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Author SHA1 Message Date
Sharlatan Hellseher
c2861537a8
gnu: python-arboreto: Migrate to pyproject. 
* gnu/packages/bioinformatics.scm (python-arboreto) [build-system]: Use
pyproject.
[native-inputs]: Add python-setuptools and python-wheel.

Change-Id: Id4b3de1b02537bbc15032d0978ef74d6c045d329
 2025-07-06 18:44:04 +01:00
Nicolas Graves
7d1f5f950f
gnu: music: Add lint-hidden-cpe-vendors property. 
* gnu/packages/bioinformatics.scm (music)[properties]: Add
lint-hidden-cpe-vendors property.

Signed-off-by: Zheng Junjie <z572@z572.online>
 2025-06-23 12:32:51 +08:00
Nicolas Graves via Guix-patches via
a1dbf22d18
gnu: express: Add lint-hidden-cpe-vendors property. 
* gnu/packages/bioinformatics.scm (express)[properties]: Add
lint-hidden-cpe-vendors property.

Signed-off-by: Zheng Junjie <z572@z572.online>
 2025-06-23 12:31:14 +08:00
Kjartan Oli Agustsson
f731d71846
gnu: tetoolkit: Run guix style 
* gnu/packages/bioinformatics.scm (tetoolkit): Run guix style.

Change-Id: I5f4c6a647a41a9d60e5bc1d2b4fbee045626dc12
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
 2025-06-22 12:54:11 +01:00
Kjartan Oli Agustsson
09a3e09fa8
gnu: tetoolkit: Use pyproject-build-system. 
* gnu/packages/bioinformatics.scm (tetoolkit): [build-system]: Use
pyproject.
[native-inputs]: Add python-setuptools and python-wheel.

Change-Id: I4fce644bee87c5d6c64a9a3cdf3581a1bae12909
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
 2025-06-22 12:54:11 +01:00
Kjartan Oli Agustsson
825ceadb5f
gnu: tbsp: Run guix style 
* gnu/packages/bioinformatics.scm (tbsp): Run guix style.

Change-Id: I3301f95963aac1f47b28e86a40374df2171732f8
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
 2025-06-22 12:54:11 +01:00
Kjartan Oli Agustsson
8ed2fcd5aa
gnu: tbsp: Use pyproject-build-system. 
* gnu/packages/bioinformatics.scm (tbsp): [build-system]: Use
pyproject.
[native-inputs]: Add python-setuptools and python-wheel.

Change-Id: I6d454d95050862378b7f06c09a42994efd9875a6
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
 2025-06-22 12:54:11 +01:00
Kjartan Oli Agustsson
abeb7cd9fa
gnu: stpipeline: Run guix style 
* gnu/packages/bioinformatics.scm (stpipeline): Run guix style.

Change-Id: I341e0b7adce82c079b1dcff94a2128d3e1773a4a
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
 2025-06-22 12:54:10 +01:00
Kjartan Oli Agustsson
3bb992a357
gnu: stpipeline: Use pyproject-build-system. 
* gnu/packages/bioinformatics.scm (stpipeline): [build-system]: Use
pyproject.
[native-inputs]: Add python-setuptools and python-wheel.

Change-Id: Ibfeea2feb08878d14becf15be5408689ba4c7c3f
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
 2025-06-22 12:54:10 +01:00
Kjartan Oli Agustsson
18d5c62c6a
gnu: python-vireosnp: Run guix style 
* gnu/packages/bioinformatics.scm (python-vireosnp): Run guix style.

Change-Id: I301322fbfa45b3ef7cb1c82eadc60aa1de33d442
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
 2025-06-22 12:54:10 +01:00
Kjartan Oli Agustsson
b7ec773e5a
gnu: python-vireosnp: Use pyproject-build-system. 
* gnu/packages/bioinformatics.scm (python-vireosnp): [build-system]: Use
pyproject.
[native-inputs]: Add python-setuptools and python-wheel.

Change-Id: Id49911001b3672402a17f0902a7e5a565168ab61
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
 2025-06-22 12:54:10 +01:00
Kjartan Oli Agustsson
002d6e4109
gnu: python-velocyto: Run guix style 
* gnu/packages/bioinformatics.scm (python-velocyto): Run guix style.

