JakeHillion/nixpkgs
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31f5dd3f36
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540 Commits

Author SHA1 Message Date
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
Sandro Jäckel
a8d360eca3
raxml: cleanup 2021-01-04 11:02:16 +01:00
github-actions[bot]
07165c7226
Merge staging-next into staging 2021-01-03 18:38:32 +00:00
John Ericson
b03fdcc7f9
Merge pull request #108300 from siraben/parallel-cmake 
treewide: remove enableParallelBuilding = true if using cmake
 2021-01-03 13:22:09 -05:00
Pavol Rusnak
77364ac7c0
Merge pull request #108251 from prusnak/bowtie2 
bowtie2: 2.3.5.1 -> 2.4.2
 2021-01-03 13:47:45 +01:00
github-actions[bot]
0649757570
Merge staging-next into staging 2021-01-03 12:24:59 +00:00
Ben Siraphob
3ae5e6ce03 treewide: remove enableParallelBuilding = true if using cmake 2021-01-03 18:37:40 +07:00
Pavol Rusnak
9139eb5aee bowtie2: 2.3.5.1 -> 2.4.2 2021-01-02 22:18:32 +01:00
Pavol Rusnak
03b99f0721 bowtie: init at at 1.3.0 2021-01-02 19:46:59 +01:00
Ben Siraphob
b04fc593e7 treewide: cmake buildInputs to nativeBuildInputs, minor cleanups 2021-01-01 11:52:33 +07:00
Justin Bedo
3a65e29d4b
SPAdes: add python dependency 2020-12-21 08:29:57 +11:00
Mario Rodas
7666fb25d0
Merge pull request #106856 from jbedo/delly 
delly: 0.8.5 -> 0.8.6
 2020-12-14 08:10:03 -05:00
Justin Bedo
6ce06dccfc
delly: 0.8.5 -> 0.8.6 2020-12-14 09:55:57 +11:00
R. RyanTM
aa2148eb1f picard-tools: 2.23.8 -> 2.23.9 2020-12-10 23:06:36 +00:00
Ryan Mulligan
4ce30eb63a
Merge pull request #105672 from r-ryantm/auto-update/hmmer 
hmmer: 3.3.1 -> 3.3.2
 2020-12-02 05:45:57 -08:00
R. RyanTM
6f50c5b18e hmmer: 3.3.1 -> 3.3.2 2020-12-02 09:00:15 +00:00
Ben Darwin
ee7d83e648 ants: unbreak on Darwin 2020-12-01 14:17:54 -05:00
Justin Bedo
5fc6258043
bwa: expand supported platforms 2020-11-30 09:46:51 +11:00
R. RyanTM
212ba486d6 igv: 2.8.12 -> 2.8.13 2020-11-28 02:18:00 +00:00
Sandro
c2d728f195
Merge pull request #102140 from SuperSandro2000/patch-2 2020-11-26 01:00:22 +01:00
Sandro
d8b570e6c8
Merge pull request #98363 from jbedo/mosdepth 
mosdepth: 0.2.9 -> 0.3.1
 2020-11-25 23:55:47 +01:00
Sandro
e166f22759
tebreak: Fix tests 2020-11-25 21:36:38 +01:00
Sandro
5f2997686c
deeptools: Fix tests 2020-11-25 21:36:37 +01:00
R. RyanTM
3b17793827 star: 2.7.5c -> 2.7.6a 2020-11-23 20:40:05 +01:00
Ryan Mulligan
80b6df2a17
Merge pull request #103525 from r-ryantm/auto-update/samblaster 
samblaster: 0.1.24 -> 0.1.26
 2020-11-16 19:03:03 -08:00
Ryan Mulligan
47fe890182
Merge pull request #103751 from r-ryantm/auto-update/last 
last: 1133 -> 1145
 2020-11-14 15:08:46 -08:00
R. RyanTM
a698dfa0a2 last: 1133 -> 1145 2020-11-13 23:30:53 +00:00
R. RyanTM
82d1113013 igv: 2.8.11 -> 2.8.12 2020-11-13 18:25:51 +00:00
R. RyanTM
d1baaef83d samblaster: 0.1.24 -> 0.1.26 2020-11-12 01:43:02 +00:00
Ryan Mulligan
ba3fc8bf47
Merge pull request #102707 from r-ryantm/auto-update/picard-tools 
picard-tools: 2.23.4 -> 2.23.8
 2020-11-04 06:11:08 -08:00
R. RyanTM
6391d3c1b5 picard-tools: 2.23.4 -> 2.23.8 2020-11-04 04:53:50 +00:00
Kevin Cox
d7a0daf2a1
Merge pull request #102420 from freezeboy/remove-plink 
plink: remove (broken since 2014)
 2020-11-03 07:49:09 -05:00
R. RyanTM
8ef46be2a4 igv: 2.8.9 -> 2.8.11 2020-11-02 10:16:32 +00:00
freezeboy
1f7e201e9e plink: remove (broken since 2014) 2020-11-02 03:24:16 +01:00
Justin Bedo
32573f4b6e
last: 1066 -> 1133 2020-10-31 10:59:02 +11:00
Renato Alves
6e19ed0a52
lumpy: 0.3.0 -> 0.3.1 2020-10-30 01:28:00 +01:00
Renato Alves
a28e5b0a4f
samtools: 1.10 -> 1.11 2020-10-29 18:27:22 +01:00