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1054 commits

Author SHA1 Message Date
R. Ryantm d564dfa4d0 sambamba: 1.0.0 -> 1.0.1 2023-08-25 06:20:00 +00:00
OTABI Tomoya 21943b1829
Merge pull request #248172 from alxsimon/bwa 
bwa-mem2: init at version 2.2.1
 2023-08-24 09:28:34 +09:00
Alexis Simon 556dac0725 bwa-mem2: init at version 2.2.1 
Co-authored-by: OTABI Tomoya <tomoya.otabi@gmail.com>
 2023-08-23 15:02:06 -07:00
OTABI Tomoya 325b09c1b5
Merge pull request #249878 from jbedo/last 
last: 1460 -> 1471
 2023-08-21 16:09:10 +09:00
Emery Hemingway ed353dc721 mosdepth: build with Nim-2 2023-08-21 07:32:46 +01:00
Emery Hemingway 9025a583b1 nimPackages.hts: 0.3.4 -> 0.3.23, rename from hts-nim 2023-08-21 07:32:46 +01:00
Justin Bedo 8d9f56ac2d
last: 1460 -> 1471 
Diff: https://gitlab.com/mcfrith/last/-/compare/refs/tags/1460...1471
 2023-08-18 14:11:53 +10:00
natsukium 5462f67cc8
bamtools: init at 2.5.2 2023-08-18 00:17:15 +09:00
Theodore Ni 851d2f6b95
macs2: 2.2.8 -> 2.2.9.1 2023-08-11 14:45:45 -07:00
R. Ryantm 6d530a6389 seqkit: 2.5.0 -> 2.5.1 2023-08-10 04:42:38 +00:00
R. Ryantm a303664816 samtools: 1.17 -> 1.18 2023-08-07 01:22:06 +00:00
Mario Rodas 156a49aa49
Merge pull request #236810 from natsukium/cmtk/update 
cmtk: 3.3.1 -> 3.3.2; fix darwin build
 2023-08-06 11:51:18 -05:00
Weijia Wang 5c9ba9e55c
Merge pull request #246863 from r-ryantm/auto-update/picard-tools 
picard-tools: 3.0.0 -> 3.1.0
 2023-08-04 21:17:27 +02:00
Jan Malakhovski 5852f26bdc treewide: noop: refer to src.name or similar in sourceRoot where appropriate, part 1: trivial cases 2023-08-03 16:32:03 +00:00
R. Ryantm 29a0a9e29a picard-tools: 3.0.0 -> 3.1.0 2023-08-02 22:03:03 +00:00
Weijia Wang 66aedfd010
Merge pull request #246815 from r-ryantm/auto-update/veryfasttree 
veryfasttree: 4.0.1 -> 4.0.2
 2023-08-02 21:56:37 +02:00
Weijia Wang e4e313aeff
Merge pull request #246485 from r-ryantm/auto-update/bcftools 
bcftools: 1.17 -> 1.18
 2023-08-02 19:51:47 +02:00
Pol Dellaiera 9a772d7658
veryfasttree: use finalAttrs pattern 2023-08-02 18:51:11 +02:00
R. Ryantm 1fd16883d4 veryfasttree: 4.0.1 -> 4.0.2 2023-08-02 16:13:45 +00:00
Weijia Wang 23332e13fe
Merge pull request #243407 from natsukium/paml/update 
paml: 4.9j -> 4.10.7
 2023-08-01 22:09:44 +02:00
R. Ryantm 487c6ac2bd bcftools: 1.17 -> 1.18 2023-08-01 03:38:31 +00:00
R. Ryantm 40b736f0e8 last: 1456 -> 1460 2023-07-25 04:34:13 +00:00
github-actions[bot] 449a683b10
Merge master into staging-next 2023-07-24 00:02:26 +00:00
natsukium e54f06de69
dssp: 4.3.1 -> 4.4.2 
Diff: https://github.com/PDB-REDO/dssp/compare/refs/tags/v4.3.1...v4.4.2

Changelog: https://github.com/PDB-REDO/libcifpp/releases/tag/refs/tags/v4.4.2
 2023-07-23 21:24:23 +09:00
Tobias Mayer ba2ce6e73b
various packages: pin boost179 
Taken from PR #244831 and vcunat amended the miopen override.
 2023-07-22 16:54:22 +02:00
R. Ryantm 7a9d01d44c seqkit: 2.4.0 -> 2.5.0 2023-07-17 11:15:14 +00:00
natsukium d2c506948b
paml: refactor 2023-07-14 15:08:14 +09:00
natsukium f6e2b68122
paml: 4.9j -> 4.10.7 
Diff: d59d538939...4.10.7
Changelog: https://github.com/abacus-gene/paml/releases/tag/4.10.7
 2023-07-14 15:08:08 +09:00
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