JakeHillion/nixpkgs
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576 Commits

Author SHA1 Message Date
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
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
R. RyanTM
12cde5ea85 messer-slim: 3.2.1 -> 3.6 2021-03-04 18:40:37 +00:00
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]
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
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
Jan Tojnar
e6c0c98940
Merge branch 'master' into staging-next 
zynaddsubfx conflict has been updated to 3.0.1, which conflicted with rewrite after 3.0.5 update on a different branch.
 2021-01-08 02:07:34 +01:00
Sandro
7ae17783a7
Merge pull request #108432 from jbedo/fastp 
fastp: init 0.20.1
 2021-01-07 21:44:33 +01:00
Jan Tojnar
f19eb635b4
Merge branch 'master' into staging-next 
b04fc593e7 seems to have accidentally changed mkDerivation function for dfilemanager and solarus-quest-editor so I have reverted that here.
 2021-01-07 13:04:31 +01:00
Justin Bedo
bdf3d727ca
fastp: init 0.20.1 2021-01-07 18:24:19 +11:00
Sandro
0af4d59732
Merge pull request #108437 from jbedo/varscan 
varscan: 2.4.2 -> 2.4.4
 2021-01-06 00:19:30 +01:00
Sandro
31d6b1cd06
Merge pull request #108435 from jbedo/last 
last: 1145 -> 1170
 2021-01-06 00:18:41 +01:00
Justin Bedo
56dd3fa172
varscan: 2.4.2 -> 2.4.4 2021-01-05 10:55:28 +11:00
Justin Bedo
62432c855f
last: 1145 -> 1170 2021-01-05 10:29:31 +11:00