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
Zheng Junjie
18a69ddbf3
gnu: bwa: Fix cross-compiling.
...
* gnu/packages/bioinformatics.scm (bwa)[arguments]<#:make-flags>: Use
CC-FOR-TARGET.
Change-Id: I63dd0f13f337fbf84967f1ef1b6332ce3391ae97
2024-07-30 15:53:58 +08:00
Spencer King
471c4322df
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
2024-07-30 15:44:36 +08:00
guix@mawumag.com
ddce6b2303
gnu: Add python-muon.
...
* gnu/packages/bioinformatics.scm (python-muon): New variable.
Change-Id: I21431b089d1f404828b78d79124d96e7d36d5a2d
Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
2024-07-01 16:18:34 +02:00
guix@mawumag.com
58ead4baf9
gnu: Add python-mofapy2.
...
* gnu/packages/bioinformatics.scm (python-mofapy2): New variable.
Change-Id: Ide92878258511b3daf4e56d5faa94d190fdee62f
Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
2024-07-01 15:55:33 +02:00
Afkhami, Navid
b77491909b
gnu: Add r-anpan.
...
* gnu/packages/bioinformatics.scm (r-anpan): New variable.
Change-Id: Ia01ba3be7424306674b9c9b2904f1f0cfa66d818
Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
2024-07-01 15:43:56 +02:00
Afkhami, Navid
1731b45c51
gnu: Add r-cmdstanr.
...
* gnu/packages/bioinformatics.scm (r-cmdstanr): New variable.
Change-Id: Ic9e83486f7ab7f0e7075343af630c4dcecf597b5
Signed-off-by: Andreas Enge <andreas@enge.fr>
2024-06-30 10:48:50 +02:00
Efraim Flashner
4b67b38a79
gnu: jellyfish: Enable building on all 64bit platforms.
...
* gnu/packages/bioinformatics.scm (jellyfish)[supported-systems]: Mark
all 64bit platforms as supported.
Change-Id: Ia79d8052bf6ff347422e4b1ce38dc379d45a9be6
2024-06-30 10:15:03 +03:00
Afkhami, Navid
385fb14f64
gnu: Add r-rphyloxml.
...
* gnu/packages/bioinformatics.scm (r-rphyloxml): New variable.
Co-authored-by: Ricardo Wurmus <rekado@elephly.net>
Change-Id: I5b799986064f2af5fe74454f2e78fea7d9947260
2024-06-28 22:37:36 +02:00
Afkhami, Navid
6a7d5cda17
gnu: Add r-rnacrosslinkoo.
...
* gnu/packages/bioinformatics.scm (r-rnacrosslinkoo): New variable.
Change-Id: I1ca6dcef9c093627c3743d1176e587cf40053ba0
2024-06-28 11:53:19 +02:00
Afkhami, Navid
30dbc8e7b0
gnu: Add r-scent.
...
* gnu/packages/bioinformatics.scm (r-scent): New variable.
Change-Id: Ie517c0619683590f630013982e831fad528c1dea
2024-06-18 09:24:53 +02:00
Ricardo Wurmus
01de17143c
gnu: Add python-celltypist.
...
* gnu/packages/bioinformatics.scm (python-celltypist): New variable.
Change-Id: I196b7a07955224fe4c641d79729f0facb6367adb
2024-05-31 07:43:12 +02:00
Ricardo Wurmus
9f9127e80a
gnu: ensembl-vep: Update to 112.
...
* gnu/packages/bioinformatics.scm (ensembl-vep): Update to 112.
[propagated-inputs]: Add perl-list-moreutils.
[native-inputs]: Add perl-test-deep and perl-test-warnings.
Change-Id: I8c7de9f3dbc8c6fe4d1383f9dc215aeba018af0d
2024-05-22 17:44:49 +02:00
Efraim Flashner
58614c9b4b
gnu: samtools: Fix build on i686-linux.
...
* gnu/packages/bioinformatics.scm (samtools)[arguments]: When building
for i686-linux adjust the make-flags to specifically use the sse math
libraries.
Change-Id: I322d521cbe87e10db7c23db8e68bb377db966aa7
2024-05-19 16:10:47 +03:00
Ricardo Wurmus
2b161f6130
gnu: pigx-rnaseq: Update to 0.1.1.
...
* gnu/packages/bioinformatics.scm (pigx-rnaseq): Update to 0.1.1.
Change-Id: I16db332e3559bed5b302f08bd85f31c6c40e9619
2024-05-15 09:37:29 +02:00
Ricardo Wurmus
be235a3092
gnu: Add r-anndatar.
...
* gnu/packages/bioinformatics.scm (r-anndatar): New variable.
Change-Id: I6060c5c15a46c064aa03ec2431a72ea88f925706
2024-05-13 16:12:12 +02:00
Efraim Flashner
39059b9390
gnu: minimap2: Remove included file from gcc.
...
* gnu/packages/bioinformatics.scm (minimap2)[arguments]: Adjust custom
'install phase to remove included emmintrin.h header.
