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1158 Commits

Author SHA1 Message Date
R. Ryantm
b3249dde09 igv: 2.16.2 -> 2.17.0 2024-01-08 05:30:06 +00:00
Weijia Wang
a9c97eaee7
Merge pull request #276101 from r-ryantm/auto-update/delly 
delly: 1.1.8 -> 1.2.6
 2024-01-03 18:29:26 +01:00
Fabián Heredia Montiel
8f080df5b7
Merge pull request #276231 from r-ryantm/auto-update/samtools 
samtools: 1.18 -> 1.19
 2023-12-24 01:50:02 -06:00
R. Ryantm
02ddd820f8 seqkit: 2.6.0 -> 2.6.1 2023-12-23 08:17:11 +00:00
R. Ryantm
d4211ea181 samtools: 1.18 -> 1.19 2023-12-23 06:46:26 +00:00
R. Ryantm
eb84f26482 delly: 1.1.8 -> 1.2.6 2023-12-22 18:36:25 +00:00
OTABI Tomoya
9db0d0a0ec
Merge pull request #274810 from r-ryantm/auto-update/messer-slim 
messer-slim: 4.0.1 -> 4.1
 2023-12-21 10:58:25 +09:00
Justin Bedő
7dcf6462dd
Merge pull request #275350 from r-ryantm/auto-update/last 
last: 1518 -> 1519
 2023-12-20 10:04:19 +11:00
R. Ryantm
0ecf097e92 last: 1518 -> 1519 2023-12-19 07:59:25 +00:00
OTABI Tomoya
bda147b4f6
Merge pull request #273915 from r-ryantm/auto-update/bcftools 
bcftools: 1.18 -> 1.19
 2023-12-19 15:57:58 +09:00
R. Ryantm
dfa0eb5286 messer-slim: 4.0.1 -> 4.1 2023-12-16 20:13:33 +00:00
R. Ryantm
c618d890bc gatk: 4.4.0.0 -> 4.5.0.0 2023-12-15 04:20:42 +00:00
R. Ryantm
bb215123da bcftools: 1.18 -> 1.19 2023-12-13 06:48:21 +00:00
Weijia Wang
9a67c36f6d
Merge pull request #273382 from wegank/strelka-aarch64 
strelka: add aarch64-linux support
 2023-12-12 01:51:59 +01:00
OTABI Tomoya
bea3c001fd
Merge pull request #273485 from r-ryantm/auto-update/kalign 
kalign: 3.3.5 -> 3.4.0
 2023-12-12 08:56:04 +09:00
Weijia Wang
3ce2a25e50 strelka: add aarch64-linux support 2023-12-11 13:37:17 +01:00
R. Ryantm
0cd6e601a6 kalign: 3.3.5 -> 3.4.0 2023-12-11 06:26:11 +00:00
Aaron Jheng
930b7d743f
poretools: mark as broken 2023-12-11 04:28:39 +00:00
Sergei Trofimovich
a92211886b strelka: fix build on gcc-12 
Without the change build fails as:

    src/c++/lib/calibration/IndelErrorModel.hh💯33: error: 'numeric_limits' is not a member of 'std'
      100 |     double logErrorRate = -std::numeric_limits<double>::infinity();
          |                                 ^~~~~~~~~~~~~~
 2023-12-10 17:44:19 +01:00
R. Ryantm
5d669c5d95 last: 1499 -> 1518 2023-12-05 14:44:08 +00:00
Weijia Wang
e420273763
Merge pull request #266665 from r-ryantm/auto-update/seqkit 
seqkit: 2.5.1 -> 2.6.0
 2023-12-04 02:43:42 +01:00
Weijia Wang
e4a901b362
Merge pull request #264994 from r-ryantm/auto-update/kallisto 
kallisto: 0.50.0 -> 0.50.1
 2023-12-04 01:43:00 +01:00
Doron Behar
df20638983
Merge pull request #186462 from apraga/bio-bigfile-1.07 
bio-bigfile: init 1.07
 2023-11-30 13:39:01 +00:00
Emery Hemingway
0f089515b1 mosdepth: build with a lockfile 2023-11-28 16:48:10 +02:00
Stian Lågstad
54f913f862 igv: Fix missing wrapGAppsHook causing causing GLib-GIO-ERROR 
Fixes https://github.com/NixOS/nixpkgs/issues/270226
 2023-11-26 19:57:18 +01:00
OTABI Tomoya
09fecf05a2
Merge pull request #269640 from natsukium/dssp/update 
dssp: 4.4.4.1 -> 4.4.5
 2023-11-25 18:35:26 +09:00
natsukium
87a4074d00
dssp: 4.4.4.1 -> 4.4.5 
Diff: https://github.com/PDB-REDO/dssp/compare/refs/tags/v4.4.4.1...v4.4.5

