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1044 commits

Author SHA1 Message Date
R. Ryantm 7c4e31bb4c igv: 2.16.0 -> 2.16.1 2023-05-31 13:33:15 +00:00
R. Ryantm 71a23afb45 iqtree: 2.2.2.4 -> 2.2.2.6 2023-05-30 01:13:17 +00:00
R. Ryantm bebbc418d4 seqtk: 1.3 -> 1.4 2023-05-28 06:48:51 +00:00
R. Ryantm 216e1726da blast: 2.13.0 -> 2.14.0 2023-05-26 00:23:49 +00:00
figsoda 8014b08ee0 treewide/applications: use top-level fetchPypi 2023-05-25 10:51:30 -04:00
Weijia Wang 6d71b5d6de iqtree: set platforms 2023-05-22 11:14:57 +03:00
R. Ryantm b36979ec74 iqtree: 2.2.0.4 -> 2.2.2.4 2023-05-22 04:48:16 +00:00
Weijia Wang 7c6ca2791b
Merge pull request #231635 from natsukium/bwa/build-on-aarch64 
bwa: 0.7.17 -> unstable-2022-09-23
 2023-05-18 01:10:14 +03:00
Nick Cao 906c7dd78c
Merge pull request #231975 from jbedo/fastp 
fastp: 0.23.2 -> 0.23.3
 2023-05-15 05:11:28 -06:00
natsukium 04dd7f41e7
bwa: add runHook 2023-05-15 16:13:49 +09:00
natsukium c85dced23e
bwa: update license 2023-05-15 16:13:49 +09:00
natsukium 01ddcaa879
bwa: 0.7.17 -> unstable-2022-09-23 
Diff: https://github.com/lh3/bwa/compare/v0.7.17...139f68fc4c3747813783a488aef2adc86626b01b
 2023-05-15 16:13:45 +09:00
Ryan Lahfa 308ee09f2f
Merge pull request #231598 from natsukium/truvari/disable-tests-darwin 
truvari: disable some tests on darwin
 2023-05-15 09:09:09 +02:00
Justin Bedo 60c69da248
fastp: 0.23.2 -> 0.23.3 2023-05-15 15:03:24 +10:00
natsukium 7edb72db10
truvari: add patches to fix truvari anno 2023-05-15 10:01:38 +09:00
Ben Booth fed8eeba5c jbrowse: init at 2.5.0 2023-05-12 11:24:26 -07:00
Justin Bedo c7a6773f8e
subread: 2.0.5 -> 2.0.6 2023-05-10 22:30:35 +10:00
Alexis Praga e027a5d836 kent: package headers too. 
This is needed for perlPackages.BioBigFile.
Removing NIX_BUILD_TOP.
 2023-05-06 19:48:14 +02:00
R. Ryantm be4b60bf4f minimap2: 2.25 -> 2.26 2023-05-03 19:38:48 +00:00
Ben Darwin cf573698b1 ants: 2.4.3 -> 2.4.4 2023-05-02 12:29:21 -04:00
R. Ryantm 54a5899734 minimap2: 2.24 -> 2.25 2023-04-29 21:45:58 +00:00
R. Ryantm 395db2896e bedtools: 2.30.0 -> 2.31.0 2023-04-29 03:05:55 +00:00
natsukium 8d40a0ecaa
bedops: fix build on darwin 2023-04-24 22:11:47 +09:00
Nick Cao ab7c128e3c
Merge pull request #227207 from natsukium/kent/update 
kent: 404 -> 446
 2023-04-24 10:03:16 +08:00
Sandro 9bc9cfe51d
Merge pull request #222660 from natsukium/hh-suite/init 2023-04-23 23:42:38 +02:00
Nick Cao 99c4e7b895
Merge pull request #227170 from jbedo/subread 
subread: 2.0.4 -> 2.0.5
 2023-04-22 11:05:37 +08:00
Robert Schütz 2362848adf truvari: add natsukium to maintainers 2023-04-21 13:43:26 -07:00
Robert Schütz ea468d9691 truvari: 2.1.1 -> 4.0.0 
Diff: https://github.com/spiralgenetics/truvari/compare/v2.1.1...v4.0.0
 2023-04-21 13:43:26 -07:00
natsukium 23205d28d2
kent: add missing information to the meta 2023-04-20 16:06:09 +09:00
natsukium 5b62152599
kent: add runHooks 2023-04-20 16:06:08 +09:00
natsukium 1e68ff3ee9
kent: 404 -> 446 
https://github.com/ucscGenomeBrowser/kent/compare/v404_base...v446_base
 2023-04-20 16:05:44 +09:00
Justin Bedo 718170ed41
subread: 2.0.4 -> 2.0.5 2023-04-20 10:25:20 +10:00
natsukium e201b1556f
tandem-aligner: add changelog to meta 2023-04-19 21:23:21 +09:00
natsukium 14d7a73714
tandem-aligner: unstable-2022-09-17 -> 0.1 
https://github.com/seryrzu/tandem_aligner/releases/tag/v0.1
 2023-04-19 21:22:18 +09:00
natsukium a272606614
hh-suite: init at 3.3.0 2023-04-19 10:32:35 +09:00
Artturi 9a1f5d4248
Merge pull request #226889 from Artturin/fixlints2 2023-04-18 21:52:21 +03:00
Artturin eac28f38d6 treewide: fix lints 
Arg to lib.optional is a list

