From 1ac797861b1e020c433ccda24b3ea74032fc7354 Mon Sep 17 00:00:00 2001
From: Justin Bedo <cu@cua0.org>
Date: Tue, 7 Mar 2017 16:33:04 +1100
Subject: SnpEff: init at 4.3i

---
 .../science/biology/snpeff/default.nix             | 31 ++++++++++++++++++++++
 1 file changed, 31 insertions(+)
 create mode 100644 pkgs/applications/science/biology/snpeff/default.nix

(limited to 'pkgs/applications/science/biology')

diff --git a/pkgs/applications/science/biology/snpeff/default.nix b/pkgs/applications/science/biology/snpeff/default.nix
new file mode 100644
index 000000000000..6c7a6b969ee6
--- /dev/null
+++ b/pkgs/applications/science/biology/snpeff/default.nix
@@ -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;
+  };
+
+}
-- 
cgit 1.4.1