Changelog: https://github.com/PDB-REDO/libcifpp/releases/tag/refs/tags/v4.4.5
 2023-11-24 22:34:06 +09:00
Alexis Praga
75fc8ae0f4 perlPackages.BioBigFile: Addressing reviewer change 2023-11-21 23:16:39 +01:00
Alexis Praga
cc4bd30387 perlPackages.BioBigfile: init at 1.07 
Perl interface to manipulate BigWig and BigBeg files (for genomics)
This will be used to package VEP : uttps://www.ensembl.org/info/docs/tools/vep/script/vep_download.html

For that, only kent version 335 works at the moment.
For this commit, 2 commits for kent are needed
- e027a5d836 : packaging kent header
- 2b2c6f4c28 : enabling patches in kent
 2023-11-21 23:16:12 +01:00
Adam Joseph
c7e0f6b905 treewide: s_targetPlatform_hostPlatform_ in non-compiler packages 
stdenv.targetPlatform really shouldn't be used by software that
doesn't generate or manipulate binaries.  I reviewed all uses of
targetPlatform outside of pkgs/development/compilers and pkgs/stdenv
and replaced those which weren't involved in something which fits
these criteria.
 2023-11-17 08:07:34 +00:00
R. Ryantm
282aede4e4 picard-tools: 3.1.0 -> 3.1.1 2023-11-15 14:35:32 +00:00
Alexis Praga
2b2c6f4c28 kent: enable patches if needed. 
This is required by BioBigFile, which needs an older Kent version.
 2023-11-12 21:46:39 +01:00
R. Ryantm
a7b54e1136 seqkit: 2.5.1 -> 2.6.0 2023-11-10 12:50:42 +00:00
R. Ryantm
70bc041b9c bedtools: 2.31.0 -> 2.31.1 2023-11-09 06:18:08 +00:00
Justin Bedő
5cd7971391
Merge pull request #264872 from r-ryantm/auto-update/last 
last: 1471 -> 1499
 2023-11-08 09:21:48 +11:00
Adam Joseph
bc2d598878 treewide: change pythonForBuild to pythonOnBuildForHost 2023-11-05 17:42:12 -08:00
OTABI Tomoya
9b586ea68f
Merge pull request #243431 from natsukium/kssd/update 
kssd: 1.1 -> 2.21; enable aarch64-linux support
 2023-11-03 20:15:48 +09:00
natsukium
10c3a40621
kssd: enable aarch64-linux support & tests 2023-11-03 19:34:28 +09:00
natsukium
847c506eae
kssd: refactor 2023-11-03 19:34:28 +09:00
natsukium
fdc1ddd305
kssd: 1.1 -> 2.21 
Diff: https://github.com/yhg926/public_kssd/compare/v1.1...v2.21
 2023-11-03 19:34:28 +09:00
R. Ryantm
901dcdf4df kallisto: 0.50.0 -> 0.50.1 2023-11-02 11:02:00 +00:00
R. Ryantm
c783a977dc last: 1471 -> 1499 2023-11-01 19:08:21 +00:00
R. Ryantm
454e029519 mmseqs2: 14-7e284 -> 15-6f452 2023-11-01 09:19:34 +00:00
Guillaume Girol
97da6c943d
Merge pull request #262311 from scalavision/update-deeptools 
deeptools: 3.5.1 -> 3.5.4
 2023-10-28 16:51:14 +02:00
OTABI Tomoya
ae84a36b66
Merge pull request #262697 from natsukium/dssp/update 
dssp: 4.4.3 -> 4.4.4.1; libcifpp: 5.2.1 -> 5.2.2
 2023-10-28 12:20:29 +09:00
Weijia Wang
90e0e54124
Merge pull request #261508 from r-ryantm/auto-update/raxml 
raxml: 8.2.12 -> 8.2.13
 2023-10-28 03:30:42 +02:00
R. Ryantm
bda407e1c8 delly: 1.1.7 -> 1.1.8 2023-10-25 10:07:12 +00:00
natsukium
30e00f04e3
dssp: 4.4.3 -> 4.4.4.1 
Diff: https://github.com/PDB-REDO/dssp/compare/refs/tags/v4.4.3...v4.4.4.1

Changelog: https://github.com/PDB-REDO/libcifpp/releases/tag/refs/tags/v4.4.4.1
 2023-10-22 18:22:11 +09:00
OTABI Tomoya
0686263a23
Merge pull request #227090 from natsukium/bowtie2/aarch64 
bowtie2: fix build on aarch64
 2023-10-21 10:29:31 +09:00
Dmitry Kalinkin
6392f18258
Merge pull request #262351 from h7x4/remove-nix-exec-bits 
treewide: remove execute bit for non-executable `*.nix` files
 2023-10-20 14:45:16 -04:00