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varscan: init at 2.4.2

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Justin Bedo 2017-03-07 16:24:06 +11:00 committed by Robert Helgesson
parent 4bb50fd08c
commit 076e513b94
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2 changed files with 38 additions and 0 deletions
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36
pkgs/applications/science/biology/varscan/default.nix Normal file
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@ -0,0 +1,36 @@
{stdenv, fetchurl, jre, makeWrapper}:
stdenv.mkDerivation rec {
name = "varscan-${version}";
version = "2.4.2";
src = fetchurl {
url = "https://github.com/dkoboldt/varscan/releases/download/${version}/VarScan.v${version}.jar";
sha256 = "0cfhshinyqgwc6i7zf8lhbfybyly2x5anrz824zyvdhzz5i69zrl";
};
buildInputs = [ jre makeWrapper ];
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 stdenv.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;
};
}

2
pkgs/top-level/all-packages.nix
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@ -17008,6 +17008,8 @@ with pkgs;
samtools = callPackage ../applications/science/biology/samtools/default.nix { };
varscan = callPackage ../applications/science/biology/varscan/default.nix { };
bwa = callPackage ../applications/science/biology/bwa/default.nix { };
### SCIENCE/MATH