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4386 Commits

Author SHA1 Message Date
Hartmut Goebel
83012bd39a gnu: biobambam2: Update to 2.0.185. 
* gnu/packages/bioinformatics.scm (biobambam2): Update to 2.0.185.

Change-Id: I462959cbdf938cc6e798132fff521645dd4a6d04
 2026-01-25 18:52:42 +01:00
Hartmut Goebel
f4bf35a92b gnu: libmaus2: Update to 2.0.813. 
* gnu/packages/bioinformatics.scm (libmaus2): Update to 2.0.813.
  [source]: Add patch. [inputs]: Add boost.
* gnu/packages/patches/libmauss-fix-gcc-13-require-include-cstdint.patch: New file.
* gnu/local.mk (dist_patch_DATA): Register new patch file.

Change-Id: I607773a7c7b7a43c0bd037bc8b99666c89e9c429
 2026-01-25 18:52:42 +01:00
Arun Isaac
7d326824a1 gnu: ccwl: Update to 0.5.0. 
* gnu/packages/bioinformatics.scm (ccwl): Update to 0.5.0.
[native-inputs]: Add guile-run64.
 2026-01-13 02:01:29 +00:00
Cayetano Santos
bb106f7b85 gnu: flexbar: Update to 3.5.0. 
* gnu/packages/bioinformatics.scm (flexbar): Update to 3.5.0.
[arguments]: Use G-Expressions.

Change-Id: If8a61ea506d30eebf29ae1116d7950fce497cb19
 2026-01-09 14:51:18 +01:00
Simon Tournier
a17221bb95 gnu: hh-suite: Adjust for GCC@14. 
* gnu/packages/bioinformatics.scm (hh-suite)[arguments]: New phase.

Change-Id: Ic1c6078febbffe6a81393c8a114ac4b41d269cda
 2026-01-08 19:59:50 +01:00
Simon Tournier
b9724d5bf0 gnu: phyml: Add font required by documentation. 
* gnu/packages/bioinformatics.scm (phyml):
[native-inputs]: Add texlive-ec.
[arguments]<phases>: Replace /homeless-shelter by /tmp.

Change-Id: I2a1d1fb343d2dd333846093fece511fe8af1cd6e
 2026-01-08 19:57:00 +01:00
Simon Tournier
108182dbb5 gnu: velvet: Adjust for GCC@14 and documentation building. 
* gnu/packages/bioinformatics.scm (velvet)
[arguments]:<make-flags>: Add incompatible-pointer-types.
<phases>: Allow TeXlive to create font.
[native-inputs]: Add texlive-ec.

Fixes: guix/guix#5471
Change-Id: I0d44b763a77a64c900f09efdea30d8a89d3b2496
Signed-off-by: Andreas Enge <andreas@enge.fr>
 2026-01-08 19:54:30 +01:00
Andreas Enge
d190f22813 gnu: Remove khmer. 
* gnu/packages/bioinformatics.scm (khmer): Delete variable.

Fixes: guix/guix#4489
Change-Id: I88aca5be768690b236343f2e959ecb71b4a5c984
 2026-01-05 17:11:14 +01:00
Sharlatan Hellseher
cf4296ecb1 gnu: cnvkit: Fix tests. 
* gnu/packages/bioinformatics.scm (cnvkit):
[arguments] <phases>: Add 'fix-pytest-config.
[propagated-inputs]: Remove python-future.

Change-Id: I845709c8e91e8ed86dcc25a9d5dc0469e8005f0b
 2025-12-31 17:33:28 +00:00
Nicolas Graves
f0a4086fad gnu: tadbit: Switch to pyproject. 
* gnu/packages/bioinformatics.scm (tadbit):
[build-system]: Switch to pyproject-build-system.
[arguments]<#:test-backend, #:test-flags>: Migrate from 'check phase.
[native-inputs]: Add python-setuptools.

