1353 Commits

Author	SHA1	Message	Date
R. Ryantm	7decc89f3e	bcftools: 1.20 -> 1.21	2024-09-13 06:20:40 +00:00
Peder Bergebakken Sundt	f99890f31f	minc-tools: unstable-2020-07-25 -> 2.3.06-unstable-2023-08-12 (#340340)	2024-09-13 01:41:06 +02:00
Weijia Wang	d4d144b8f2	jbrowse: 2.14.0 -> 2.15.0 (#339549)	2024-09-11 00:24:42 +02:00
Weijia Wang	7127eff86d	iqtree: 2.3.5 -> 2.3.6 (#331537)	2024-09-09 23:31:22 +02:00
Ben Darwin	6718a1b70f	minc-tools: unstable-2020-07-25 -> 2.3.06-unstable-2023-08-12	2024-09-07 13:57:40 -04:00
Ben Darwin	5297d8f429	minc-tools: apply nixfmt	2024-09-07 12:46:46 -04:00
Aleksana	6b045549f1	igv: only replace actual java commands with the full path (#338340)	2024-09-06 23:11:25 +08:00
R. Ryantm	17a622b98e	jbrowse: 2.14.0 -> 2.15.0	2024-09-04 14:00:01 +00:00
Nick Cao	1cb6cb8df1	jbrowse: 2.13.1 -> 2.14.0 (#338101)	2024-09-03 15:17:57 -04:00
electric-castle	5d19a9ed86	Only replace actual java commands with the full path	2024-08-29 23:51:23 -07:00
Peder Bergebakken Sundt	ebc2389134	treewide: remove refs/tags/ from github release meta.changelog urls ... diff of `jq <packages.json 'to_entries[]|"\(.key) \(.value.meta.changelog)"' -r`: https://gist.github.com/pbsds/49b2e2ae5c9b967a0972bbc3c2597c12	2024-08-29 22:45:00 -04:00
R. Ryantm	747970800e	jbrowse: 2.13.1 -> 2.14.0	2024-08-29 04:33:48 +00:00
Peder Bergebakken Sundt	925c7fa7b8	Merge pull request #331743 from r-ryantm/auto-update/kallisto ... kallisto: 0.50.1 -> 0.51.0	2024-08-16 01:57:02 +02:00
R. Ryantm	ce2698d6c3	jbrowse: 2.12.3 -> 2.13.1	2024-08-07 10:53:57 +00:00
Philip Taron	57b45852e3	Merge pull request #331864 from emilazy/push-posunwslrptx ... febio: 3.6 -> 4.7; febio-studio: 1.6.1 -> 2.7	2024-08-05 21:38:59 -07:00
Nick Cao	1570486e98	Merge pull request #329292 from r-ryantm/auto-update/last ... last: 1548 -> 1550	2024-08-05 19:31:14 -04:00
tomberek	b93e52ddd5	Merge pull request #331891 from r-ryantm/auto-update/nest ... nest: 3.7 -> 3.8	2024-08-04 14:50:27 -04:00
tomberek	ed0a541703	Merge pull request #329924 from r-ryantm/auto-update/python312Packages.neuronpy ... python312Packages.neuronpy: 8.2.4 -> 8.2.6	2024-08-04 14:39:29 -04:00
amesgen	dd2019b0c0	tandem-aligner: move to by-name	2024-08-04 13:37:12 +02:00
R. Ryantm	9913cedc5b	nest: 3.7 -> 3.8	2024-08-03 02:21:53 +00:00
Emily	aa4aae33c5	febio-studio: move to pkgs/by-name	2024-08-02 23:12:31 +01:00
Emily	a600cdfb4a	febio-studio: 1.6.1 -> 2.7	2024-08-02 23:12:31 +01:00
Emily	c0f739e784	febio-studio: format with nixfmt-rfc-style	2024-08-02 23:12:31 +01:00
R. Ryantm	1213f4e3f2	kallisto: 0.50.1 -> 0.51.0	2024-08-02 11:16:03 +00:00
R. Ryantm	dd3fd18213	iqtree: 2.3.5 -> 2.3.6	2024-08-01 14:11:09 +00:00
Florian	bc95156d37	Merge pull request #326174 from t4ccer/t4/sratoolkit-3.1.1 ... sratoolkit: 2.11.3 -> 3.1.1, build from source	2024-07-29 21:16:34 +02:00
t4ccer	35db6ff3e7	sratoolkit: build from source	2024-07-29 11:25:25 -06:00