Change-Id: Ieda2b56cf13ae519e539ecef286ef63595532a7a
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
 2025-06-22 12:54:10 +01:00
Kjartan Oli Agustsson
5853163fbf
gnu: python-velocyto: Use pyproject-build-system. 
* gnu/packages/bioinformatics.scm (python-velocyto): [build-system]: Use
pyproject.
[native-inputs]: Add python-setuptools and python-wheel.

Change-Id: Ie5e605136a7eb7a1acd3850313f2796bf7c83c31
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
 2025-06-22 12:54:10 +01:00
Kjartan Oli Agustsson
5eebea1b76
gnu: python-slamdunk: Run guix style 
* gnu/packages/bioinformatics.scm (python-slamdunk): Run guix style.

Change-Id: I5235a49f7c2d128df6c903f35908fefe022fd50a
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
 2025-06-22 12:54:10 +01:00
Kjartan Oli Agustsson
9aff205c4f
gnu: python-slamdunk: Use pyproject-build-system. 
* gnu/packages/bioinformatics.scm (python-slamdunk): [build-system]: Use
pyproject.
[native-inputs]: Add python-setuptools and python-wheel.

Change-Id: I935dd9a0a7c08985dfb7ca989346783ebf024d50
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
 2025-06-22 12:54:10 +01:00
Kjartan Oli Agustsson
15c4134067
gnu: python-scanorama: Run guix style 
* gnu/packages/bioinformatics.scm (python-scanorama): Run guix style.

Change-Id: I43bfbe845f6e54dab94c6e0055ee811f70026ab4
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
 2025-06-22 12:54:10 +01:00
Kjartan Oli Agustsson
492035dfa8
gnu: python-scanorama: Use pyproject-build-system. 
* gnu/packages/bioinformatics.scm (python-scanorama): [build-system]: Use
pyproject.
[native-inputs]: Add python-setuptools and python-wheel.

Change-Id: Ie437414bff54c361ab61ee2e9baea670762c9ce5
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
 2025-06-22 12:54:10 +01:00
Kjartan Oli Agustsson
673a485a6b
gnu: python-pyliftover: Run guix style 
* gnu/packages/bioinformatics.scm (python-pyliftover): Run guix style.

Change-Id: I45bf0066db834fd99a2bbc1e64d4bc3e20e92cde
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
 2025-06-22 12:54:09 +01:00
Kjartan Oli Agustsson
66ab4c5bc1
gnu: python-pyliftover: Use pyproject-build-system. 
* gnu/packages/bioinformatics.scm (python-pyliftover): [build-system]: Use
pyproject.
[native-inputs]: Add python-setuptools and python-wheel.

Change-Id: Ifcdbfba497527edd82625a20e4baf6b2504f3f92
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
 2025-06-22 12:54:09 +01:00
Kjartan Oli Agustsson
0809db9016
gnu: python-pyfit-sne: Use pyproject-build-system. 
* gnu/packages/bioinformatics.scm (python-pyfit-sne): [build-system]: Use
pyproject.
[native-inputs]: Add python-setuptools and python-wheel.

Change-Id: I8f62f2dc30d2bd182a791830bb835adf778d2ecf
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
 2025-06-22 12:54:09 +01:00
Kjartan Oli Agustsson
247afd63f2
gnu: python-ikarus: Run guix style 
* gnu/packages/bioinformatics.scm (python-ikarus): Run guix style.

Change-Id: I493beb55986808a8ba27eadcc48d8a2a20b1678e
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
 2025-06-22 12:54:09 +01:00
Kjartan Oli Agustsson
1ff6229402
gnu: python-ont-fast5-api: Use pyproject-build-system. 
* gnu/packages/bioinformatics.scm (python-ont-fast5-api): [build-system]: Use
pyproject.
[native-inputs]: Add python-setuptools and python-wheel.

Change-Id: Idb3b5a65767998e232fcc31534cb923ea6f5fed8
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
 2025-06-22 12:54:09 +01:00
Kjartan Oli Agustsson
7c405b8da9
gnu: python-ikarus: Use pyproject-build-system. 
* gnu/packages/bioinformatics.scm (python-ikarus): [build-system]: Use
pyproject.
[native-inputs]: Add python-setuptools and python-wheel.

Change-Id: Idb3b5a65767998e232fcc31534cb923ea6f5fed8
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
 2025-06-22 12:54:09 +01:00
Kjartan Oli Agustsson
78039c3e61
gnu: porechop: Use pyproject-build-system. 
* gnu/packages/bioinformatics.scm (porechop): [build-system]: Use
pyproject.
[native-inputs]: Add python-setuptools, python-wheel, and python-pytest.

