R. Ryantm
8fc55ae4ab
iqtree: 2.3.4 -> 2.3.5
2024-06-30 14:49:34 +00:00
R. Ryantm
3efbea1593
gatk: 4.5.0.0 -> 4.6.0.0
2024-06-30 01:17:34 +00:00
R. Ryantm
c5db4f6b96
picard-tools: 3.1.1 -> 3.2.0
2024-06-28 01:41:05 +00:00
github-actions[bot]
2f3bfad6d2
Merge master into staging-next
2024-06-28 00:02:11 +00:00
R. Ryantm
ab4851ec2b
jbrowse: 2.11.2 -> 2.12.2
2024-06-27 10:09:32 +00:00
github-actions[bot]
27074b7d07
Merge master into staging-next
2024-06-26 00:02:13 +00:00
Weijia Wang
992070ffdd
Merge pull request #319985 from r-ryantm/auto-update/last
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last: 1544 -> 1548
2024-06-26 00:49:56 +02:00
Martin Weinelt
de245ec4a5
Merge remote-tracking branch 'origin/master' into staging-next
2024-06-25 13:00:25 +02:00
R. Ryantm
fda000ee3a
kent: 466 -> 467
2024-06-25 05:23:39 +00:00
natsukium
d80d5059c1
macs2: refactor
2024-06-24 12:18:27 +02:00
natsukium
41577bd4e2
macs2: pin to python311
2024-06-24 12:18:27 +02:00
Aleksana
a12b153874
Merge pull request #316782 from aaronjheng/poretools
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poretools: remove
2024-06-18 13:41:58 +08:00
Zitrone
63b875e099
SPAdes: refactor
2024-06-16 20:18:13 -03:00
R. Ryantm
9ffeef4612
last: 1544 -> 1548
2024-06-15 05:29:39 +00:00
R. Ryantm
2a5d67ff74
kent: 465 -> 466
2024-06-13 08:40:27 +00:00
Aaron Jheng
8b4e935052
poretools: remove
2024-06-11 10:16:51 +08:00
Weijia Wang
14df049746
Merge pull request #318689 from r-ryantm/auto-update/ants
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ants: 2.5.1 -> 2.5.2
2024-06-10 16:52:14 +02:00
Peder Bergebakken Sundt
91fed2bd84
Merge pull request #316965 from r-ryantm/auto-update/jbrowse
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jbrowse: 2.11.1 -> 2.11.2
2024-06-10 15:47:47 +02:00
R. Ryantm
27993b515e
ants: 2.5.1 -> 2.5.2
2024-06-10 04:29:13 +00:00
Alexis Hildebrandt
f8c4a98e8e
treewide: Remove the definite article from meta.description
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nix run nixpkgs#silver-searcher -- -G '\.nix$' -0l 'description.*"([Tt]he)? ' pkgs \
| xargs -0 nix run nixpkgs#gnused -- -i '' -Ee 's/(description.*")[Tt]he (.)/\1\U\2/'
2024-06-09 23:08:46 +02:00
Alexis Hildebrandt
755b915a15
treewide: Remove indefinite article from meta.description
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nix run nixpkgs#silver-searcher -- -G '\.nix$' -0l 'description.*"[Aa]n?' pkgs \
| xargs -0 nix run nixpkgs#gnused -- -i '' -Ee 's/(description.*")[Aa]n? (.)/\1\U\2/'
2024-06-09 23:07:45 +02:00
Alexis Hildebrandt
bf995e3641
treewide: Remove ending period from meta.description
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nix run nixpkgs#silver-searcher -- -G '\.nix$' -0l 'description.*".*\.";' pkgs \
| xargs -0 nix run nixpkgs#gnused -- -i '' -Ee 's/(description.*)\.";/\1";/'
2024-06-09 23:04:51 +02:00
Connor Baker
d63eb88a50
neuron: 8.2.3 -> 8.2.4; fixup
2024-06-04 22:29:48 +00:00
R. Ryantm
6f871a7736
