim Cournoyer |
| 2024-08-31 | 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>
| Bruno Victal |
| 2024-07-30 | 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
| Zheng Junjie |
| 2024-07-30 | gnu: bwa: Fix cross-compiling....* gnu/packages/bioinformatics.scm (bwa)[arguments]<#:make-flags>: Use
CC-FOR-TARGET.
Change-Id: I63dd0f13f337fbf84967f1ef1b6332ce3391ae97
| Zheng Junjie |
| 2024-07-30 | 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
| Spencer King |
| 2024-07-01 | gnu: Add python-muon....* gnu/packages/bioinformatics.scm (python-muon): New variable.
Change-Id: I21431b089d1f404828b78d79124d96e7d36d5a2d
Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
| guix@mawumag.com |
| 2024-07-01 | gnu: Add python-mofapy2....* gnu/packages/bioinformatics.scm (python-mofapy2): New variable.
Change-Id: Ide92878258511b3daf4e56d5faa94d190fdee62f
Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
| guix@mawumag.com |
| 2024-07-01 | gnu: Add r-anpan....* gnu/packages/bioinformatics.scm (r-anpan): New variable.
Change-Id: Ia01ba3be7424306674b9c9b2904f1f0cfa66d818
Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
| Afkhami, Navid |