Change-Id: I77444786f3e64591c2dc526fb030cecdbb30a3c1
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
 2025-06-22 12:54:09 +01:00
Kjartan Oli Agustsson
c1b7cf51dc
gnu: gdc-client: Run guix style 
* gnu/packages/bioinformatics.scm (gdc-client): Run guix style.

Change-Id: I5dc3f65e622354a66ff71365f6dfd052da951297
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
 2025-06-22 12:54:09 +01:00
Kjartan Oli Agustsson
81e55bc0d5
gnu: gdc-client: Use pyproject-build-system. 
* gnu/packages/bioinformatics.scm (gdc-client): [build-system]: Use
pyproject.
[native-inputs]: Add python-setuptools and python-wheel.

Change-Id: Ifa6ddfab7ddfc90ecdc5838484b3763f1f653e81
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
 2025-06-22 12:54:09 +01:00
Kjartan Oli Agustsson
50ece4e78f
gnu: crossmap: Run guix style 
* gnu/packages/bioinformatics.scm (crossmap): Run guix style.

Change-Id: I56a0ba0e7f5fd24e02a5a769efa7b7e6bda5603b
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
 2025-06-22 12:54:08 +01:00
Kjartan Oli Agustsson
1a5fa2c3b2
gnu: crossmap: Use pyproject-build-system. 
* gnu/packages/bioinformatics.scm (crossmap): [build-system]: Use
pyproject.
[native-inputs]: Add python-setuptools and python-wheel.

Change-Id: I1750685ad8037d004fc1d5fc4f7f76613f257c17
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
 2025-06-22 12:54:08 +01:00
Kjartan Oli Agustsson
313519348b
gnu: clipper-peak: Run guix style 
* gnu/packages/bioinformatics.scm (clipper-peak): Run guix style.

Change-Id: I93c3aea922b1d493d004b401eb312cba63ae4d74
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
 2025-06-22 12:54:08 +01:00
Kjartan Oli Agustsson
a694de3938
gnu: clipper-peak: Use pyproject-build-system. 
* gnu/packages/bioinformatics.scm (clipper-peak): [build-system]: Use
pyproject.
[native-inputs]: Add python-setuptools and python-wheel.

Change-Id: I6cae7d463a412b6736413e80346e377ccb14c290
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
 2025-06-22 12:54:08 +01:00
Kjartan Oli Agustsson
1eda883414
gnu: ciri-long: Run guix style 
* gnu/packages/bioinformatics.scm (ciri-long): Run guix style.

Change-Id: I97e5bd025474ea4ba4f2781f523bc7f5c38fb8e8
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
 2025-06-22 12:54:08 +01:00
Kjartan Oli Agustsson
dbfce79477
gnu: ciri-long: Use pyproject-build-system. 
* gnu/packages/bioinformatics.scm (ciri-long): [build-system]: Use pyproject.

Change-Id: Ie4ff2f95cfe1988bb2b75eb78bda77b8c4259105
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
 2025-06-22 12:54:08 +01:00
Kjartan Oli Agustsson
aeb5fd0a24
gnu: checkm: Use pyproject-build-system. 
* gnu/packages/bioinformatics.scm (checkm): Run guix style.
[build-system]: Use pyproject.
[native-inputs]: Add python-setuptools and python-wheel.

Change-Id: I7d3214c29a7e2b3a6065336632f534a2c4cefbbc
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
 2025-06-22 12:54:04 +01:00
Nicolas Graves
01ad0cf43e
gnu: ruby: Populating (gnu packages ruby-check/ruby-xyz). 
* gnu/packages/ruby.scm: Move all packages except different versions
of ruby and mruby, to either (gnu packages ruby-check) or
(gnu packages ruby-xyz).

