Commit graph

592 commits

Author SHA1 Message Date
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
Ryan Mulligan 64c446d0ba
Merge pull request #112021 from r-ryantm/auto-update/picard-tools
picard-tools: 2.24.1 -> 2.24.2
2021-02-07 14:57:32 -08:00
github-actions[bot] aaaf1218bf
Merge master into staging-next 2021-02-07 00:37:36 +00:00
R. RyanTM ef6ed50cb4 star: 2.7.6a -> 2.7.7a 2021-02-06 19:50:22 +00:00
Orivej Desh 8d0af26e1d blast: 2.10.0 -> 2.11.0
Fixes build with gcc10.
2021-02-06 19:20:56 +00:00
R. RyanTM 0adfe0f108 picard-tools: 2.24.1 -> 2.24.2 2021-02-05 12:35:00 +00:00
R. RyanTM ad28c0fb42 last: 1170 -> 1178 2021-01-30 07:52:29 +00:00
Phillip Cloud bba47f95f1 sortmerna: mark broken on darwin 2021-01-26 12:55:33 -05:00
Pavol Rusnak a6ce00c50c
treewide: remove stdenv where not needed 2021-01-25 18:31:47 +01:00
Sandro ad445d3728
Merge pull request #110735 from jbedo/bedtools
bedtools: 2.29.2 -> 2.30.0
2021-01-25 11:04:30 +01:00
Ryan Mulligan afebf1cc9a
Merge pull request #110529 from r-ryantm/auto-update/picard-tools
picard-tools: 2.24.0 -> 2.24.1
2021-01-24 18:06:28 -08:00
Justin Bedo d81e79af15
bedtools: 2.29.2 -> 2.30.0 2021-01-25 13:06:22 +11:00
volth bc0d605cf1 treewide: fix double quoted strings in meta.description
Signed-off-by: Ben Siraphob <bensiraphob@gmail.com>
2021-01-24 19:56:59 +07:00
Pavol Rusnak 90f7338112
treewide: stdenv.lib -> lib 2021-01-24 01:49:49 +01:00
Markus Kowalewski 6dba41fbcb
mpi: use mpi attribute consistently as the default MPI implementations
Use the attribute mpi to provide a system wide default MPI
implementation. The default is openmpi (as before).
This now allows for overriding the MPI implentation by using
the overlay mechanism. Build all packages with mpich instead
of the default openmpi can now be achived like this:
self: super:
 {
   mpi = super.mpich;
 }

All derivations that have been using "mpi ? null" to provide optional
building with MPI have been change in the following way to allow for
optional builds with MPI:
{ ...
, mpi
, useMpi ? false
}
2021-01-23 12:15:13 +01:00
R. RyanTM e1ea0a237a picard-tools: 2.24.0 -> 2.24.1 2021-01-22 19:10:27 +00:00
zowoq 932941b79c treewide: editorconfig fixes
- remove trailing whitespace
- use spaces for indentation
2021-01-21 13:29:54 +10:00