Change-Id: Ib32b92c308fae375095c0c3a14df1c8bea1f7969
Modified-by: Sharlatan Hellseher <sharlatanus@gmail.com>
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
 2025-12-31 13:53:03 +00:00
Sharlatan Hellseher
48983fab8d gnu: python-mappy: Fix indentation. 
* gnu/packages/bioinformatics.scm (python-mappy): Fix indentation.

Change-Id: Ib6fbe26b7ba54e559093699b6b31e9a27b60ea96
 2025-12-17 23:32:23 +00:00
Hugo Buddelmeijer
14ab247ece gnu: python-mappy: Switch to pyproject. 
* gnu/packages/bioinformatics.scm (python-mappy):
[source]: Switch to git-fetch.
[build-system]: Switch to pyproject-build-system.
[arguments]<#test-backend, #test-flags>: Replace check phase with
example (no tests).
[native-inputs]: Add python-setuptools.

Change-Id: I9561de7e0ee94dbd1134c23c608d262169407456
Modified-by: Sharlatan Hellseher <sharlatanus@gmail.com>
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
 2025-12-17 23:30:57 +00:00
Hugo Buddelmeijer
82aa5d47fb gnu: python-strawc: Switch to pyproject-build-system. 
* gnu/packages/bioinformatics.scm (python-strawc): Switch to
pyproject-build-system.
[build-system]: Switch to pyproject-build-system.
[native-inputs]: Add python-setuptools.

Change-Id: I49f697f9a968a141e5009ea8f860f0662500e0fd
Signed-off-by: Andreas Enge <andreas@enge.fr>
 2025-12-17 11:20:21 +01:00
Hugo Buddelmeijer
146da6cf12 gnu: python-pypairix: Update to 0.3.9. 
* gnu/packages/bioinformatics.scm (python-pypairix): Update to 0.3.9.
[build-system]: Switch to pyproject-build-system.
[native-inputs]: Add python-pytest and python-setuptools.

Change-Id: I0fbe88438fcdcb304e12eac4156e94959e6db174
Signed-off-by: Andreas Enge <andreas@enge.fr>
 2025-12-17 11:20:21 +01:00
Sharlatan Hellseher
0a2dfdb6d7 gnu: tetoolkit: Update to 2.2.3. 
* gnu/packages/bioinformatics.scm (tetoolkit): Update to 2.2.3.
[arguments] <tests?>: No tests.
[native-inputs]: Remove python-wheel.

Change-Id: Idc5994a58115653447abb02d676b800d27ffe16e
 2025-12-17 11:20:20 +01:00
Sharlatan Hellseher
08b18b4422 gnu: gdc-client: Update to 2.3, fix build. 
* gnu/packages/bioinformatics.scm (gdc-client): Update to 2.3.
[arguments] <phases>: Rework 'relax-requirements for the refresh
criteria; add 'fix-pytest-config.
[inputs]: Remove python-cryptography, python-ndg-httpsclient,
python-pyasn1, and python-pyopenssl; add python-importlib-metadata.
[native-inputs]: Remove python-wheel; add python-flask, python-httmock,
python-moto, python-pytest, and python-requests-mock.

Change-Id: Ia51c934fcac473f0b88e1d69077c66fbf62e0ebc
 2025-12-04 21:23:38 +00:00
Ricardo Wurmus
8983dd5394 gnu: pigx-rnaseq: Add missing input. 
* gnu/packages/bioinformatics.scm (pigx-rnaseq)[inputs]: Add r-genomeinfodb.

Change-Id: I358d6dca2acde401eaf6cdd370109cd9aa0b558d
 2025-12-03 12:41:05 +01:00
Nicolas Graves
290a91c5cb gnu: seqmagick: Fix build and remove python-nose. 
* gnu/packages/bioinformatics.scm (seqmagick)
[arguments]<#:phases>: Add phase 'set-version.
[native-inputs]: Remove python-wheel.  Replace python-nose by
python-pynose.

