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891 commits

Author SHA1 Message Date
Sandro ab78a72cd0
Merge pull request #198872 from jiegec/nest 
nest: init at 3.3
 2023-02-17 13:53:52 +01:00
Felix Buehler cdb39a86e0 treewide: use optionalString 2023-02-13 21:52:34 +01:00
Felix Bühler fb2c37b576
Merge pull request #216064 from Stunkymonkey/treewide-pname-version-1 
inormalize/minc-widgets/gimp-plugins: use pname & version
 2023-02-13 19:25:08 +01:00
Alyssa Ross c6c7493c3b
Merge remote-tracking branch 'origin/master' into staging-next 
Conflicts:
	pkgs/development/python-modules/pyarrow/default.nix
 2023-02-13 00:15:28 +00:00
Felix Buehler db348eb0d6 inormalize/minc-widgets/gimp-plugins: use pname & version 2023-02-12 22:21:44 +01:00
R. Ryantm 10c93d977d last: 1445 -> 1447 2023-02-12 17:14:30 +00:00
github-actions[bot] 15bfb025ab
Merge master into staging-next 2023-02-11 18:01:19 +00:00
R. Ryantm cc7591f90e eggnog-mapper: 2.1.9 -> 2.1.10 2023-02-11 08:43:59 +00:00
github-actions[bot] 9be52f693f
Merge master into staging-next 2023-02-10 12:01:38 +00:00
R. Ryantm b64bc146ed diamond: 2.1.0 -> 2.1.1 2023-02-10 02:56:54 +00:00
github-actions[bot] b30088fc3f
Merge master into staging-next 2023-02-07 00:02:12 +00:00
R. Ryantm 38e3d21824 stacks: 2.60 -> 2.62 2023-02-06 21:36:49 +01:00
github-actions[bot] b2a1140ada
Merge master into staging-next 2023-02-06 06:01:25 +00:00
R. Ryantm 0fd2901e31 varscan: 2.4.4 -> 2.4.5 2023-02-05 13:38:28 +00:00
github-actions[bot] cb231fb28d
Merge master into staging-next 2023-02-05 06:01:18 +00:00
R. Ryantm eadaccaa42 igv: 2.15.5 -> 2.16.0 2023-02-04 18:01:58 +00:00
github-actions[bot] 6d7be19afb
Merge master into staging-next 2023-02-02 18:01:08 +00:00
Sandro a9cadfb7b8
Merge pull request #213490 from OPNA2608/refactor/yaml-cpp 
yaml-cpp*: Refactor, rename, adopt
 2023-02-02 17:32:34 +01:00
Vladimír Čunát 9287f4461d
Merge #206907: stdenv: gcc11 -> gcc12 2023-02-01 16:54:44 +01:00
OPNA2608 c9b4c7dccd treewide: Rename libyamlcpp* to yaml-cpp* 2023-01-31 16:22:54 +01:00
Nick Cao c84edce4ec
Merge pull request #213063 from r-ryantm/auto-update/diamond 
diamond: 2.0.15 -> 2.1.0
 2023-01-31 16:47:56 +08:00
Fabián Heredia Montiel 0cf5d85f0c treewide: add gcc12 flags 2023-01-27 21:20:52 -06:00
R. Ryantm 01c2d762f3 diamond: 2.0.15 -> 2.1.0 2023-01-28 02:58:32 +00:00
Ben Darwin b27838807e ants: unpin vtk dependency 2023-01-27 00:21:26 -05:00
Fabian Affolter bf0a5df606
Merge pull request #212793 from fabaff/last-fix 
last: 1422 -> 1445
 2023-01-26 20:06:44 +01:00
Fabian Affolter e14e8f5f31 last: 1422 -> 1445 2023-01-26 16:10:25 +01:00
R. Ryantm 422b1c5144 igv: 2.15.4 -> 2.15.5 2023-01-25 17:03:16 +00:00
Justin Bedő ed15930675
Merge pull request #211057 from r-ryantm/auto-update/last 
last: 1411 -> 1422
 2023-01-23 22:22:52 +00:00
Sandro 7726aa9ce6
Merge pull request #206287 from amesgen/add-TandemAligner 2023-01-23 23:12:36 +01:00
Weijia Wang 02d3fe6418
Merge pull request #212113 from r-ryantm/auto-update/sambamba 
sambamba: 0.8.2 -> 1.0.0
 2023-01-23 21:01:50 +01:00
Nick Cao 06d76bd44e
Merge pull request #210641 from r-ryantm/auto-update/star 
star: 2.7.10a -> 2.7.10b
 2023-01-23 16:16:01 +08:00
Weijia Wang 90e2800173
Merge pull request #198962 from r-ryantm/auto-update/bowtie2 
bowtie2: 2.4.5 -> 2.5.1
 2023-01-23 05:32:54 +01:00
Weijia Wang 6bfeb6aa68
Merge pull request #195005 from r-ryantm/auto-update/picard-tools 
picard-tools: 2.27.4 -> 2.27.5
 2023-01-22 22:40:27 +01:00
R. Ryantm 2166bf1bfe sambamba: 0.8.2 -> 1.0.0 2023-01-22 13:54:41 +00:00
Weijia Wang 218c4c526e
Merge pull request #212002 from mothsART/feature/replace_http_by_https 
treewide: replace http by https when https is a permanent redirection
 2023-01-22 03:26:02 +01:00
Ferry Jérémie 65d7e87fdb treewide: replace http by https when https is a permanent redirection 2023-01-22 02:46:49 +01:00
R. Ryantm 2660299f54 bowtie2: 2.4.5 -> 2.5.1 2023-01-21 21:19:00 +00:00
Guillaume Girol 33afbf39f6 treewide: switch to nativeCheckInputs 
checkInputs used to be added to nativeBuildInputs. Now we have
nativeCheckInputs to do that instead. Doing this treewide change allows
to keep hashes identical to before the introduction of
nativeCheckInputs.
 2023-01-21 12:00:00 +00:00
R. Ryantm d269d79261 last: 1411 -> 1422 2023-01-16 09:13:32 +00:00
R. Ryantm fc65d6e66e star: 2.7.10a -> 2.7.10b 2023-01-14 06:06:52 +00:00
github-actions[bot] 33aa224777
Merge master into staging-next 2023-01-09 18:01:24 +00:00
R. Ryantm e0db41ab1a ants: 2.4.2 -> 2.4.3 2023-01-09 09:48:53 -06:00
Robert Schütz b3241be75d python310Packages.levenshtein: don't use alias 2023-01-09 06:09:31 -08:00
R. Ryantm 605d013aac igv: 2.15.1 -> 2.15.4 2023-01-03 14:36:54 +08:00
Ben Darwin 9c748218f2 itk: unstable -> 5.3.0 2022-12-27 09:06:37 +01:00
Sandro b20fb264cc
Merge pull request #197575 from thyol/sratoolkit-init 2022-12-24 02:58:47 +01:00
amesgen d499bc2447
tandem-aligner: init at unstable-2022-09-17 2022-12-15 20:48:53 +01:00
Weijia Wang fa19b16e93 ecopcr: 0.8.0 -> 1.0.1 2022-12-08 04:35:53 +01:00
Jonas Heinrich 20193b6d86
Merge pull request #202395 from thyol/muscle 
muscle: 3.8.31 -> 5.1.0
 2022-11-24 15:47:12 +01:00
Jonas Heinrich 57728b51cf
Merge pull request #202404 from thyol/veryfasttree 
veryfasttree: init at 3.1.1
 2022-11-24 15:14:13 +01:00