build time tool in buildInputs

*Flags not a list

https://github.com/nix-community/nixpkgs-lint
 2023-04-18 20:20:56 +03:00
Sandro 555daa9d33
Merge pull request #221957 from natsukium/dssp/update 
dssp: 4.0.5 -> 4.2.2.1
 2023-04-18 16:34:17 +02:00
natsukium 62943901dd
dssp: 4.0.5 -> 4.2.2.1 
https://github.com/PDB-REDO/dssp/compare/v4.0.5...v4.2.2.1
 2023-04-14 11:35:48 +09:00
Nick Cao 2833fc3981
Merge pull request #225841 from natsukium/mafft/update 
mafft: 7.515 -> 7.520
 2023-04-13 09:15:12 +08:00
Robert Scott 2107f7de60
Merge pull request #225865 from bzizou/samtools 
samtools: 1.13 -> 1.17
 2023-04-13 00:10:42 +01:00
Bruno Bzeznik d69d242b7b Samtools: 1.13 -> 1.17 
Changelogs:
 - https://github.com/samtools/samtools/releases/tag/1.14
 - https://github.com/samtools/samtools/releases/tag/1.15
 - https://github.com/samtools/samtools/releases/tag/1.15.1
 - https://github.com/samtools/samtools/releases/tag/1.16
 - https://github.com/samtools/samtools/releases/tag/1.16.1
 - https://github.com/samtools/samtools/releases/tag/1.17
 2023-04-12 12:00:25 +02:00
natsukium f962206f94
mafft: 7.515 -> 7.520 
https://gitlab.com/sysimm/mafft/-/tags/v7.520
 2023-04-12 13:28:24 +09:00
R. Ryantm 8fcdc3f62c varscan: 2.4.5 -> 2.4.6 2023-04-05 14:55:31 +00:00
Weijia Wang 150dcd7ce7
Merge pull request #224345 from natsukium/blast/darwin 
blast-bin: init at 2.13.0
 2023-04-03 09:59:08 +03:00
natsukium cddb4a24ba
blast-bin: init at 2.13.0 2023-04-03 12:39:17 +09:00
Justin Bedo e739dc5088
last: 1447 -> 1453 2023-04-03 08:38:27 +10:00
github-actions[bot] cead7e3e73
Merge master into staging-next 2023-03-25 00:02:20 +00:00
Weijia Wang 2ce97f2bf9
Merge pull request #222464 from r-ryantm/auto-update/diamond 
diamond: 2.1.5 -> 2.1.6
 2023-03-24 20:56:17 +02:00
github-actions[bot] 0537539006
Merge master into staging-next 2023-03-22 12:01:22 +00:00
Nick Cao 6c4095e7af
Merge pull request #222331 from r-ryantm/auto-update/seqkit 
seqkit: 2.3.1 -> 2.4.0
 2023-03-22 16:08:39 +08:00
R. Ryantm 4c2324cf14 diamond: 2.1.5 -> 2.1.6 2023-03-22 03:09:40 +00:00
R. Ryantm a6f33bd62f seqkit: 2.3.1 -> 2.4.0 2023-03-21 10:45:22 +00:00
