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SnpEff: init at 4.3i

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Justin Bedo 2017-03-07 16:33:04 +11:00 committed by Robert Helgesson
parent 076e513b94
commit 1ac797861b
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2 changed files with 33 additions and 0 deletions
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31
pkgs/applications/science/biology/snpeff/default.nix Normal file
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@ -0,0 +1,31 @@
{stdenv, fetchurl, jre, unzip, makeWrapper}:
stdenv.mkDerivation rec {
name = "snpeff-${version}";
version = "4.3i";
src = fetchurl {
url = "mirror://sourceforge/project/snpeff/snpEff_latest_core.zip";
sha256 = "0i1slg201c8yjfr4wrg4xcgzwi0c8b9l3fb1i73fphq6q6zdblzb";
};
buildInputs = [ unzip jre makeWrapper ];
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 stdenv.lib; {
description = "Genetic variant annotation and effect prediction toolbox.";
license = licenses.lgpl3;
homepage = http://snpeff.sourceforge.net/;
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 { }; samtools = callPackage ../applications/science/biology/samtools/default.nix { };
snpeff = callPackage ../applications/science/biology/snpeff/default.nix { };
varscan = callPackage ../applications/science/biology/varscan/default.nix { }; varscan = callPackage ../applications/science/biology/varscan/default.nix { };
bwa = callPackage ../applications/science/biology/bwa/default.nix { }; bwa = callPackage ../applications/science/biology/bwa/default.nix { };