Jan Tojnar
457f28f6f8
Merge branch 'master' into staging-next
...
; Conflicts:
; pkgs/development/tools/codespell/default.nix
codespell 2.2.2 switched to pyproject & setuptools_scm:
https://github.com/codespell-project/codespell/pull/2523
2022-10-19 05:24:28 +02:00
R. Ryantm
4ab06e3223
ants: 2.4.1 -> 2.4.2
2022-10-19 09:19:31 +08:00
github-actions[bot]
f52955a521
Merge master into staging-next
2022-10-16 18:01:42 +00:00
R. Ryantm
00b3b4ee24
gatk: 4.2.6.1 -> 4.3.0.0
2022-10-16 21:48:30 +08:00
Martin Weinelt
51fcbf5bb7
Merge remote-tracking branch 'origin/master' into staging-next
2022-10-16 00:18:40 +02:00
Jonas Heinrich
9259c4b841
Merge pull request #195990 from r-ryantm/auto-update/angsd
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angsd: 0.938 -> 0.940
2022-10-15 09:33:23 +02:00
github-actions[bot]
886633ba43
Merge master into staging-next
2022-10-15 00:04:00 +00:00
R. Ryantm
4cee9b9ddb
angsd: 0.938 -> 0.940
2022-10-14 14:50:26 +00:00
Artturi
e66d2fd89d
Merge pull request #194256 from Artturin/treewides2
2022-10-13 00:08:01 +03:00
Markus S. Wamser
c9d167f174
pkgs.applications: remove unused args
2022-10-12 16:00:16 +02:00
Martin Weinelt
cf7f4393f3
Merge pull request #193494 from NixOS/staging-next
2022-10-11 01:12:59 +02:00
Alexis Praga
2ce78bd571
gatk: add java and python to PATH
...
gatk is actually a python script that starts either the local or spark
.jar file according to a fixed setup.
In the initial commit, neither java nor python were present in PATH.
2022-10-10 23:06:01 +02:00
Artturin
7e49471316
treewide: optional -> optionals where the argument is a list
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the argument to optional should not be list
2022-10-10 15:40:21 +03:00
github-actions[bot]
f18d801779
Merge staging-next into staging
2022-09-28 18:05:53 +00:00
R. Ryantm
ddf9f1800a
delly: 1.1.3 -> 1.1.5
2022-09-27 11:26:09 +00:00
Artturin
0734f54ef2
treewide: move pkg-config, autoreconfHook, intltool to nativeBuildInputs
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found with nixpkgs-lint
2022-09-26 17:53:26 +03:00
Justin Bedő
d21b5ac044
Merge pull request #192211 from r-ryantm/auto-update/last
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last: 1409 -> 1411
2022-09-26 11:49:30 +10:00
Brad Langhorst
2beb26b45b
seqtk: init at 1.3
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Co-authored-by: Anderson Torres <torres.anderson.85@protonmail.com>
2022-09-25 19:55:58 -04:00
R. Ryantm
1008651931
last: 1409 -> 1411
2022-09-21 08:24:01 +00:00
Christian Kögler
e06e88d003
Merge pull request #189923 from r-ryantm/auto-update/igv
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igv: 2.14.0 -> 2.14.1
2022-09-18 15:59:16 +02:00
R. Ryantm
9da745bfaf
messer-slim: 4.0 -> 4.0.1
2022-09-15 22:25:51 +00:00
Sandro
785031e430
Merge pull request #185819 from apraga/gatk-4.2.6.1
2022-09-10 21:31:42 +02:00
natsukium
9e65d09e3d
mafft: 7.505 -> 7.508
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changed to fetch from new gitlab repository
2022-09-09 13:26:38 +09:00
R. Ryantm
c7832514ef
igv: 2.14.0 -> 2.14.1
2022-09-05 22:29:15 +00:00
Sandro
ef987a9604
Merge pull request #189329 from bcdarwin/itk4-removal
2022-09-05 16:05:51 +02:00
Sandro
73bf7a0ca0
Merge pull request #181954 from bzizou/treemix
2022-09-05 15:57:48 +02:00
Bruno Bzeznik
7c09cfdc1a
treemix: init at 1.13
2022-09-05 06:55:03 +02:00
Jonas Heinrich
eb3d3b2e90
Merge pull request #175449 from bzizou/iqtree
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iqtree: init at 2.2.0.4
2022-09-04 23:58:04 +02:00
Ben Darwin
1280129aab
EZminc: itk4 -> itk (formally; package is broken)
2022-09-04 13:36:24 -04:00
Ben Darwin
961b308fe1
ants: 2.2.0 -> 2.4.1
2022-09-04 13:36:24 -04:00
Alexis Praga
95da303902
gatk : init at 4.2.6.1
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GATK is the industry standard for genetics analysis, more precisely for
identifying SNPs and indels in germline DNA and RNAseq data .
