Nick Cao
d2e6f60e02
Merge pull request #309432 from r-ryantm/auto-update/messer-slim
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messer-slim: 4.2.1 -> 4.2.2
2024-05-06 10:34:40 -04:00
OTABI Tomoya
5656abaea3
Merge pull request #308676 from natsukium/dssp/update
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dssp: 4.4.5 -> 4.4.7, libcifpp: 7.0.3 -> 7.0.4
2024-05-06 23:20:52 +09:00
R. Ryantm
d5edb2e2f5
messer-slim: 4.2.1 -> 4.2.2
2024-05-06 01:54:25 +00:00
Weijia Wang
b8cb60c6fe
Merge pull request #306674 from r-ryantm/auto-update/jbrowse
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jbrowse: 2.5.0 -> 2.11.0
2024-05-04 15:49:20 +02:00
natsukium
7d27d397a5
dssp: 4.4.5 -> 4.4.7
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Diff: https://github.com/PDB-REDO/dssp/compare/refs/tags/v4.4.5...v4.4.7
Changelog:
https://github.com/PDB-REDO/libcifpp/releases/tag/refs/tags/v4.4.7
2024-05-03 10:51:52 +09:00
Vladimír Čunát
725f48a252
Merge branch 'master' into staging-next
2024-05-02 09:05:49 +02:00
R. RyanTM
a16ec6bad3
last: 1542 -> 1543 ( #307730 )
2024-05-01 22:49:48 +02:00
github-actions[bot]
67f8ba4a30
Merge master into staging-next
2024-05-01 18:01:22 +00:00
R. Ryantm
ecfbb79ecd
igv: 2.17.3 -> 2.17.4
2024-05-01 11:59:31 +00:00
K900
a9c7210d0b
Merge branch 'master' into staging-next
2024-05-01 09:37:47 +03:00
Nick Cao
cd5f33f23d
seqtk: fix cross compilation, drop custom installPhase
2024-04-29 17:04:29 -04:00
github-actions[bot]
69117017f0
Merge master into staging-next
2024-04-28 18:01:03 +00:00
natsukium
ce0af18702
mafft: enable simple test
2024-04-28 13:57:47 +09:00
natsukium
4b3081c5e0
mafft: prettify
2024-04-28 13:46:23 +09:00
natsukium
5cb77278a4
mafft: 7.525 -> 7.526
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Diff: https://gitlab.com/sysimm/mafft/-/compare/v7.525...v7.526
2024-04-28 13:42:08 +09:00
Jan Tojnar
eb04659fc2
treewide: wrapGAppsHook → wrapGAppsHook3
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This was achieved using the following command:
sd 'wrapGAppsHook\b' wrapGAppsHook3 (rg -l 'wrapGAppsHook\b')
And then manually reverted the following changes:
- alias in top-level.nix
- function name in wrap-gapps-hook.sh
- comment in postFixup of at-spi2-core
- comment in gtk4
- comment in preFixup of 1password-gui/linux.nix
- comment in postFixup of qgis/unwrapped-ltr.nix and qgis/unwrapped.nix
- comment in postFixup of telegram-desktop
- comment in postFixup of fwupd
- buildCommand of mongodb-compass
- postFixup of xflux-gui
- comment in a patch in kdePackages.kde-gtk-config and plasma5Packages.kde-gtk-config
- description of programs.sway.wrapperFeatures.gtk NixOS option (manual rebuild)
2024-04-27 02:23:22 +02:00
Yt
f2157c2a34
Merge pull request #305974 from onny/rocksdb-update
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rocksdb: 8.3.2 -> 9.1.0, rocksdb_8_3: init at 8.3.2
2024-04-25 01:38:37 +00:00
R. Ryantm
8566ec559a
jbrowse: 2.5.0 -> 2.11.0
2024-04-25 01:29:38 +00:00
Peder Bergebakken Sundt
985aa8174d
treewide: unbreak appimageTools.wrapType2 builds
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`appimageTools.wrapType2` no longer creates a binary `$out/bin/${name}` if `pname` and `version` is provided.
Derivations that have worked around this behavior with a `mv $out/bin/{${name},${pname}}` broke as a result.