Martin Weinelt 9959ec97f8
Merge remote-tracking branch 'origin/master' into staging-next 
Conflicts:
- pkgs/development/python-modules/wxPython/4.0.nix
- pkgs/development/python-modules/wxPython/4.1.nix
 2023-03-20 15:07:36 +01:00
Weijia Wang 802b7ac3e7
Merge pull request #221743 from r-ryantm/auto-update/gatk 
gatk: 4.3.0.0 -> 4.4.0.0
 2023-03-20 14:33:37 +02:00
github-actions[bot] 84c97a9e91
Merge master into staging-next 2023-03-19 18:00:59 +00:00
natsukium 21affa5ff1
trf: init at 4.09.1 2023-03-19 22:25:42 +09:00
github-actions[bot] c70342c89c
Merge master into staging-next 2023-03-19 00:02:27 +00:00
Weijia Wang 7574e25ef3
Merge pull request #221864 from natsukium/mafft/update 
mafft: 7.508 -> 7.515
 2023-03-19 00:03:19 +02:00
github-actions[bot] 403b148aa5
Merge master into staging-next 2023-03-18 18:01:02 +00:00
natsukium f3b75ef3ce
mafft: 7.508 -> 7.515 2023-03-19 00:42:29 +09:00
Fabian Affolter 109f8ccdfe
nest: specify license 2023-03-18 11:23:52 +01:00
Fabian Affolter c7ec291235
nest: add changelog to meta 2023-03-18 11:23:06 +01:00
Weijia Wang ea847dd1a0 nest: 3.3 -> 3.4 2023-03-18 12:13:46 +02:00
R. Ryantm 0d44f838ca gatk: 4.3.0.0 -> 4.4.0.0 2023-03-18 01:10:14 +00:00
github-actions[bot] f5629a4518
Merge master into staging-next 2023-03-17 06:01:16 +00:00
R. Ryantm 2a35b86739 subread: 2.0.3 -> 2.0.4 2023-03-16 23:09:44 +00:00
Vladimír Čunát 0f9354bfee
Merge #218309: ffmpeg: ffmpeg_4 → ffmpeg_5 
...into staging
 2023-03-16 11:11:31 +01:00
Martin Weinelt 6b67186fe9
Merge remote-tracking branch 'origin/master' into staging-next 
Conflicts:
- pkgs/development/python-modules/crownstone-cloud/default.nix
- pkgs/development/python-modules/exrex/default.nix
- pkgs/development/python-modules/mkdocs-minify/default.nix
- pkgs/development/python-modules/myjwt/default.nix
- pkgs/development/tools/analysis/checkov/default.nix
 2023-03-14 08:14:26 +01:00
Artturi b978bf0f0f
Merge pull request #220570 from Artturin/fixlints1 2023-03-14 02:15:55 +02:00
Atemu 9bd2506458 treewide: make ffmpeg_4-dependant packages depend on ffmpeg_4 
These packages were identified as broken when ffmpeg = ffmpeg_5.