Jörg Thalheim	5356420466	treewide: remove unused with statements from maintainer lists ... $ find -type f -name '*.nix' -print0 | xargs -P "$(nproc)" -0 sed -i \ -e 's!with lib.maintainers; \[ *\];![ ];!' \ -e 's!with maintainers; \[ *\];![ ];!'	2024-07-29 10:06:20 +08:00
Aleksana	84a53ad8e2	Merge pull request #328741 from Sigmanificient/remove-unused-arguments-pkgs-app ... pkgs/applications: remove unused arguments	2024-07-26 22:05:49 +08:00
Sigmanificient	2ee703dccb	pkgs/applications: remove unused arguments	2024-07-26 11:36:49 +02:00
R. Ryantm	3dc43c3821	python312Packages.neuronpy: 8.2.4 -> 8.2.6	2024-07-25 15:04:43 +00:00
R. Ryantm	077b396406	ants: 2.5.2 -> 2.5.3	2024-07-25 02:08:42 +00:00
Franz Pletz	7c693006a7	Merge pull request #327543 from r-ryantm/auto-update/kent	2024-07-23 23:12:37 +02:00
R. Ryantm	055a00a203	last: 1548 -> 1550	2024-07-23 00:58:03 +00:00
Peder Bergebakken Sundt	6f65a24431	Merge pull request #325860 from bcdarwin/bump-dcm2niix ... dcm2niix: 1.0.20230411 -> 1.0.20240202	2024-07-21 01:18:30 +02:00
R. Ryantm	5c3ad3f895	kent: 467 -> 468	2024-07-16 04:00:44 +00:00
aleksana	592e3845c4	treewide: sha256 -> hash attribute for fetchgit	2024-07-14 19:10:08 +08:00
éclairevoyant	0926bdbf98	treewide: fix uses of finalAttrs.pname in source urls	2024-07-12 20:23:39 -04:00
OTABI Tomoya	72966ff6cf	Merge pull request #324590 from natsukium/truvari/update ... truvari: 4.1.0 -> 4.2.2; abpoa: init at 1.5.1	2024-07-12 14:37:07 +09:00
t4ccer	530a1191a2	sratoolkit: 2.11.3 -> 3.1.1	2024-07-10 13:01:15 -06:00
Ben Darwin	81756aaba1	dcm2niix: 1.0.20230411 -> 1.0.20240202	2024-07-09 10:18:52 -04:00
Weijia Wang	777a74274c	Merge pull request #324258 from r-ryantm/auto-update/jbrowse ... jbrowse: 2.12.2 -> 2.12.3	2024-07-08 22:45:00 +02:00
natsukium	45b23644da	truvari: 4.1.0 -> 4.2.2 ... Diff: https://github.com/ACEnglish/truvari/compare/v4.1.0...v4.2.2 Changelog: https://github.com/ACEnglish/truvari/releases/tag/v4.2.2	2024-07-04 21:38:05 +09:00
github-actions[bot]	6c668cb3e5	Merge master into staging-next	2024-07-03 09:24:52 +00:00
R. Ryantm	8e39ff657e	jbrowse: 2.12.2 -> 2.12.3	2024-07-03 08:35:09 +00:00
R. Ryantm	1854940a5d	trimal: 1.4.1 -> 1.5.0	2024-07-02 19:20:38 +00:00
K900	665f1d6183	Merge remote-tracking branch 'origin/master' into staging-next	2024-07-02 08:32:46 +03:00
h7x4	445ae2940d	Merge pull request #323605 from r-ryantm/auto-update/iqtree ... iqtree: 2.3.4 -> 2.3.5	2024-07-01 23:34:08 +02:00
Martin Weinelt	9b79a05ae1	Merge remote-tracking branch 'origin/master' into staging-next ... Conflicts: - pkgs/development/python-modules/flexcache/default.nix - pkgs/development/python-modules/flexparser/default.nix - pkgs/development/python-modules/odp-amsterdam/default.nix - pkgs/development/python-modules/pint/default.nix - pkgs/development/python-modules/uncertainties/default.nix - pkgs/top-level/python-packages.nix	2024-07-01 01:07:21 +02:00
Matthias Beyer	ed95ea87ad	Merge pull request #323064 from r-ryantm/auto-update/picard-tools ... picard-tools: 3.1.1 -> 3.2.0	2024-06-30 17:17:28 +02:00