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1076 Commits

Author SHA1 Message Date
natsukium
7cec88e50f
delly: enable openmp 2023-07-14 00:20:20 +09:00
natsukium
ae95c0d5a5
delly: refactor 2023-07-14 00:18:27 +09:00
natsukium
61be2ca18a
delly: enable darwin support 
- add passthru.tests
 2023-07-13 23:54:39 +09:00
natsukium
e7c8cbc2b1
cmtk: fix format 
- use finalAttrs instead of rec
- fix license
- remove trailing space from description
 2023-07-11 17:50:47 +09:00
natsukium
7014b723d9
cmtk: enable some compile options 
- use system zlib
- enabled bzip2
- enabled fftw
- enabled openmp for clang

- still disabled Grand Central Dispatch for linux because of build failure
- still disabled CUDA because of build failure
- still disabled mxml because of build failure
- still disabled lzma because of lack of lzmadec.h
- still disabled dcmtk because of build failure
 2023-07-11 17:50:47 +09:00
natsukium
6bf04fc9c9
cmtk: fix darwin build 2023-07-11 17:50:43 +09:00
R. Ryantm
b5e04f0bc7 kallisto: 0.48.0 -> 0.50.0 2023-07-09 17:19:43 +00:00
Weijia Wang
6d506a9d51
Merge pull request #242302 from r-ryantm/auto-update/nest-mpi 
nest-mpi: 3.4 -> 3.5
 2023-07-09 12:21:22 +03:00
R. Ryantm
ead7b7800d nest-mpi: 3.4 -> 3.5 2023-07-08 16:03:30 +00:00
R. Ryantm
47d5bee543 veryfasttree: 4.0 -> 4.0.1 2023-07-08 07:27:05 +00:00
Weijia Wang
1e0d363214
Merge pull request #241136 from r-ryantm/auto-update/veryfasttree 
veryfasttree: 3.1.1 -> 4.0
 2023-07-03 17:17:51 +03:00
Weijia Wang
82d4f6b43d veryfasttree: fix build on darwin 2023-07-03 12:29:44 +03:00
Martin Weinelt
bb40b8c205
Merge pull request #235322 from natsukium/dssp/update 
dssp: 4.2.2.1 -> 4.3.1; libcifpp: 5.0.8 -> 5.1.0.1; libmcfp: 1.2.3 -> 1.2.4
 2023-07-02 23:12:49 +02:00
figsoda
50acc2d57a pkgs/applications: replace "${version}" with version 2023-07-02 14:39:50 -04:00
R. Ryantm
cb16c50571 veryfasttree: 3.1.1 -> 4.0 2023-07-02 15:55:36 +00:00
natsukium
7b49fced0f
dssp: fix format 
- add changelog to meta
- use finalAttrs
 2023-07-01 16:40:29 +09:00
natsukium
fba5a4d702
dssp: 4.2.2.1 -> 4.3.1 
Diff: https://github.com/PDB-REDO/dssp/compare/v4.2.2.1...v4.3.1
 2023-07-01 16:36:36 +09:00
R. Ryantm
abfcd95c63 mosdepth: 0.3.3 -> 0.3.4 2023-06-28 10:52:42 +00:00
Weijia Wang
826bdb7214
Merge pull request #239691 from r-ryantm/auto-update/diamond 
diamond: 2.1.7 -> 2.1.8
 2023-06-26 07:46:03 +02:00
R. Ryantm
fa6b5a3cb3 last: 1453 -> 1456 2023-06-25 11:01:07 -03:00
R. Ryantm
754d578555 diamond: 2.1.7 -> 2.1.8 2023-06-25 04:35:30 +00:00
Mario Rodas
2bd4a56ee1
Merge pull request #237950 from bcdarwin/bppsuite-fix-homepage 
bppsuite: fix homepage
 2023-06-16 18:28:27 -05:00
Ben Darwin
9120f78e06 bppsuite: fix homepage 
Old homepage is down, so point to GitHub instead.
 2023-06-15 12:18:11 -04:00
natsukium
7b36afffd6
kalign: init at 3.3.5 2023-06-14 21:05:58 +09:00
natsukium
3d1b9f0819 macs2: rename from MACS2 2023-06-13 21:47:47 +00:00
natsukium
12cab182ae MACS2: 2.2.7.1 -> 2.2.8 
Diff: https://github.com/macs3-project/MACS/compare/v2.2.7.1...v2.2.8
changelog: https://github.com/macs3-project/MACS/releases/tag/v2.2.8
 2023-06-13 21:47:47 +00:00
natsukium
597e4e8652
aragorn: fix format 
- use finalAttrs instead of rec
- add runHook
 2023-06-08 18:42:29 +09:00
natsukium
bb317093e8
aragorn: 1.2.38 -> 1.2.41 
- change the source and homepage
- change the license
 2023-06-08 18:42:24 +09:00
natsukium
f2d7b3381b
cmtk: 3.3.1 -> 3.3.2 2023-06-08 15:34:29 +09:00
Weijia Wang
bff97d5215
Merge pull request #235727 from r-ryantm/auto-update/diamond 
diamond: 2.1.6 -> 2.1.7
 2023-06-04 19:10:45 +02:00
R. Ryantm
1f231abe57 fastp: 0.23.3 -> 0.23.4 2023-06-04 03:21:21 +00:00
R. Ryantm
33d8777af9 diamond: 2.1.6 -> 2.1.7 2023-06-03 08:46:43 +00:00
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