From 27960b6acfd00fa67acfaf345da3fb3e4f7fac4e Mon Sep 17 00:00:00 2001
From: Justin Bedo <cu@cua0.org>
Date: Tue, 31 Jul 2018 13:11:16 +1000
Subject: [PATCH] strelka: init 2.9.5

---
 .../science/biology/strelka/default.nix       | 37 +++++++++++++++++++
 pkgs/top-level/all-packages.nix               |  2 +
 2 files changed, 39 insertions(+)
 create mode 100644 pkgs/applications/science/biology/strelka/default.nix

diff --git a/pkgs/applications/science/biology/strelka/default.nix b/pkgs/applications/science/biology/strelka/default.nix
new file mode 100644
index 000000000000..1527f5d3ddad
--- /dev/null
+++ b/pkgs/applications/science/biology/strelka/default.nix
@@ -0,0 +1,37 @@
+{stdenv, fetchFromGitHub, cmake, zlib, python2}:
+
+stdenv.mkDerivation rec {
+  name = "strelka-${version}";
+  version = "2.9.5";
+
+  src = fetchFromGitHub {
+    owner = "Illumina";
+    repo = "strelka";
+    rev = "v${version}";
+    sha256 = "0x4a6nkx1jnyag9svghsdjz1fz6q7qx5pn77wphdfnk81f9yspf8";
+  };
+
+  buildInputs = [ cmake zlib python2 ];
+
+  preConfigure = ''
+    sed -i 's|/usr/bin/env python|${python2}/bin/python|' src/python/lib/makeRunScript.py
+    patchShebangs .
+  '';
+
+  postFixup = ''
+    pushd $out/lib/python/pyflow
+    sed -i 's|/bin/bash|${stdenv.shell}|' pyflowTaskWrapper.py
+    rm pyflowTaskWrapper.pyc
+    echo "import pyflowTaskWrapper" | python2
+    popd
+  '';
+
+  meta = with stdenv.lib; {
+    description = "Germline and small variant caller";
+    license = licenses.gpl3;
+    homepage = https://github.com/Illumina/strelka;
+    maintainers = with maintainers; [ jbedo ];
+    platforms = [ "x86_64-linux" ];
+  };
+
+}
diff --git a/pkgs/top-level/all-packages.nix b/pkgs/top-level/all-packages.nix
index dde837269367..53ea7cb5ded0 100644
--- a/pkgs/top-level/all-packages.nix
+++ b/pkgs/top-level/all-packages.nix
@@ -20393,6 +20393,8 @@ with pkgs;
 
   star = callPackage ../applications/science/biology/star { };
 
+  strelka = callPackage ../applications/science/biology/strelka { };
+
   varscan = callPackage ../applications/science/biology/varscan { };
 
   hmmer = callPackage ../applications/science/biology/hmmer { };