Change-Id: I5a10d7702d59c6f837761ff96e11f0ff470e0626
Modified-by: Sharlatan Hellseher <sharlatanus@gmail.com>
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
 2025-12-02 11:18:02 +00:00
Nicolas Graves
988d0a2f74 gnu: rseqc: Disable tests. 
python-nose runs 0 tests, let's remove it and disable tests instead.

* gnu/packages/bioinformatics.scm (rseqc)
[arguments]<#:tests?>: Disable them.
[native-inputs]: Remove python-nose.
[propagated-inputs]: Remove python-wheel.

Change-Id: I5be4019f6093478b5ab28f07a52319c7cfbd7cd8
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
 2025-12-02 11:18:02 +00:00
Nicolas Graves
84978f7277 gnu: crossmap: Disable tests. 
python-nose runs 0 tests, let's remove it and disable tests instead.

* gnu/packages/bioinformatics.scm (crossmap)
[arguments]<#:tests?>: Disable them.
[native-inputs]: Remove python-nose, python-wheel.

Change-Id: I2fbbefac935901c4bafea3b8c941b81d3e404a23
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
 2025-12-02 11:18:02 +00:00
Nicolas Graves
ff846b8635 gnu: clipper-peak: Adjust native-inputs. 
* gnu/packages/bioinformatics.scm (clipper-peak)[native-inputs]:
Remove python-wheel; replace python-nose by python-pynose; sort a->z.

Change-Id: Id8fa425960c4d8675f3e863e0576dc407c383d8f
Modified-by: Sharlatan Hellseher <sharlatanus@gmail.com>
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
 2025-12-02 11:18:02 +00:00
Nicolas Graves
ad5929ab70 gnu: ciri-long: Replace python-nose by python-pynose. 
* gnu/packages/bioinformatics.scm (ciri-long)
[arguments]: Run guix style -S arguments.
[native-inputs]: Replace python-nose by python-pynose.

Change-Id: If028b5e1eb3915019aa6f4798aaf73d4cd13797f
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
 2025-12-02 11:18:02 +00:00
Ricardo Wurmus
328d27e116 gnu: r-cytoexplorer: Skip tests using with_mock. 
* gnu/packages/bioinformatics.scm (r-cytoexplorer)[arguments]: Adjust phase
'skip-bad-tests.

Change-Id: I677fb4bdc709bd9ab463ab1e7c9c3c187ff76723
 2025-11-29 12:21:36 +01:00
Ricardo Wurmus
1464b58032 gnu: r-gchain: Update to 0.2.0-2.19f8bb9. 
* gnu/packages/bioinformatics.scm (r-gchain): Update to 0.2.0-2.19f8bb9.
[arguments]: Add phase 'biostrings-compatibility; adjust phase
'skip-bad-tests.

Change-Id: Ia8719400b555625dd0067179ee3d142ee2d59ccc
 2025-11-29 12:21:35 +01:00
Ricardo Wurmus
eec6a55ed4 gnu: r-gutils: Add missing input and patch for testthat compatibility. 
* gnu/packages/bioinformatics.scm (r-gutils)[arguments]: Add phase
'testthat-compatibility.
[native-inputs]: Add r-xvector.

Change-Id: I6178bb62486167445921069e0f40e122f10c838e
 2025-11-29 12:21:33 +01:00
Greg Hogan
1aebfc74f1 gnu: boost: Update to 1.89.0. 
* gnu/packages/boost.scm (boost-for-source-highlight): Rename this ...
(boost-1.83): ... to this.
(boost-numpy): Inherit from boost-1.83.
* gnu/packages/pretty-print.scm (source-highlight): Update accordingly.

* gnu/packages/boost.scm (boost): Update to 1.89.0.
[source]: Remove patches.

* gnu/packages/boost.scm (mdds)
[propagated-inputs]: Replace boost with boost-1.83.

