lumpy: Initial packaging

pkgs/all-packages.nix

@@ -24,6 +24,8 @@ self: super: pkgs: with pkgs; {
   libxc4 = libxc404;
   libxc = libxc4;
 
+  lumpy = callPackage ./lumpy.nix { };
+
   #meraculous = callPackage ./meraculous.nix { let stdenv49 = overrideCC stdenv gcc49; in stdenv = stdenv49; boost = boost159.override { stdenv = stdenv49 }; };
 
   minia = callPackage ./minia.nix { };

pkgs/lumpy.nix

@@ -0,0 +1,55 @@
+{ stdenv, fetchFromGitHub, which, autoconf, automake
+, zlib, curl
+, python, hexdump, sambamba, samblaster, samtools }:
+
+stdenv.mkDerivation rec {
+  version = "0.3.0";
+  name = "lumpy-${version}";
+
+  src = fetchFromGitHub {
+    inherit name;
+    owner = "arq5x";
+    repo = "lumpy-sv";
+    rev = version;
+    fetchSubmodules = true;
+    sha256 = "1r6sssbnz017jpnsfb6dfjj0y7bzxgxxdikz4rak569m6kqkawqq";
+  };
+
+  installPhase = ''
+    mkdir -p "$out"
+    cp -r bin "$out"
+    substituteInPlace "$out/bin/lumpyexpress.config" \
+      --replace "$PWD/" "$out"
+    mkdir -p "$out/lib/lumpy"
+    for script in \
+      pairend_distro.py \
+      bamkit/bamgroupreads.py \
+      bamkit/bamfilterrg.py \
+      bamkit/bamlibs.py
+    do
+      cp "scripts/$script" "$out/lib/lumpy"
+      substituteInPlace "$out/bin/lumpyexpress.config" \
+        --replace "$out/scripts/$script" "$out/lib/lumpy/$script"
+    done
+  '';
+
+  buildInputs = [
+    which
+    autoconf
+    automake
+    zlib
+    curl
+    (python.withPackages (packages: with packages; [ numpy pysam ]))
+    hexdump
+    sambamba
+    samblaster
+    samtools
+  ];
+
+  meta = with stdenv.lib; {
+    description = "A probabilistic framework for structural variant discovery.";
+    homepage = https://github.com/arq5x/lumpy-sv;
+    platforms = platforms.all;
+    license = licenses.mit;
+  };
+}