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

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{lib, stdenv, fetchurl, jre, makeWrapper}:
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stdenv.mkDerivation rec {
pname = "varscan";
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version = "2.4.4";
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src = fetchurl {
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url = "https://github.com/dkoboldt/varscan/raw/master/VarScan.v${version}.jar";
sha256 = "sha256-+yO3KrZ2+1qJvQIJHCtsmv8hC5a+4E2d7mrvTYtygU0=";
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};
nativeBuildInputs = [ makeWrapper ];
buildInputs = [ jre ];
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phases = [ "installPhase" ];
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; {
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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";
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maintainers = with maintainers; [ jbedo ];
platforms = platforms.all;
};
}