* gnu/packages/astronomy.scm (aoflagger),
* gnu/packages/embedded.scm (cc-tool),
* gnu/packages/games.scm (0ad, vcmi),
* gnu/packages/image.scm (gpick),
* gnu/packages/maths.scm (highfive),
* gnu/packages/plotutils.scm (asymptote)
[native-inputs]: Replace boost with boost-1.83.

* gnu/packages/audio.scm (guitarix, supercollider),
* gnu/packages/bioconductor.scm (r-mzr),
* gnu/packages/bioinformatics.scm (ataqv, bless, express, isolator,
metabat, r-velocytom, rsem, sailfish, salmon),
* gnu/packages/bittorrent.scm (libtorrent-rasterbar),
* gnu/packages/code.scm (sourcetrail),
* gnu/packages/compression.scm (innoextract),
* gnu/packages/cpp.scm (lager),
* gnu/packages/crypto.scm (cryfs),
* gnu/packages/electronics.scm (nextpnr, prjpeppercorn, prjtrellis,
pulseview),
* gnu/packages/emulators.scm (mupen64plus-video-glide64mk2),
* gnu/packages/engineering.scm (cadabra2, freecad, libigl,
openscad, prusa-slicer),
* gnu/packages/file-systems.scm (snapper),
* gnu/packages/finance.scm (ledger),
* gnu/packages/game-development.scm (dds),
* gnu/packages/games.scm (colobot, fifengine, knightsgame, leela-zero,
pokerth, supertux, wesnoth, wesnoth-server),
* gnu/packages/geo.scm (gplates),
* gnu/packages/gnucash.scm (gnucash),
* gnu/packages/graph.scm (python-graph-tool),
* gnu/packages/graphics.scma (openshadinglanguage),
* gnu/packages/i2p.scm (i2pd),
* gnu/packages/image-viewers.scm (luminance-hdr),
* gnu/packages/kde-graphics.scm (krita),
* gnu/packages/mail.scm (astroid),
* gnu/packages/medical.scm (orthanc, orthanc-mysql,
orthanc-postgresql),
* gnu/packages/messaging.scm (libphonenumber),
* gnu/packages/mpd.scm (ncmpcpp),
* gnu/packages/networking.scm (kismet),
* gnu/packages/opencog.scm (cogutil),
* gnu/packages/photo.scm (hugin),
* gnu/packages/poedit.scm (poedit),
* gnu/packages/radio.scm (gnuradio),
* gnu/packages/rdf.scm (lucene++),
* gnu/packages/serialization.scm (avro-cpp),
* gnu/packages/simulation.scm (fenics-dolfin),
* gnu/packages/version-control.scm (gource),
* gnu/packages/video.scm (aegisub, mkvtoolnix),
* gnu/packages/web.scm (websocketpp)
[inputs]: Replace boost with boost-1.83.

* gnu/packages/libreoffice.scm (libcmis): Update to 0.6.2-00a85bf6.
(librevenge): Update to 0.0.5.
[arguments]<#:configure-flags>: Remove reference to boost system
component for which the compatibility stub has been removed.
* gnu/packages/serialization.scm (msgpack-cxx): Update to 7.0.0.

Change-Id: I247f3eaecde3de3fe227586b840f0312b4797ee1
 2025-11-28 12:26:24 +00:00
Nicolas Graves
023bba9441 gnu: python-pybiomart: Remove python-sphinx-autobuild native-input. 
This is a development-only input.

* gnu/packages/bioinformatics.scm (python-pybiomart)[native-inputs]:
Remove python-sphinx-autobuild.

Change-Id: Ie806c28dcbe7e139f79476ec8086b7af24ec527c
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
 2025-11-27 00:02:30 +00:00
Arun Isaac
e5c746b905 gnu: ravanan: Update to 0.2.0. 
* gnu/packages/bioinformatics.scm (ravanan): Update to 0.2.0.
[native-inputs]: Add guile-run64.
[home-page]: Update.
 2025-11-24 19:39:19 +00:00
Andreas Enge
480d78c4c4 gnu: Remove htslib-1.14. 
* gnu/packages/bioinformatics.scm (htslib-1.14): Delete variable.

