37 lines
1.2 KiB
Nix
37 lines
1.2 KiB
Nix
{lib, stdenv, fetchurl, jre, makeWrapper}:
|
|
|
|
stdenv.mkDerivation rec {
|
|
pname = "varscan";
|
|
version = "2.4.4";
|
|
|
|
src = fetchurl {
|
|
url = "https://github.com/dkoboldt/varscan/raw/master/VarScan.v${version}.jar";
|
|
sha256 = "sha256-+yO3KrZ2+1qJvQIJHCtsmv8hC5a+4E2d7mrvTYtygU0=";
|
|
};
|
|
|
|
nativeBuildInputs = [ makeWrapper ];
|
|
buildInputs = [ jre ];
|
|
|
|
dontUnpack = true;
|
|
|
|
installPhase = ''
|
|
mkdir -p $out/libexec/varscan
|
|
cp $src $out/libexec/varscan/varscan.jar
|
|
mkdir -p $out/bin
|
|
makeWrapper ${jre}/bin/java $out/bin/varscan --add-flags "-jar $out/libexec/varscan/varscan.jar"
|
|
'';
|
|
|
|
meta = with lib; {
|
|
description = "Variant calling and somatic mutation/CNV detection for next-generation sequencing data";
|
|
# VarScan 2 is free for non-commercial use by academic,
|
|
# government, and non-profit/not-for-profit institutions. A
|
|
# commercial version of the software is available, and licensed
|
|
# through the Office of Technology Management at Washington
|
|
# University School of Medicine.
|
|
license = licenses.unfree;
|
|
homepage = "https://github.com/dkoboldt/varscan";
|
|
maintainers = with maintainers; [ jbedo ];
|
|
platforms = platforms.all;
|
|
};
|
|
|
|
}
|