This package does not ship the Spark version.
Apply suggestions from code review
Co-authored-by: Sandro <sandro.jaeckel@gmail.com>
2022-09-04 15:34:30 +02:00
Jonas Heinrich
3b3a01e3f9
Merge pull request #188785 from jbedo/last
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last: 1406 -> 1409
2022-09-04 12:40:30 +02:00
Justin Bedo
d9acf90371
last: 1406 -> 1409
2022-09-04 10:36:01 +10:00
Sandro
9b214e6dad
Merge pull request #177830 from r-ryantm/auto-update/eggnog-mapper
2022-09-03 22:43:11 +02:00
Jonas Heinrich
ed227dc9fb
Merge pull request #168109 from r-ryantm/auto-update/bcftools
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bcftools: 1.15 -> 1.16
2022-08-27 08:51:34 +02:00
Jonas Heinrich
21ba29f226
Merge pull request #181338 from thyol/diamond
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diamond: 0.8.36 -> 2.0.15
2022-08-25 15:25:03 +02:00
Jonas Heinrich
b8e0c9b652
Merge pull request #183253 from r-ryantm/auto-update/angsd
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angsd: 0.937 -> 0.938
2022-08-24 10:35:05 +02:00
Jonas Heinrich
c199cfabff
Merge pull request #184694 from r-ryantm/auto-update/SPAdes
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SPAdes: 3.15.4 -> 3.15.5
2022-08-23 20:21:42 +02:00
Jonas Heinrich
5cb64f6046
Merge pull request #186958 from r-ryantm/auto-update/igv
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igv: 2.13.2 -> 2.14.0
2022-08-21 21:11:49 +02:00
R. Ryantm
49f4071f30
eggnog-mapper: 2.1.7 -> 2.1.9
2022-08-21 12:45:21 +00:00
Jonas Heinrich
8508d5decf
Merge pull request #183724 from r-ryantm/auto-update/picard-tools
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picard-tools: 2.26.11 -> 2.27.4
2022-08-21 10:03:42 +02:00
R. Ryantm
98d1f4c35d
bcftools: 1.15 -> 1.16
2022-08-18 18:44:42 +00:00
R. Ryantm
f4c3ff2d7f
igv: 2.13.2 -> 2.14.0
2022-08-16 13:24:02 +00:00
R. Ryantm
c37112d2d0
messer-slim: 3.7.1 -> 4.0
2022-08-14 14:11:37 +00:00
Mario Rodas
0cab4c8f8a
Merge pull request #183012 from bcdarwin/update-mni-autoreg
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mni_autoreg: unstable-2017-09-22 -> unstable-2022-05-20
2022-08-13 01:05:26 -05:00
Mario Rodas
6aeb44c32e
Merge pull request #185211 from r-ryantm/auto-update/delly
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delly: 1.0.3 -> 1.1.3
2022-08-13 00:41:48 -05:00
kilianar
0442ab82e0
igv: 2.8.13 -> 2.13.2
...
- https://software.broadinstitute.org/software/igv/2.9.x
- https://software.broadinstitute.org/software/igv/2.10.x
- https://software.broadinstitute.org/software/igv/2.11.x
- https://software.broadinstitute.org/software/igv/2.12.x
- https://software.broadinstitute.org/software/igv/2.13.x
2022-08-07 17:53:06 +02:00
Bobby Rong
934c6c9a95
Merge pull request #184334 from r-ryantm/auto-update/mafft
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mafft: 7.490 -> 7.505
2022-08-07 16:18:05 +08:00
R. Ryantm
8b7c09d0e6
delly: 1.0.3 -> 1.1.3
2022-08-05 08:58:15 +00:00
Sandro
e9984bc607
Merge pull request #182705 from luispedro/no_test_samtools_on_cross_compile
2022-08-02 23:20:38 +02:00