Change-Id: Ic009b3ea5bd2b718461dc049df2f71e8e14f0864
 2025-11-24 11:23:45 +01:00
Andreas Enge
c4ebcd5629 gnu: Remove htslib-1.9. 
* gnu/packages/bioinformatics.scm (htslib-1.9): Delete variable.

Change-Id: I4961b197f6357880e82a856ad3f661435eb980db
 2025-11-24 11:19:53 +01:00
Andreas Enge
792d935233 gnu: perl-bio-db-hts: Swap outdated input. 
* gnu/packages/bioinformatics.scm (perl-bio-db-hts)[propagated-inputs]:
Replace htslib-1.9 by htslib.

Change-Id: I509e2ee9165d70c04753b467852fe40c805e6ea7
 2025-11-24 11:17:39 +01:00
Andreas Enge
9103fbd2e6 gnu: Remove pbcopper. 
* gnu/packages/bioinformatics.scm (pbcopper): Delete variable.

Fixes: guix/guix#3781
Change-Id: Ibde3554af08d72f2e3d64c9e1a4226871402bbec
 2025-11-24 11:11:51 +01:00
Andreas Enge
1ffec44bf2 gnu: Remove pbbam. 
* gnu/packages/bioinformatics.scm (pbbam): Delete variable.

Change-Id: I75ff8816ca4c37508864890ee2561b3947a53dc1
 2025-11-24 11:11:10 +01:00
Andreas Enge
e371d6bbf1 gnu: Remove blasr-libcpp. 
* gnu/packages/bioinformatics.scm (blasr-libcpp): Delete variable.

Change-Id: I93cbb12041bd544d381851e44b17d3bd1596e4cf
 2025-11-24 11:10:38 +01:00
Andreas Enge
220329e73c gnu: Remove blasr. 
* gnu/packages/bioinformatics.scm (blasr): Delete variable.

Change-Id: I7c10109d4a168c868f1a7c8587584ad738378506
 2025-11-24 11:10:04 +01:00
Ricardo Wurmus
c2e28c1ac4 gnu: Add r-genenmf. 
* gnu/packages/bioinformatics.scm (r-genenmf): New variable.

Change-Id: Ic17308d94bd5d9ec0484acc82cc738a3c67fb632
 2025-11-21 18:33:48 +01:00
Andreas Enge
56fe9a8bd6 gnu: Remove eigensoft. 
* gnu/packages/bioinformatics.scm (eigensoft): Delete variable.

Fixes: guix/guix#3710
Change-Id: I9cfc472dbadd078d4a35afed4a86c806bba6c64d
 2025-11-21 10:52:32 +01:00
Sharlatan Hellseher
70bca483a6 gnu: scvelo: Reduce closure size. 
* gnu/packages/bioinformatics.scm (scvelo):
[propagated-inputs]: Remove python-isort.
[native-inputs]: Remove python-black, python-flake8, python-hypothesis,
and python-wheel; add python-setuptools.

Change-Id: Ieefb91cbe3481c64d7d9e5588d934216ef17f974
 2025-11-20 01:06:42 +00:00
Nicolas Graves
ac103f7fff gnu: python-gseapy: Extend with (pyproject-guile-json). 
* gnu/packages/bioinformatics.scm (python-gseapy)[arguments]
<#:phases>: Extend with (pyproject-guile-json).

Change-Id: I6969e5d71d77d4d95a41fea0a0c2b572a8f1276c
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
 2025-11-20 01:06:35 +00:00
Nicolas Graves
0cb15c6f63 gnu: python-bed-reader: Extend with (pyproject-guile-json). 
* gnu/packages/bioinformatics.scm (python-bed-reader)[arguments]
<#:phases>: Extend with (pyproject-guile-json).