* gnu/packages/ruby-check.scm (bundler, ruby-builder, ruby-cucumber-ci-environment,
ruby-cucumber-compatibility-kit,
ruby-cucumber-compatibility-kit-bootstrap, ruby-cucumber-core,
ruby-cucumber-expressions, ruby-cucumber-gherkin,
ruby-cucumber-html-formatter, ruby-cucumber-messages,
ruby-cucumber-tag-expressions, ruby-cucumber-wire, ruby-diff-lcs,
ruby-docile, ruby-fivemat, ruby-given-core, ruby-hoe, ruby-hoe-3,
ruby-json, ruby-mime-types, ruby-mime-types-data, ruby-mini-portile,
ruby-mini-portile-2, ruby-minitest, ruby-minitest-bonus-assertions,
ruby-minitest-focus, ruby-minitest-hooks, ruby-minitest-moar,
ruby-multi-test, ruby-rake, ruby-rake-compiler,
ruby-rake-compiler-dock, ruby-rspec, ruby-rspec-2, ruby-rspec-core,
ruby-rspec-core-2, ruby-rspec-expectations, ruby-rspec-expectations-2,
ruby-rspec-mocks, ruby-rspec-mocks-2, ruby-rspec-support, ruby-sequel,
ruby-simplecov-json-formatter, ruby-simplecov, ruby-simplecov-html,
ruby-sorcerer, ruby-unindent): Moved from (gnu packages ruby).
 (ruby-asciidoctor/minimal): New variable, to allow more minimal
 import of only (gnu packages ruby-check) in a lot of modules.
 (ruby-rubocop/minimal): New variable to build cucumber with a lot
 less dependencies.
 (cucumber-ruby-core)[native-inputs]: Replace ruby-rubocop by
 ruby-rubocop/minimal. Remove ruby-coveralls.

* gnu/packages/ruby-xyz.scm: Move all other packages from
(gnu packages ruby).

* gnu/packages/admin.scm
* gnu/packages/bioinformatics.scm
* gnu/packages/databases.scm
* gnu/packages/emacs-xyz.scm
* gnu/packages/gnome-xyz.scm
* gnu/packages/gnome.scm
* gnu/packages/groff.scm
* gnu/packages/kde-systemtools.scm
* gnu/packages/libffi.scm
* gnu/packages/mail.scm
* gnu/packages/maths.scm
* gnu/packages/mpd.scm
* gnu/packages/ntp.scm
* gnu/packages/package-management.scm
* gnu/packages/plotutils.scm
* gnu/packages/protobuf.scm
* gnu/packages/rails.scm
* gnu/packages/ruby-check.scm
* gnu/packages/ruby-xyz.scm
* gnu/packages/ruby.scm
* gnu/packages/shellutils.scm
* gnu/packages/statistics.scm
* gnu/packages/tex.scm
* gnu/packages/virtualization.scm:
    Adapt module imports accordingly.

* gnu/packages/backup.scm (btrbk):
* gnu/packages/ccache.scm (ccache):
* gnu/packages/cluster.scm (drbd-utils):
* gnu/packages/compton.scm (picom):
* gnu/packages/cryptsetup.scm (cryptsetup):
* gnu/packages/engineering.scm (kicad-doc):
* gnu/packages/games.scm (warzone2100):
* gnu/packages/irc.scm (open-adventure):
* gnu/packages/ntp.scm (weechat):
* gnu/packages/password-utils.scm (keepassxc):
* gnu/packages/radio.scm (wsjtx, jtdx):
* gnu/packages/syndication.scm (newsboat):
* gnu/packages/task-management.scm (timewarrior):
* gnu/packages/version-control.scm (git-lfs):
    [native-inputs]: Replace ruby-asciidoctor by
    ruby-asciidoctor/minimal. Adapt module imports accordingly.

* gnu/packages/text-editors.scm: Remove (gnu packages ruby) import.

Signed-off-by: Andreas Enge <andreas@enge.fr>
 2025-06-20 20:40:02 +02:00
Sharlatan Hellseher
4db91aa852
gnu: packages: Remove redundant (gnu packages golang) from some modules. 
* gnu/packages/android.scm: Remove redundant (gnu packages golang) from
used modules.
* gnu/packages/bioinformatics.scm: Likewise.
* gnu/packages/check.scm: Likewise.
* gnu/packages/configuration-management.scm: Likewise.
* gnu/packages/databases.scm: Likewise.
* gnu/packages/emacs-xyz.scm: Likewise.
* gnu/packages/file-systems.scm: Likewise.
* gnu/packages/golang-check.scm: Likewise.
* gnu/packages/hardware.scm: Likewise.
* gnu/packages/hyperledger.scm: Likewise.
* gnu/packages/irc.scm: Likewise.
* gnu/packages/mail.scm: Likewise.
* gnu/packages/messaging.scm: Likewise.
* gnu/packages/networking.scm: Likewise.
* gnu/packages/password-utils.scm: Likewise.
* gnu/packages/radio.scm: Likewise.
* gnu/packages/terminals.scm: Likewise.
* gnu/packages/tor-browsers.scm: Likewise.
* gnu/packages/video.scm: Likewise.
* gnu/packages/vpn.scm: Likewise.

