nixpkgs/pkgs/applications/science/biology/snpeff/default.nix
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

34 lines
986 B
Nix

{lib, stdenv, fetchurl, jre, unzip, makeWrapper}:
stdenv.mkDerivation rec {
pname = "snpeff";
version = "4.3t";
src = fetchurl {
url = "mirror://sourceforge/project/snpeff/snpEff_v${builtins.replaceStrings [ "." ] [ "_" ] version}_core.zip";
sha256 = "0i12mv93bfv8xjwc3rs2x73d6hkvi7kgbbbx3ry984l3ly4p6nnm";
};
buildInputs = [ unzip jre makeWrapper ];
sourceRoot = "snpEff";
installPhase = ''
mkdir -p $out/libexec/snpeff
cp *.jar *.config $out/libexec/snpeff
mkdir -p $out/bin
makeWrapper ${jre}/bin/java $out/bin/snpeff --add-flags "-jar $out/libexec/snpeff/snpEff.jar"
makeWrapper ${jre}/bin/java $out/bin/snpsift --add-flags "-jar $out/libexec/snpeff/SnpSift.jar"
'';
meta = with lib; {
description = "Genetic variant annotation and effect prediction toolbox";
license = licenses.lgpl3;
homepage = "http://snpeff.sourceforge.net/";
maintainers = with maintainers; [ jbedo ];
platforms = platforms.all;
};
}