Change-Id: Ie67b640629f33654e6953bf95f81fe4ad2190c9a
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
 2025-11-20 01:06:35 +00:00
Andreas Enge
1d739bcc15 gnu: Remove vbz-compression. 
* gnu/packages/bioinformatics.scm (vbz-compression): Delete variable.

Fixes: guix/guix#3640
Change-Id: I996c211af44a7342cb83249c0a9347f11d324069
 2025-11-18 17:52:31 +01:00
Andreas Enge
7564f8620a gnu: Remove python-ont-fast5-api. 
* gnu/packages/bioinformatics.scm (python-ont-fast5-api): Delete variable.

Change-Id: I32baf50001cc86436a8b07b035b595f8084306bd
 2025-11-18 17:51:56 +01:00
Andreas Enge
932cabe2c7 gnu: Remove cellsnp-lite. 
* gnu/packages/bioinformatics.scm (cellsnp-lite): Delete variable.

Fixes: guix/guix#3638
Change-Id: I559bb31c2ddf1940414a20891ffb7459ec4d7e28
 2025-11-18 17:50:41 +01:00
Ricardo Wurmus
2a3b2b6f91 gnu: r-skitools: Update to 0.0.0.9000-2.ba322dc. 
* gnu/packages/bioinformatics.scm (r-skitools): Update to 0.0.0.9000-2.ba322dc.

Change-Id: Ic006e4178ccaae57e7f4b25e07bb63db42585cb3
 2025-11-13 11:16:24 +01:00
Ricardo Wurmus
4436b2ee8e gnu: r-skitools: Disable one test. 
* gnu/packages/bioinformatics.scm (r-skitools)[arguments]: Add phase
'disable-bad-test.

Change-Id: I5c79aa28e343266a83522afe6635b3a714dadcc1
 2025-11-13 11:16:24 +01:00
Ricardo Wurmus
af1ca83cf9 gnu: r-sigfit: Fix build with GCC@14 
* gnu/packages/bioinformatics.scm (r-sigfit)[arguments]: Add phase
'gcc-14-compatibility.

Change-Id: Iaa00ecdf00dcf76330f3b1f904da6263b82e0617
 2025-11-13 11:16:24 +01:00
Jake Forster
91188daed7 gnu: gdcm: Fix reference in exported target. 
* gnu/packages/bioinformatics.scm (gdcm)
[arguments]<#:phases>{refer-to-charls}: New phase.

Change-Id: I0671b71471c123b041156940640f0f745464052d
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
 2025-11-11 18:40:49 +00:00
Ricardo Wurmus
d271fd7fd7 gnu: r-saige: Update to 1.3.4-2.44c8dd4. 
* gnu/packages/bioinformatics.scm (r-saige): Update to 1.3.4-2.44c8dd4.
[arguments]: Add phases 'add-missing-include and 'link-with-plink2.
[inputs]: Add plink-ng.
[properties]: Add r-lintools and r-survival.

Change-Id: I61b8ca6cc5384d30eabf94cbe95cecf6b97623e7
 2025-11-09 21:28:30 +01:00
Ricardo Wurmus
ae1918a75b gnu: plink-ng: Update to 2.0.0-a.6.16. 
* gnu/packages/bioinformatics.scm (plink-ng): Update to 2.0.0-a.6.16.
[arguments]: Use G-expression; add phases 'patch-headers and 'build-library;
update 'install phase to install headers and library.
[inputs]: Add libdeflate.
[native-inputs]: Remove plink.

Change-Id: Ifba65c6c312e6098e36800b3e0bb9158ccd7873a
 2025-11-09 21:28:30 +01:00
Ricardo Wurmus
6f1e42cac3 gnu: megahit: Add missing header include. 
* gnu/packages/bioinformatics.scm (megahit)[arguments]: Add phase 'fix-headers.

Closes guix/guix#3641

Change-Id: I9f8e872e4c6a58c85d05257b5349547063dcf310
 2025-11-08 08:20:54 +01:00