This should fix most instances.
contex: #271071
2024-04-24 15:26:52 +02:00
Jonas Heinrich
f7709cf1b3
treewide: switch from rocksdb -> rocksdb_8_3
2024-04-22 13:02:14 +02:00
Weijia Wang
5bc788216a
nest: fix hash
2024-04-20 10:17:24 +02:00
Vladimír Čunát
8c0c955a09
Merge branch 'master' into staging-next
2024-04-19 07:52:28 +02:00
Weijia Wang
2e5299f478
Merge pull request #303357 from r-ryantm/auto-update/iqtree
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iqtree: 2.3.1 -> 2.3.2
2024-04-18 20:54:50 +02:00
github-actions[bot]
5c2b2d5b74
Merge master into staging-next
2024-04-17 18:01:04 +00:00
Aleksana
e1e418e67a
Merge pull request #304395 from r-ryantm/auto-update/bcftools
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bcftools: 1.19 -> 1.20
2024-04-17 21:16:25 +08:00
github-actions[bot]
a459b363de
Merge master into staging-next
2024-04-16 12:01:11 +00:00
Weijia Wang
72e43a6c65
Merge pull request #303754 from r-ryantm/auto-update/messer-slim
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messer-slim: 4.2 -> 4.2.1
2024-04-16 12:51:51 +02:00
R. Ryantm
c48e90fd63
bcftools: 1.19 -> 1.20
2024-04-16 00:22:42 +00:00
github-actions[bot]
097ced11fa
Merge master into staging-next
2024-04-16 00:02:03 +00:00
R. Ryantm
25a9517a84
messer-slim: 4.2 -> 4.2.1
2024-04-13 01:13:01 +00:00
R. Ryantm
15b7dddaba
python311Packages.nest: 3.6 -> 3.7
2024-04-12 13:50:38 +00:00
github-actions[bot]
35713de428
Merge master into staging-next
2024-04-12 12:01:18 +00:00
Weijia Wang
3e0325206d
Merge pull request #301677 from r-ryantm/auto-update/minimap2
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minimap2: 2.27 -> 2.28
2024-04-12 10:20:56 +02:00
R. Ryantm
636999c359
iqtree: 2.3.1 -> 2.3.2
2024-04-11 13:08:33 +00:00
Weijia Wang
3f59355d84
Merge branch 'staging-next' into staging
2024-04-09 08:26:23 +02:00
R. Ryantm
c4128f9b05
seqkit: 2.8.0 -> 2.8.1
2024-04-07 14:35:21 +00:00
R. Ryantm
a9be06cc4d
minimap2: 2.27 -> 2.28
2024-04-04 23:45:37 +00:00
Martin Weinelt
ea1480099d
Merge pull request #299223 from NixOS/python-updates
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[python-updates] 2024-03-24 - selective updates
2024-03-28 05:01:55 +01:00
Martin Weinelt
528354e66c
python312Packages.cython: 0.29.36 -> 3.0.9
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Folds the cython_3 attribute into the primary cython attribute and
migrates all packages from the versioned attribute.
The old version will be provided through the cython_0 attribute in an
effort to phase it out.
2024-03-27 18:35:05 +01:00
R. Ryantm
60daff4b19
iqtree: 2.2.2.7 -> 2.3.1
2024-03-26 08:23:46 +00:00
R. Ryantm
9229eb6e7e
messer-slim: 4.1 -> 4.2
2024-03-22 17:12:15 +00:00
Jussi Kuokkanen
82b45bf454
treewide: remove licenses.agpl3
2024-03-21 18:09:24 +02:00
jopejoe1
3c57e34690
conglomerate: change license to hpndUc
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found at https://github.com/BIC-MNI/conglomerate/blob/master/COPYING
2024-03-20 20:49:33 +01:00
TomaSajt
25ea922a4b
astral: make deterministic and clean up
2024-03-19 11:24:39 +01:00
Pol Dellaiera
186c3e34a7
Merge pull request #296549 from TomaSajt/strip-java-archives-hook
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add stripJavaArchivesHook and use treewide
2024-03-19 05:41:08 +01:00
stuebinm
ff1a94e523
treewide: add meta.mainProgram to packages with a single binary
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The nixpkgs-unstable channel's programs.sqlite was used to identify
packages producing exactly one binary, and these automatically added
to their package definitions wherever possible.
2024-03-19 03:14:51 +01:00
Weijia Wang
2e911ea73b
Merge pull request #294471 from r-ryantm/auto-update/deeptools
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deeptools: 3.5.4 -> 3.5.5
2024-03-17 15:20:16 +01:00
TomaSajt
0e20953796
treewide: use stripJavaArchivesHook instead of canonicalize-jars-hook
2024-03-17 13:35:12 +01:00
OTABI Tomoya
7fc13a0d56
Merge pull request #295598 from r-ryantm/auto-update/mafft
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mafft: 7.520 -> 7.525
2024-03-17 11:56:50 +09:00
Nick Cao
86e812c02a
Merge pull request #295472 from r-ryantm/auto-update/minimap2
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minimap2: 2.26 -> 2.27
2024-03-15 14:04:43 -04:00