Tested _only_ by building them. If you are a maintainer of one of these
packages, please test whether your package still works.
 2023-03-13 16:42:22 -06:00
Vladimír Čunát 1dd94ad62f
Merge branch 'master' into staging-next 2023-03-12 09:06:28 +01:00
R. Ryantm 77c83ddbc9 diamond: 2.1.4 -> 2.1.5 2023-03-11 18:22:58 +00:00
Artturin cab4a24c34 treewide: fix lints 
Arg to lib.optional is a list

build time tool in buildInputs
 2023-03-11 00:55:17 +02:00
Martin Weinelt 8a085cd8e3 Merge remote-tracking branch 'origin/master' into staging-next 2023-03-05 15:36:16 +01:00
R. Ryantm e175a2ea68 diamond: 2.1.3 -> 2.1.4 2023-03-04 15:44:53 +00:00
Martin Weinelt d0286ecd24 Merge remote-tracking branch 'origin/staging' into staging-next 2023-03-04 01:42:06 +00:00
R. Ryantm 99785ee90e picard-tools: 2.27.5 -> 3.0.0 2023-03-01 14:43:38 +00:00
Weijia Wang ccd9d6da1e
Merge pull request #218118 from r-ryantm/auto-update/diamond 
diamond: 2.1.1 -> 2.1.3
 2023-02-27 21:28:18 +02:00
Artturi 1c6a1e5650
Merge pull request #218500 from alyssais/pythonForBuild 2023-02-27 18:17:27 +02:00
Weijia Wang 21bb99733d
Merge pull request #218342 from r-ryantm/auto-update/bcftools 
bcftools: 1.16 -> 1.17
 2023-02-27 18:02:55 +02:00
Alyssa Ross 2bfa93e01c
treewide: python{ => .pythonForBuild}.interpreter 
It won't be enough to fix cross in all cases, but it is in at least
one: pywayland.  I've only made the change in cases I'm confident it's
correct, as it would be wrong to change this when python.interpreter
is used in wrappers, and possibly when it's used for running tests.
 2023-02-26 20:26:17 +00:00
R. Ryantm f2465e1ecf neuron-full: 8.2.1 -> 8.2.2 2023-02-26 05:18:37 +00:00
R. Ryantm 95ca5f576c bcftools: 1.16 -> 1.17 2023-02-25 23:02:27 +00:00
Weijia Wang c8ba046415
Merge pull request #217897 from DavidCromp/nest 
nest: fix Python & Darwin
 2023-02-25 19:47:22 +02:00
DavidCromp 5ce4a02687 nest: fix Python & Darwin 
Removed auto-patch-elf and replaced with find command that moves
libraries where they are expected by nest. Auto-patchelf isn't
supported on aarch64, so I copied my local derivation fix I've been
using.

PyNEST also requires numpy, so that has been added to
propagatedbuildinputs.

Also added support for OpenMP on Darwin.
 2023-02-25 10:28:59 -05:00
Artturi 8e027ec1d1
Merge pull request #218240 from amesgen/tandem-aligner-fix-build-gcc-12 2023-02-25 15:35:12 +02:00
amesgen a85b73c514
tandem-aligner: fix build with GCC 12 2023-02-25 13:40:11 +01:00
R. Ryantm 60ee2eaf54 diamond: 2.1.1 -> 2.1.3 2023-02-24 23:46:09 +00:00
Artturin f9fdf2d402 treewide: move NIX_CFLAGS_COMPILE to the env attrset 
with structuredAttrs lists will be bash arrays which cannot be exported
which will be a issue with some patches and some wrappers like cc-wrapper

this makes it clearer that NIX_CFLAGS_COMPILE must be a string as lists
in env cause a eval failure
 2023-02-22 21:23:04 +02:00
Artturin 6f6cc4a22d treewide: use toString on list NIX_CFLAGS_COMPILE 
with structuredAttrs lists will be bash arrays which cannot be exported
which will be a issue with some patches and some wrappers like cc-wrapper
 2023-02-22 21:23:04 +02:00
DavidCrompton1192@gmail.com 77aed40027 neuron: 7.5 -> 8.2.1 2023-02-21 13:52:34 -05:00
Ferry Jérémie bfac2d0034 treewide:replace http by https when https is a permanent redirection 2023-02-19 21:47:59 +01:00
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