dev/nixpkgs
1
0
Fork 0
Code Issues Pull Requests Actions 2 Packages Projects Releases Wiki Activity
558,296 Commits 3 Branches 0 Tags 4.3 GiB
930b7d743f
Commit Graph

1140 Commits

Author SHA1 Message Date
Aaron Jheng
930b7d743f
poretools: mark as broken 2023-12-11 04:28:39 +00:00
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
h7x4
e6321d2788
treewide: remove execute bit for non-executable *.nix files 2023-10-20 19:55:39 +02:00
OTABI Tomoya
0a18e1f929
Merge pull request #249750 from natsukium/bioawk/init 
bioawk: init at unstable-2017-09-11
 2023-10-20 17:59:30 +09:00
natsukium
056f9e21c0
bowtie2: enable tests 2023-10-20 17:08:20 +09:00
natsukium
13fe1effaf
bowtie2: fix build on aarch64 2023-10-20 17:07:55 +09:00
natsukium
aae51697be
bowtie2: refactor 2023-10-20 17:06:09 +09:00
scalavision
9fd3ea0f76 deeptools: 3.5.1 -> 3.5.4 2023-10-18 19:06:01 +02:00
R. Ryantm
355e594816 raxml: 8.2.12 -> 8.2.13 2023-10-16 22:16:12 +00:00
R. Ryantm
d89c2af58a bowtie2: 2.5.1 -> 2.5.2 2023-10-14 10:06:32 +00:00
OTABI Tomoya
e8f331680d
Merge pull request #259418 from natsukium/blast-bin/update 
blast-bin: 2.13.0 -> 2.14.1
 2023-10-12 23:49:59 +09:00
natsukium
d60c85fb75
blast-bin: add sourceProvenance to meta 2023-10-07 10:12:24 +09:00
natsukium
3dc0f1e7b7
blast-bin: 2.13.0 -> 2.14.1 
Changelog: https://www.ncbi.nlm.nih.gov/books/NBK131777/#_Blast_ReleaseNotes_BLAST_2_14_1_August_2_
 2023-10-07 01:59:18 +09:00
natsukium
96178c29a4
truvari: 4.0.0 -> 4.1.0 
Diff: https://github.com/ACEnglish/truvari/compare/v4.0.0...v4.1.0

Changelog: https://github.com/ACEnglish/truvari/releases/tag/v4.1.0
 2023-10-07 01:30:27 +09:00
natsukium
776b2694a3
truvari: add meta.changelog 2023-10-07 01:30:27 +09:00
Justin Bedo
e347cca9f8
delly: 1.1.6 -> 1.1.7 
Diff: https://github.com/dellytools/delly/compare/v1.1.6...1.1.7
 2023-10-06 14:12:05 +11:00
Weijia Wang
0396d3b0fb
Merge pull request #258254 from r-ryantm/auto-update/nest-mpi 
nest-mpi: 3.5 -> 3.6
 2023-10-01 03:53:05 +02:00
Weijia Wang
d2f79d7443
Merge pull request #257369 from r-ryantm/auto-update/stacks 
stacks: 2.62 -> 2.65
 2023-10-01 03:20:19 +02:00
Weijia Wang
293062bbdb stacks: set platforms 2023-10-01 02:26:34 +02:00
Weijia Wang
00d57438ab
Merge pull request #256805 from r-ryantm/auto-update/neuron-mpi 
neuron-mpi: 8.2.2 -> 8.2.3
 2023-10-01 00:44:58 +02:00