Change-Id: Id994dd2bd4a98e8d1c162c4e011fc77b9d5565d2
2024-05-12 09:59:55 +03:00
Ricardo Wurmus
6745d692d4
gnu: rcas-web: Update to latest commit.
...
The latest commit fixes a problem in configure.ac.
* gnu/packages/bioinformatics.scm (rcas-web)[source]: Fetch from git.
[arguments]: Remove 'find-RCAS phase; use G-expression.
[inputs]: Drop labels. Use Guile 3.0.
[native-inputs]: Add autoconf and automake.
Change-Id: I6f1d300df589a99b9493b2857f58d49e468b210e
2024-05-08 12:53:43 +02:00
Ricardo Wurmus
babafe251c
gnu: r-icellnet: Update to 2.2.1-1.e10ee4a.
...
* gnu/packages/bioinformatics.scm (r-icellnet): Update to 2.2.1-1.e10ee4a.
[propagated-inputs]: Add r-complexheatmap and r-circlize.
Change-Id: Ib844f83cb1ca4f88259593153d9e66289307dccc
2024-05-08 12:53:43 +02:00
Efraim Flashner
51c711a328
gnu: bitmapperbs: Limit to x86_64-linux.
...
* gnu/packages/bioinformatics.scm (bitmapperbs)[supported-systems]: New
field.
Change-Id: I03484413e5af8e779fe0e5199e456eaab124e8b7
2024-05-07 01:31:20 +03:00
Efraim Flashner
0a5929033f
gnu: minimap2: Fix make-flags.
...
* gnu/packages/bioinformatics.scm (minimap2)[arguments]: Adjust the
make-flags to contain actual build flags for all architectures.
Change-Id: I5b4077a25d6d46172ff566ceaa16629ebf066721
2024-05-06 23:53:04 +03:00
Efraim Flashner
6571231f2d
gnu: minimap2: Update to 2.28.
...
* gnu/packages/bioinformatics.scm (minimap2): Update to 2.28.
[arguments]: Adjust custom 'install phase to not delete non-existent
file. Remove trailing #t from phase.
Change-Id: Ie6cc21f2b761532f08967efea54d3a12b944f213
2024-05-06 23:42:22 +03:00
Efraim Flashner
a4c0a58594
gnu: proteinortho: Add tunable property.
...
* gnu/packages/bioinformatics.scm (proteinortho)[properties]: Add
tunable? flag.
Change-Id: If59d5785c8c8e4aedb5b88479da6fba0e9754640
2024-05-06 23:16:57 +03:00
Efraim Flashner
dd23efe020
gnu: proteinortho: Update to 6.3.2.
...
* gnu/packages/bioinformatics.scm (proteinortho): Update to 6.3.2.
[source]: Adjust snippet to also delete lapack source tarball.
[arguments]: Rewrite using g-expressions. Add flag to run tests
sequentially. Adjust make-flags for cross-compiling and to set PREFIX.
Delete 'configure and custom 'configure phase. Remove trailing #t from
phases.
Change-Id: I40249e5ac92c26223119b81b4677c08d5ab230e6
2024-05-06 23:16:56 +03:00
Ricardo Wurmus
f736a784e1
gnu: trust4: Update to 1.1.0.
...
* gnu/packages/bioinformatics.scm (trust4): Update to 1.1.0.
Change-Id: I4780038a5db110514e27f07a576166def4063da7
2024-05-06 12:36:53 +02:00
Mădălin Ionel Patrașcu
709e87caff
gnu: Add trust4.
...
gnu/packages/bioinformatics.scm (trust4): New variable.
Change-Id: I6a0fd339a0f761a473f50c7da74c26cfac7b1caf
2024-05-06 11:47:05 +02:00
Mădălin Ionel Patrașcu
57769fb0b3
gnu: Add r-seraster.
...
* gnu/packages/bioinformatics.scm (r-seraster): New variable.
Change-Id: I9f9fd24a9aa563f7c74154e613b85dee46bdcf79
2024-05-06 11:38:17 +02:00
Mădălin Ionel Patrașcu
64fcc49dc5
gnu: Add r-metadeconfoundr.
...
* gnu/packages/bioinformatics.scm (r-metadeconfoundr): New variable.
Change-Id: I733fb464d2a3c7fd1335826be9f23e2610e6fd60
2024-05-06 11:26:54 +02:00
nafkhamdc
00aa6b5a3c
gnu: Add python-pyrodigal.
...
* gnu/packages/bioinformatics.scm (python-pyrodigal): New variable.
Co-authored-by: Ricardo Wurmus <rekado@elephly.net>
Change-Id: Iaa0bdb4b918d93f990d5b904f1df3a3f910726b0
2024-05-06 10:37:41 +02:00
nafkhamdc
e33bf0bbe6
gnu: Add python-pyahocorasick.
...
* gnu/packages/bioinformatics.scm (python-pyahocorasick): New variable.
Change-Id: I468bed450351b49cf81344a328841cd77f67cb4e
Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
2024-05-06 00:07:40 +02:00
