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608 commits

Author SHA1 Message Date
Sandro d5bd34ebf2
treewide: convert phases that contain ":" to dont* = true (#130500) 2021-07-18 23:42:48 +02:00
R. RyanTM 7177212409 bcftools: 1.11 -> 1.13 2021-07-10 10:15:10 +00:00
scalavision c6ca3545ae
truvari: 2.0.2 -> 2.1.1 (#126839) 
Co-authored-by: Sandro <sandro.jaeckel@gmail.com>
 2021-06-15 22:14:20 +02:00
R. RyanTM 089915f634 bowtie2: 2.4.3 -> 2.4.4 2021-05-26 23:43:08 -07:00
Stéphan Kochen c47425a230 sambamba: fix darwin build 2021-05-22 20:56:09 +02:00
Stéphan Kochen 20f36556dc samblaster: fix darwin build 2021-05-18 13:41:51 +02:00
Sandro 83c5d21320
Merge pull request #123083 from stephank/fix-est-sfs-darwin 
est-sfs: fix darwin build
 2021-05-17 18:58:33 +02:00
R. RyanTM 9528bf9fd9 bowtie2: 2.4.2 -> 2.4.3 2021-05-16 02:53:03 -04:00
Stéphan Kochen d707979a73 est-sfs: fix darwin build 2021-05-15 12:10:05 +02:00
Stéphan Kochen 2adca7ae14
cd-hit: fix darwin build (#123026) 2021-05-14 17:27:16 -04:00
Justin Bedo 40eeb2c6d3
octopus: 0.7.3 -> 0.7.4 2021-05-11 08:46:00 +10:00
Luke Granger-Brown 884cf29501 dcm2niix: 1.0.20201102 -> 1.0.20210317 2021-05-02 11:10:40 +00:00
R. RyanTM ad5f251230 dcm2niix: 1.0.20200331 -> 1.0.20201102 2021-05-02 03:14:11 +00:00
Justin Bedo def7c82f88
octopus: 0.7.1 -> 0.7.3 2021-04-20 10:13:25 +10:00
Sandro 28fb287d4b
Merge pull request #118610 from GregorySchwartz/init/macs2 2021-04-14 21:15:38 +02:00
Gregory W. Schwartz b7763a8287 macs2: init at 2.2.7.1 
Update pkgs/applications/science/biology/macs2/default.nix

Co-authored-by: Sandro <sandro.jaeckel@gmail.com>

Update pkgs/applications/science/biology/macs2/default.nix

Co-authored-by: Sandro <sandro.jaeckel@gmail.com>

Update pkgs/applications/science/biology/macs2/default.nix

Co-authored-by: Sandro <sandro.jaeckel@gmail.com>

Update pkgs/applications/science/biology/macs2/default.nix

Co-authored-by: Sandro <sandro.jaeckel@gmail.com>

Renamed package, updated version, set pypi, and added import test.

Update pkgs/applications/science/biology/MACS2/default.nix

Co-authored-by: Sandro <sandro.jaeckel@gmail.com>

Add comment about error for checking.

