sambamba: Add package from asobhani/nix-bioinfo-pkgs-sharcnet

pkgs/sambamba/default.nix

@@ -0,0 +1,72 @@
+{ stdenv, fetchFromGitHub, callPackage
+, bash, python, glibc, dmd, which, rdmd, zlib }:
+
+let
+
+  ldc = callPackage ./ldc.nix { };
+
+in
+
+  stdenv.mkDerivation rec {
+    version = "0.6.6";
+    name = "sambamba-${version}";
+
+    srcs = [
+        (fetchFromGitHub {
+          owner = "lomereiter";
+          repo = "sambamba";
+          rev = "63cfd5c7b3053e1f7045dec0b5a569f32ef73d06";
+          sha256 = "0mla4d8pn3gcdxpwk1dpk7xcxm5dkv1af1z6lq5v2hk8wg7gc58p";
+          fetchSubmodules = true;
+        })
+        (fetchFromGitHub {
+          owner = "dlang";
+          repo = "undeaD";
+          rev = "7684274512a5610ac8536780f7a1cdd24d7087bc";
+          sha256 = "0pi7if7fjngcnyjrv4q73hl4d020fj0dkwfrw66x9m25qmf77178";
+        })
+    ];
+
+
+    sourceRoot = "sambamba-63cfd5c7b3053e1f7045dec0b5a569f32ef73d06-src";
+
+    postUnpack = ''
+       cp -av undeaD-* $sourceRoot
+       mv $sourceRoot/undeaD-* $sourceRoot/undeaD
+    '';
+
+    postPatch = ''
+      patchShebangs .
+      sed -i 's/-Bdynamic/-Bdynamic -ldl/' Makefile
+    '';
+
+    buildPhase = ''
+      make sambamba-ldmd2-64
+    '';
+
+    installPhase = ''
+      mkdir -p $out/bin
+      mv build/sambamba $out/bin
+      mv build/sambamba.debug $out/bin
+    '';
+
+    buildInputs = [
+      bash
+      python
+      glibc
+      dmd
+      ldc
+      which
+      rdmd
+      zlib
+    ];
+
+    meta = with stdenv.lib; {
+      homepage = https://github.com/lomereiter/sambamba/wiki;
+      description = "Sambamba is a set of command-line tools for working with SAM/BAM file formats which are used for storing next generation sequencing (NGS) datasets.";
+      platforms = platforms.all;
+      license = licenses.gpl2;
+    };
+
+    enableParallelBuilding = true;
+  }