40 lines
1020 B
Nix
40 lines
1020 B
Nix
|
{
|
||
|
|
lib,
|
||
|
|
stdenv,
|
||
|
|
fetchurl,
|
||
|
|
jre,
|
||
|
|
makeWrapper,
|
||
|
|
}:
|
||
|
|
|
||
|
|
stdenv.mkDerivation rec {
|
||
|
|
pname = "picard-tools";
|
||
|
|
version = "3.4.0";
|
||
|
|
|
||
|
|
src = fetchurl {
|
||
|
|
url = "https://github.com/broadinstitute/picard/releases/download/${version}/picard.jar";
|
||
|
|
sha256 = "sha256-52EowoOIn8WDyd6jOjt0SJdMBn0QLJ41vhUmQtTV+QE=";
|
||
|
|
};
|
||
|
|
|
||
|
|
nativeBuildInputs = [ makeWrapper ];
|
||
|
|
buildInputs = [ jre ];
|
||
|
|
|
||
|
|
dontUnpack = true;
|
||
|
|
|
||
|
|
installPhase = ''
|
||
|
|
mkdir -p $out/libexec/picard
|
||
|
|
cp $src $out/libexec/picard/picard.jar
|
||
|
|
mkdir -p $out/bin
|
||
|
|
makeWrapper ${jre}/bin/java $out/bin/picard --add-flags "-jar $out/libexec/picard/picard.jar"
|
||
|
|
'';
|
||
|
|
|
||
|
|
meta = with lib; {
|
||
|
|
description = "Tools for high-throughput sequencing (HTS) data and formats such as SAM/BAM/CRAM and VCF";
|
||
|
|
license = licenses.mit;
|
||
|
|
homepage = "https://broadinstitute.github.io/picard/";
|
||
|
|
sourceProvenance = with sourceTypes; [ binaryBytecode ];
|
||
|
|
maintainers = with maintainers; [ jbedo ];
|
||
|
|
mainProgram = "picard";
|
||
|
|
platforms = platforms.all;
|
||
|
|
};
|
||
|
|
}
|