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4a7f99d55d
nixpkgs/pkgs/applications/science/biology
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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
..
ants treewide: with stdenv.lib; in meta -> with lib; 2021-01-11 10:38:22 +01:00
aragorn treewide: with stdenv.lib; in meta -> with lib; 2021-01-11 10:38:22 +01:00
bayescan treewide: with stdenv.lib; in meta -> with lib; 2021-01-11 10:38:22 +01:00
bcftools treewide: with stdenv.lib; in meta -> with lib; 2021-01-11 10:38:22 +01:00
bedtools treewide: with stdenv.lib; in meta -> with lib; 2021-01-11 10:38:22 +01:00
bftools treewide: with stdenv.lib; in meta -> with lib; 2021-01-11 10:38:22 +01:00
blast treewide: with stdenv.lib; in meta -> with lib; 2021-01-11 10:38:22 +01:00
bowtie treewide: with stdenv.lib; in meta -> with lib; 2021-01-11 10:38:22 +01:00
bowtie2 treewide: with stdenv.lib; in meta -> with lib; 2021-01-11 10:38:22 +01:00
bppsuite bppsuite: init at 2.4.1 2020-05-25 21:13:02 -04:00
bwa treewide: with stdenv.lib; in meta -> with lib; 2021-01-11 10:38:22 +01:00
cd-hit treewide: with stdenv.lib; in meta -> with lib; 2021-01-11 10:38:22 +01:00
clustal-omega treewide: with stdenv.lib; in meta -> with lib; 2021-01-11 10:38:22 +01:00
cmtk treewide: with stdenv.lib; in meta -> with lib; 2021-01-11 10:38:22 +01:00
conglomerate treewide: with stdenv.lib; in meta -> with lib; 2021-01-11 10:38:22 +01:00
dcm2niix treewide: with stdenv.lib; in meta -> with lib; 2021-01-11 10:38:22 +01:00
deeptools deeptools: Fix tests 2020-11-25 21:36:37 +01:00
delly treewide: with stdenv.lib; in meta -> with lib; 2021-01-11 10:38:22 +01:00
diamond treewide: with stdenv.lib; in meta -> with lib; 2021-01-11 10:38:22 +01:00
ecopcr treewide: with stdenv.lib; in meta -> with lib; 2021-01-11 10:38:22 +01:00
eggnog-mapper treewide: with stdenv.lib; in meta -> with lib; 2021-01-11 10:38:22 +01:00
emboss emboss: fix license 2020-06-26 11:05:24 +02:00
est-sfs treewide: with stdenv.lib; in meta -> with lib; 2021-01-11 10:38:22 +01:00
exonerate treewide: with stdenv.lib; in meta -> with lib; 2021-01-11 10:38:22 +01:00
EZminc treewide: with stdenv.lib; in meta -> with lib; 2021-01-11 10:38:22 +01:00
fastp treewide: with stdenv.lib; in meta -> with lib; 2021-01-11 10:38:22 +01:00
freebayes treewide: with stdenv.lib; in meta -> with lib; 2021-01-11 10:38:22 +01:00
hisat2 treewide: with stdenv.lib; in meta -> with lib; 2021-01-11 10:38:22 +01:00
hmmer treewide: with stdenv.lib; in meta -> with lib; 2021-01-11 10:38:22 +01:00
igv treewide: with stdenv.lib; in meta -> with lib; 2021-01-11 10:38:22 +01:00
inormalize treewide: with stdenv.lib; in meta -> with lib; 2021-01-11 10:38:22 +01:00
itsx treewide: with stdenv.lib; in meta -> with lib; 2021-01-11 10:38:22 +01:00
iv treewide: Per RFC45, remove all unquoted URLs 2020-04-10 17:54:53 +01:00
kallisto treewide: with stdenv.lib; in meta -> with lib; 2021-01-11 10:38:22 +01:00
kent treewide: with stdenv.lib; in meta -> with lib; 2021-01-11 10:38:22 +01:00
kssd treewide: with stdenv.lib; in meta -> with lib; 2021-01-11 10:38:22 +01:00
last treewide: with stdenv.lib; in meta -> with lib; 2021-01-11 10:38:22 +01:00
lumpy treewide: with stdenv.lib; in meta -> with lib; 2021-01-11 10:38:22 +01:00
macse treewide: with stdenv.lib; in meta -> with lib; 2021-01-11 10:38:22 +01:00
manta treewide: with stdenv.lib; in meta -> with lib; 2021-01-11 10:38:22 +01:00
megahit treewide: with stdenv.lib; in meta -> with lib; 2021-01-11 10:38:22 +01:00
messer-slim treewide: remove enableParallelBuilding = true if using cmake 2021-01-03 18:37:40 +07:00
