Commit graph

535 commits

Author SHA1 Message Date
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
Ben Siraphob db74029e3e treewide: remove package names from prefix of descriptions 2020-10-27 09:15:07 -07:00
Ben Siraphob 683a87dbeb treewide: remove periods from end of package descriptions 2020-10-17 08:22:31 -07:00
Ryan Mulligan f9728adae7
Merge pull request #99128 from jbedo/delly
delly: 0.8.2 -> 0.8.5
2020-10-16 06:30:11 -07:00
R. RyanTM a3dca9576b deeptools: 3.4.1 -> 3.5.0 2020-10-16 00:42:47 -07:00
Doron Behar 1db3202722
Merge pull request #75843 from jbedo/lumpy 2020-10-15 19:46:13 +03:00