jbrowse: 2.11.1 -> 2.11.2
2024-06-03 16:39:21 +00:00
Pol Dellaiera
ae80850b94
Merge pull request #316556 from r-ryantm/auto-update/kent
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kent: 446 -> 465
2024-06-02 21:30:23 +02:00
Weijia Wang
026005ab69
Merge pull request #312446 from r-ryantm/auto-update/bowtie2
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bowtie2: 2.5.3 -> 2.5.4
2024-06-02 17:26:37 +02:00
R. Ryantm
32feef3965
kent: 446 -> 465
2024-06-02 01:34:52 +00:00
tomberek
757873b346
Merge pull request #311696 from Pandapip1/fix-statoolkit-license
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licenses: Add NCBI-PD
2024-05-27 00:35:44 -04:00
R. Ryantm
1cfa988a8e
last: 1543 -> 1544
2024-05-22 19:38:03 +00:00
Sigmanificient
0058552891
pkgs/applications: remove uneeded fetchpatch arguments
2024-05-21 03:12:20 +02:00
Sigmanificient
a2353716f6
treewide: remove unused occurence of fetchurl argument
2024-05-20 05:20:23 +02:00
Nick Cao
7619a8dcfe
Merge pull request #312565 from r-ryantm/auto-update/seqkit
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seqkit: 2.8.1 -> 2.8.2
2024-05-18 15:40:25 -04:00
Matthias Beyer
567bfac089
Merge pull request #310872 from r-ryantm/auto-update/jbrowse
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jbrowse: 2.11.0 -> 2.11.1
2024-05-18 09:12:55 +02:00
R. Ryantm
3f4f9b51d5
seqkit: 2.8.1 -> 2.8.2
2024-05-18 00:57:59 +00:00
R. Ryantm
62f5fe5b14
bowtie2: 2.5.3 -> 2.5.4
2024-05-17 13:49:30 +00:00
R. Ryantm
200630a75d
iqtree: 2.3.2 -> 2.3.4
2024-05-16 00:07:19 +00:00
Gavin John
438273dac7
sratoolkit: Assign correct license
2024-05-14 11:38:53 -05:00
Raghav Sood
a55e1a28c1
conglomerate: unstable-2017-09-10 -> unstable-2023-01-19
2024-05-14 14:28:10 +08:00
Raghav Sood
b8b18a2517
conglomerate: nixfmt-rfc-style and modernization
2024-05-14 14:26:29 +08:00
OTABI Tomoya
e1fce3f66f
Merge pull request #308490 from natsukium/migrate/update
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migrate: 3.7.2 -> 5.0.6
2024-05-12 10:59:02 +09:00
R. Ryantm
f56f4c9fec
jbrowse: 2.11.0 -> 2.11.1
2024-05-11 14:58:02 +00:00
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
natsukium
21c42b3d39
migrate: refactor
2024-05-02 19:36:15 +09:00
natsukium
f5d23a16ed
migrate: add meta.mainProgram
2024-05-02 19:08:25 +09:00
natsukium
e789c579c1
migrate: 3.7.2 -> 5.0.6
2024-05-02 19:07:53 +09:00
natsukium
77dc1504a2
migrate: format with nixfmt
2024-05-02 18:44:09 +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
R. Ryantm
fd5b7188ef
mafft: 7.520 -> 7.525
2024-03-13 12:21:27 +00:00
R. Ryantm
055cf7e2ac
minimap2: 2.26 -> 2.27
2024-03-13 00:30:24 +00:00
Pol Dellaiera
37b4a69489
Merge pull request #295208 from r-ryantm/auto-update/igv
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igv: 2.17.2 -> 2.17.3
2024-03-12 21:36:29 +01:00
R. Ryantm
c91acf3624
igv: 2.17.2 -> 2.17.3
2024-03-12 02:48:25 +00:00
R. Ryantm
8cc0f796eb
seqkit: 2.7.0 -> 2.8.0
2024-03-12 00:29:44 +00:00
