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
R. RyanTM
427bbe059a
picard-tools: 2.23.9 -> 2.24.0
2021-01-20 20:42:01 +00:00
zowoq
759a2cd563
ecopcr: use spaces for indentation
2021-01-20 10:53:10 +10:00
zowoq
31f5dd3f36
treewide: editorconfig fixes
...
- remove trailing whitespace
- use spaces for indentation
2021-01-20 09:11:11 +10:00
Jonathan Ringer
9bb3fccb5b
treewide: pkgs.pkgconfig -> pkgs.pkg-config, move pkgconfig to alias.nix
...
continuation of #109595
pkgconfig was aliased in 2018, however, it remained in
all-packages.nix due to its wide usage. This cleans
up the remaining references to pkgs.pkgsconfig and
moves the entry to aliases.nix.
python3Packages.pkgconfig remained unchanged because
it's the canonical name of the upstream package
on pypi.
2021-01-19 01:16:25 -08:00
Jonathan Ringer
200bb8c977
cd-hit: remove non-existent package
2021-01-19 01:16:25 -08:00
R. RyanTM
a0e1bb6a4b
delly: 0.8.6 -> 0.8.7
2021-01-18 14:22:30 +00:00
Ben Siraphob
badf51221d
treewide: stdenv.lib -> lib
2021-01-16 17:58:11 +07:00
Profpatsch
4a7f99d55d
treewide: with stdenv.lib; in meta -> with lib;
...
Part of: https://github.com/NixOS/nixpkgs/issues/108938
meta = with stdenv.lib;
is a widely used pattern. We want to slowly remove
the `stdenv.lib` indirection and encourage people
to use `lib` directly. Thus let’s start with the meta
field.
This used a rewriting script to mostly automatically
replace all occurances of this pattern, and add the
`lib` argument to the package header if it doesn’t
exist yet.
The script in its current form is available at
https://cs.tvl.fyi/depot@2f807d7f141068d2d60676a89213eaa5353ca6e0/-/blob/users/Profpatsch/nixpkgs-rewriter/default.nix
2021-01-11 10:38:22 +01:00