Change-Id: I6bb92ac0f7c68644cc9b9cc16834aa54240d8fc9
 2025-05-26 16:50:21 +01:00
nomike
8b84a2302c
gnu: Rename clipper to clipper-peak. 
There's a naming conflict with cpp/bioinformatics clipper.

* gnu/packages/bioinformatics.scm
(clipper): Delete variable, rename to clipper-peak.
(clipper-peak): New variable, renamed from clipper.

Change-Id: I1411fe0eebf4ff322e4dadfbe53758feddc36599
Signed-off-by: Christopher Baines <mail@cbaines.net>
 2025-05-26 16:00:25 +01:00
Ricardo Wurmus
b430cb1c78
gnu: r-anpan: Update to 0.3.0-1.efd4dc4. 
* gnu/packages/bioinformatics.scm (r-anpan): Update to 0.3.0-1.efd4dc4.
[properties]: Record updater-extra-native-inputs.
[propagated-inputs]: Add r-cli; remove r-mass.

Change-Id: I60ea7dae8974df81b0188164568de2fe930d1fc4
 2025-05-21 15:21:23 +02:00
Sergey Trofimov
380282f3f5
gnu: packages: Fix broken descriptions. 
A few description mistakenly use @{foo} instead of @code{foo} which
results in broken formatting in guix search.

* gnu/packages/bioinformatics.scm (umi-tools),
* gnu/packages/cran.scm (r-ggside),
* gnu/packages/crates-apple.scm: (rust-commoncrypto-0.2),
* gnu/packages/crates-io.scm: (rust-ndarray-rand-0.15),
* gnu/packages/emacs-xyz.scm (emacs-load-relative, emacs-el-x)
(emacs-helm-org-ql, emacs-consult-lsp),
* gnu/packages/golang-xyz.scm (go-github-com-songmu-gitconfig),
* gnu/packages/haskell-xyz.scm (ghc-text-short, ghc-validation),
* gnu/packages/image.scm (imgp),
* gnu/packages/perl-check.scm (perl-test-file-contents),
* gnu/packages/perl-web.scm (perl-uri-db),
* gnu/packages/perl.scm (perl-clipboard, perl-module-refresh),
* gnu/packages/python-xyz.scm (python-ddlparse, python-black-macchiato)
(python-pysendfile),
* gnu/packages/qt.scm (qt5compat),
* gnu/packages/ruby.scm (ruby-ruby-engine, ruby-httpclient),
* gnu/packages/sagemath.scm (python-memory-allocator),
* gnu/packages/spreadsheet.scm (sc-im),
* gnu/packages/time.scm (python-pendulum):
[description]: Fix malformed macros.

Change-Id: I3ed755a54aecf40bf0c5c982f9e70b7cd3689de7
Signed-off-by: Greg Hogan <code@greghogan.com>
 2025-05-13 16:35:45 +00:00
Ricardo Wurmus
8b2426a1a1
gnu: Add r-anglemania. 
* gnu/packages/bioinformatics.scm (r-anglemania): New variable.

Change-Id: I14e8df223af809cb2a0bb2e569c9a6976de35e6b
 2025-05-13 17:01:01 +02:00
Ricardo Wurmus
e4e43cebba
gnu: r-chromunity: Update to 0.0.2-2.101e30a. 
* gnu/packages/bioinformatics.scm (r-chromunity): Update to 0.0.2-2.101e30a.
[arguments]: Disable one test.

Change-Id: I522e993d86cf88914a95c9fb15d933c7af906c41
 2025-05-12 08:55:51 +02:00
Ricardo Wurmus
901020cdeb
gnu: pigx-scrnaseq: Use Snakemake 5. 
* gnu/packages/bioinformatics.scm (pigx-scrnaseq)[inputs]: Replace snakemake-7
with snakemake-5.
[arguments]: Set HOME.

Change-Id: I45257e138c4cf468d179ff35b0c705bc73046052
 2025-05-12 08:55:51 +02:00
Ricardo Wurmus
d6f9f9b585
gnu: pigx-bsseq: Set HOME. 
* gnu/packages/bioinformatics.scm (pigx-bsseq)[inputs]: Add phase 'pre-check.