Two spaces indent.
 2021-04-14 10:17:53 -04:00
Gregory Schwartz 9bf867612d
meme-suite: init at 5.1.1 (#118603) 
Co-authored-by: Sandro <sandro.jaeckel@gmail.com>
 2021-04-05 22:43:27 +02:00
Sandro Jäckel 3453b89f4b
lzma: deprecate alias 2021-04-04 19:49:52 +02:00
Ryan Mulligan f3262c2a3e
Merge pull request #117648 from r-ryantm/auto-update/picard-tools 
picard-tools: 2.25.0 -> 2.25.1
 2021-03-29 16:10:25 -07:00
Justin Bedo 76bd953162 bedops: init 2.4.39 2021-03-28 22:27:51 -04:00
R. RyanTM 49e4c1e323 picard-tools: 2.25.0 -> 2.25.1 2021-03-26 03:16:44 +00:00
Frederik Rietdijk 5a5cb718a5 bedtools: use python3 2021-03-25 10:42:32 +01:00
Frederik Rietdijk 2c00aed6b1 bcftools: use python3 2021-03-25 10:39:47 +01:00
Bruno Bzeznik f0eef16f9c SPAdes: 3.15.1 -> 3.15.2 + fix license and platform 2021-03-23 10:51:01 +01:00
Jan Tojnar 2445e9a681
Merge branch 'master' into staging-next 2021-03-18 19:24:39 +01:00
Thomas Mader 09acdfde94
sambamba: 0.7.1 -> 0.8.0 
Getting rid of dmd dependency and compile with ldc
 2021-03-18 17:41:30 +02:00
Martin Weinelt 0241873f7f
Merge branch 'master' into staging-next 2021-03-14 17:35:32 +01:00
Ryan Mulligan 0e63a1bb33
Merge pull request #115579 from r-ryantm/auto-update/stacks 
stacks: 2.53 -> 2.55
 2021-03-14 07:47:22 -07:00
Ryan Mulligan 03754f91eb
Merge pull request #115574 from r-ryantm/auto-update/SPAdes 
SPAdes: 3.14.1 -> 3.15.1
 2021-03-14 07:46:58 -07:00
github-actions[bot] aea4725648
Merge master into staging-next 2021-03-10 12:21:24 +00:00
Justin Bedo 4e1a560ae4
octopus: 0.7.0 -> 0.7.1 2021-03-10 08:44:18 +11:00
R. RyanTM cb9f13c609 stacks: 2.53 -> 2.55 2021-03-09 17:19:55 +00:00
R. RyanTM 95d96bbfe5 SPAdes: 3.14.1 -> 3.15.1 2021-03-09 17:01:01 +00:00
github-actions[bot] 5c2a7abde7
Merge master into staging-next 2021-03-08 18:22:56 +00:00
R. RyanTM 12cde5ea85 messer-slim: 3.2.1 -> 3.6 2021-03-04 18:40:37 +00:00
Robert Schütz 54757b35c1 Merge branch 'staging-next' into staging 2021-02-26 10:56:17 +01:00
Frederik Rietdijk c456a2512f Merge master into staging-next 2021-02-26 10:25:13 +01:00
R. RyanTM 615ff1b2ab star: 2.7.7a -> 2.7.8a 2021-02-23 10:38:00 +00:00
github-actions[bot] ed07c63105
Merge staging-next into staging 2021-02-22 06:17:08 +00:00
github-actions[bot] 227aa2c9b0
Merge master into staging-next 2021-02-22 06:17:05 +00:00
R. RyanTM ff27c8e0ad last: 1178 -> 1179 2021-02-21 21:24:17 +00:00
Ben Siraphob 127733211e
treewide: unzip buildInputs to nativeBuildInputs (#112302) 2021-02-20 16:01:53 -05:00
github-actions[bot] abe7db36a4
Merge staging-next into staging 2021-02-20 00:36:40 +00:00
Ben Siraphob 223f25cf4a treewide: add targetPrefix to hardcoded references to CC=cc 2021-02-20 01:01:46 +07:00
Ben Siraphob e03c068af5 treewide: makeWrapper buildInputs to nativeBuildInputs 2021-02-19 20:09:16 +07:00
github-actions[bot] 318f95e4c2
Merge master into staging-next 2021-02-13 06:16:33 +00:00
R. RyanTM d1067751c6 picard-tools: 2.24.2 -> 2.25.0 2021-02-11 21:10:44 +00:00
github-actions[bot] 30dddce5e8
Merge master into staging-next 2021-02-09 06:16:02 +00:00
Mario Rodas f9a095da28
Merge pull request #112191 from r-ryantm/auto-update/star 
star: 2.7.6a -> 2.7.7a
 2021-02-08 20:17:49 -05:00
github-actions[bot] 1c86cb40e9
Merge master into staging-next 2021-02-08 00:36:16 +00:00