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

pkgs/all-packages.nix

@@ -14,4 +14,6 @@ self: pkgs: with pkgs; {
   sumo = callPackage ./sumo.nix { };
 
   namd = callPackage ./namd.nix { };
+
+  sambamba = callPackage ./sambamba { };
 }

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;
+  }

pkgs/sambamba/ldc.nix

@@ -0,0 +1,57 @@
+{ stdenv, fetchFromGitHub
+, cmake, dmd, cacert, openssl, libconfig, libedit, zlib, libxml2, curl, llvm }:
+
+
+stdenv.mkDerivation rec {
+  version = "1.2.0";
+  name = "ldc-${version}";
+
+  src = fetchFromGitHub {
+    owner = "ldc-developers";
+    repo = "ldc";
+    rev = "e229b1d3810b4880440810c6ca0c23a762ec49cb";
+    sha256 = "0r73vdafmmd6nlxhh1wp3sz9ymni5c721svmbz23l3i0wjlc72ga";
+    fetchSubmodules = true;
+  };
+
+#  src = fetchgit {
+#    url = "https://github.com/ldc-developers/ldc.git";
+#    rev = "refs/tags/v${version}";
+#    sha256 = "12xbzc9b0hhgda8n0125yn4g545qpazhfpv8hjr26pc8qjg9rlq4";
+#    fetchSubmodules = true;
+#  };
+
+#  src = fetchurl {
+#    url = "https://github.com/ldc-developers/ldc/archive/v${version}.tar.gz";
+#    sha256 = "0plgvy9nybc4p41xx9rzrdlhxphbx2sx0sgj4xgg6ak1vac519sa";
+#  };
+
+#  postPatch = ''
+#    sed -i 's:bits/mathdef.h:math.h:' dmd2/root/port.c
+#    sed -i 's/::isnan/std::isnan/' dmd2/root/port.c
+#    sed -i 's/::isinf/std::isinf/' dmd2/root/port.c
+#  '';
+
+  buildInputs = [
+    cmake
+    dmd
+    cacert
+    openssl
+    libconfig
+    libedit
+    zlib
+    libxml2
+    curl
+    llvm
+  ];
+
+  enableParallelBuilding = true;
+
+#  cmakeFlags = [
+#    "-DCMAKE_BUILD_TYPE=Release"
+#    "-DCMAKE_CXX_FLAGS_RELEASE=-std=c++11"
+#    "-DLLVM_ROOT_DIR=${llvm}"
+#    "-DCMAKE_C_COMPILER=${gcc5}/bin/cc"
+#    "-DCMAKE_CXX_COMPILER=${gcc5}/bin/g++"
+#  ];
+}