Change-Id: Ic88976554e6e7c7955ae9ab4f0232330060446c9
 2025-05-12 08:55:50 +02:00
Ricardo Wurmus
c80e1e958b
gnu: pigx-chipseq: Set HOME. 
* gnu/packages/bioinformatics.scm (pigx-chipseq)[arguments]: Add phase 'pre-check.

Change-Id: Ia95db9209b5ea0cb340f9827197bdcc851266961
 2025-05-12 08:55:50 +02:00
Ricardo Wurmus
b0aaf60a38
gnu: pigx-rnaseq: Set HOME. 
* gnu/packages/bioinformatics.scm (pigx-rnaseq)[arguments]: Add phase 'pre-check.

Change-Id: Ibabfa8f14b8eaec6d25ae72a2cd0f33e6a7d2819
 2025-05-12 08:55:50 +02:00
Ricardo Wurmus
d05e09fb61
gnu: pigx-sars-cov-2: Use Snakemake 7. 
* gnu/packages/bioinformatics.scm (pigx-sars-cov-2)[inputs]: Replace snakemake
with snakemake-7.

Change-Id: I059ea25c0e4a45e42f8f288cd92f548b9684e624
 2025-05-12 08:55:50 +02:00
Ricardo Wurmus
fdc8303a27
gnu: pigx-scrnaseq: Use Snakemake 7. 
* gnu/packages/bioinformatics.scm (pigx-scrnaseq)[inputs]: Replace snakemake
with snakemake-7.

Change-Id: I9b903dba192e862d3b5b6ca4e0018ed88069937d
 2025-05-12 08:55:49 +02:00
Ricardo Wurmus
150ecd1579
gnu: pigx-bsseq: Use Snakemake 7. 
* gnu/packages/bioinformatics.scm (pigx-bsseq)[inputs]: Replace snakemake
with snakemake-7.

Change-Id: If82236f94d46c8e1f7f325e6eaf76f68397218d1
 2025-05-12 08:55:49 +02:00
Ricardo Wurmus
c43c9f9849
gnu: pigx-chipseq: Use Snakemake 7. 
* gnu/packages/bioinformatics.scm (pigx-chipseq)[inputs]: Replace snakemake
with snakemake-7.

Change-Id: Ib4d7d95713be3535b44ad10b655cf1a217048121
 2025-05-12 08:55:49 +02:00
Ricardo Wurmus
46ccde1476
gnu: pigx-rnaseq: Use Snakemake 7. 
* gnu/packages/bioinformatics.scm (pigx-rnaseq)[inputs]: Replace snakemake
with snakemake-7.

Change-Id: I2ab8af1438b59c3d36951b5901aeb57039b4aafc
 2025-05-12 08:55:49 +02:00
Nicolas Goaziou
1a8b36329f
gnu: texlive-libkpathsea: Tweak "texmf.cnf" variables. 
* gnu/packages/tex.scm (texlive-libkpathsea): Use XDG variables instead of
HOME for cache and user configuration.  Re-instate TEXMFLOCAL, which may be
necessary for external TeX installations.
(texlive-luatex): Re-instate TEXFLOCAL.
* gnu/packages/algebra.scm (gap):
* gnu/packages/assembly.scm (asl):
(yaehmop):
* gnu/packages/bioinformatics.scm (discrover):
* gnu/packages/chez.scm (chez-scheme-for-racket):
* gnu/packages/engineering.scm (fastcap):
* gnu/packages/fsf.scm (book-faif):
* gnu/packages/maths.scm (hypre):
(stex-boostrap):
(suitesparse-amd):
(suitesparse-camd):
(suitesparse-cholmod):
(suitesparse-klu):
(suitesparse-ldl):
(suitesparse-mongoose):
(suitesparse-spex):
(suitesparse-spqr):
(suitesparse-umfpack):
* gnu/packages/ocaml.scm (ocaml-bibtex2html):
(unison):
* gnu/packages/python-xyz.scm (python-nbconvert):
* gnu/packages/statistics.scm (r-with-tests)[arguments]: Set TEXMFVAR to
a writable location.

Change-Id: I3d2d069cf41a92214d9d6fb7f4d54fc81fe6db7a
 2025-05-06 11:25:07 +02:00