migrate treewide: Per RFC45, remove all unquoted URLs 2020-04-10 17:54:53 +01:00
minc-tools treewide: with stdenv.lib; in meta -> with lib; 2021-01-11 10:38:22 +01:00
minc-widgets treewide: with stdenv.lib; in meta -> with lib; 2021-01-11 10:38:22 +01:00
minia treewide: with stdenv.lib; in meta -> with lib; 2021-01-11 10:38:22 +01:00
minimap2 treewide: with stdenv.lib; in meta -> with lib; 2021-01-11 10:38:22 +01:00
mni_autoreg treewide: with stdenv.lib; in meta -> with lib; 2021-01-11 10:38:22 +01:00
mosdepth treewide: with stdenv.lib; in meta -> with lib; 2021-01-11 10:38:22 +01:00
mrbayes treewide: with stdenv.lib; in meta -> with lib; 2021-01-11 10:38:22 +01:00
mrtrix mrtrix: 3.0.0 -> 3.0.2 2020-09-30 22:13:18 -04:00
muscle treewide: with stdenv.lib; in meta -> with lib; 2021-01-11 10:38:22 +01:00
N3 treewide: with stdenv.lib; in meta -> with lib; 2021-01-11 10:38:22 +01:00
ncbi-tools treewide: Per RFC45, remove all unquoted URLs 2020-04-10 17:54:53 +01:00
neuron treewide: with stdenv.lib; in meta -> with lib; 2021-01-11 10:38:22 +01:00
niftyreg treewide: with stdenv.lib; in meta -> with lib; 2021-01-11 10:38:22 +01:00
niftyseg treewide: with stdenv.lib; in meta -> with lib; 2021-01-11 10:38:22 +01:00
obitools treewide: remove enableParallelBuilding = true if using cmake 2021-01-03 18:37:40 +07:00
octopus treewide: with stdenv.lib; in meta -> with lib; 2021-01-11 10:38:22 +01:00
paml treewide: Per RFC45, remove all unquoted URLs 2020-04-10 17:54:53 +01:00
picard-tools treewide: with stdenv.lib; in meta -> with lib; 2021-01-11 10:38:22 +01:00
platypus treewide: with stdenv.lib; in meta -> with lib; 2021-01-11 10:38:22 +01:00
plink-ng treewide: use blas and lapack 2020-04-17 16:24:09 -05:00
poretools treewide: Per RFC45, remove all unquoted URLs 2020-04-10 17:54:53 +01:00
prodigal treewide: with stdenv.lib; in meta -> with lib; 2021-01-11 10:38:22 +01:00
quast Quast: init at 5.0.2 2020-04-24 10:11:54 +02:00
raxml treewide: with stdenv.lib; in meta -> with lib; 2021-01-11 10:38:22 +01:00
sambamba treewide: with stdenv.lib; in meta -> with lib; 2021-01-11 10:38:22 +01:00
samblaster treewide: with stdenv.lib; in meta -> with lib; 2021-01-11 10:38:22 +01:00
samtools treewide: with stdenv.lib; in meta -> with lib; 2021-01-11 10:38:22 +01:00
seaview treewide: with stdenv.lib; in meta -> with lib; 2021-01-11 10:38:22 +01:00
snpeff treewide: with stdenv.lib; in meta -> with lib; 2021-01-11 10:38:22 +01:00
somatic-sniper treewide: with stdenv.lib; in meta -> with lib; 2021-01-11 10:38:22 +01:00
sortmerna treewide: with stdenv.lib; in meta -> with lib; 2021-01-11 10:38:22 +01:00
spades treewide: with stdenv.lib; in meta -> with lib; 2021-01-11 10:38:22 +01:00
stacks stacks: 2.52 -> 2.53 2020-05-10 09:37:29 -07:00
star treewide: with stdenv.lib; in meta -> with lib; 2021-01-11 10:38:22 +01:00
strelka treewide: with stdenv.lib; in meta -> with lib; 2021-01-11 10:38:22 +01:00
sumatools treewide: with stdenv.lib; in meta -> with lib; 2021-01-11 10:38:22 +01:00
svaba treewide: with stdenv.lib; in meta -> with lib; 2021-01-11 10:38:22 +01:00
tebreak treewide: with stdenv.lib; in meta -> with lib; 2021-01-11 10:38:22 +01:00
trimal treewide: with stdenv.lib; in meta -> with lib; 2021-01-11 10:38:22 +01:00
truvari truvari: 1.3.4 -> 2.0.2, fixing build 2020-09-20 12:25:17 +01:00
varscan treewide: with stdenv.lib; in meta -> with lib; 2021-01-11 10:38:22 +01:00
vcftools treewide: with stdenv.lib; in meta -> with lib; 2021-01-11 10:38:22 +01:00
whisper treewide: with stdenv.lib; in meta -> with lib; 2021-01-11 10:38:22 +01:00
xenomapper python.pkgs wide: fix problematic urls 2020-01-10 21:02:12 -08:00