From bcbb1ef4fb144005642c159a74bd9760b1ddd619 Mon Sep 17 00:00:00 2001
From: Tyson Whitehead <twhitehead@gmail.com>
Date: Wed, 27 Jun 2018 14:19:23 -0400
Subject: [PATCH] sambamba: Upgrade to 0.6.7 and compile with upstream ldc

Fixes new compilation issues with tupple operator being dropped
---
 pkgs/all-packages.nix     |  2 +-
 pkgs/sambamba.nix         | 49 ++++++++++++++++++++++++++
 pkgs/sambamba/default.nix | 72 ---------------------------------------
 pkgs/sambamba/ldc.nix     | 57 -------------------------------
 4 files changed, 50 insertions(+), 130 deletions(-)
 create mode 100644 pkgs/sambamba.nix
 delete mode 100644 pkgs/sambamba/default.nix
 delete mode 100644 pkgs/sambamba/ldc.nix

diff --git a/pkgs/all-packages.nix b/pkgs/all-packages.nix
index 1ac258a..950bb0f 100644
--- a/pkgs/all-packages.nix
+++ b/pkgs/all-packages.nix
@@ -33,7 +33,7 @@ self: super: pkgs: with pkgs; {
 
   namd = callPackage ./namd.nix { };
 
-  sambamba = callPackage ./sambamba { };
+  sambamba = callPackage ./sambamba.nix { };
 
   idba = callPackage ./idba.nix { };
 
diff --git a/pkgs/sambamba.nix b/pkgs/sambamba.nix
new file mode 100644
index 0000000..3a97062
--- /dev/null
+++ b/pkgs/sambamba.nix
@@ -0,0 +1,49 @@
+{ stdenv, fetchFromGitHub, ldc
+, bash, python, glibc, which, rdmd, zlib }:
+
+stdenv.mkDerivation rec {
+  version = "0.6.7";
+  name = "sambamba-${version}";
+
+  src = fetchFromGitHub {
+    owner = "lomereiter";
+    repo = "sambamba";
+    rev = "v${version}";
+    sha256 = "06fj6ayr57xcpinmsdmczfay13bbmq2f6zlvknzz9yhgsdkny9w3";
+    fetchSubmodules = true;
+  };
+
+  postPatch = ''
+    patchShebangs .
+    sed -i '1s,$, undeaD/src/undead/utf.d,' *.rsp
+  '';
+
+  buildPhase = ''
+    make sambamba-ldmd2-64
+  '';
+
+  installPhase = ''
+    mkdir -p $out/bin
+    mv build/sambamba $out/bin
+    mv build/sambamba.debug $out/bin
+  '';
+
+  buildInputs = [
+    bash
+    python
+    glibc
+    ldc
+    which
+    rdmd
+    zlib
+  ];
+
+  meta = with stdenv.lib; {
+    homepage = https://github.com/lomereiter/sambamba/wiki;
+    description = "Sambamba is a set of command-line tools for working with SAM/BAM file formats which are used for storing next generation sequencing (NGS) datasets.";
+    platforms = platforms.all;
+    license = licenses.gpl2;
+  };
+
+  enableParallelBuilding = true;
+}
diff --git a/pkgs/sambamba/default.nix b/pkgs/sambamba/default.nix
deleted file mode 100644
index dfde254..0000000
--- a/pkgs/sambamba/default.nix
+++ /dev/null
@@ -1,72 +0,0 @@
-{ stdenv, fetchFromGitHub, callPackage
-, bash, python, glibc, dmd, which, rdmd, zlib }:
-
-let
-
-  ldc = callPackage ./ldc.nix { };
-
-in
-
-  stdenv.mkDerivation rec {
-    version = "0.6.6";
-    name = "sambamba-${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 $out/bin
-    '';
-
-    buildInputs = [
-      bash
-      python
-      glibc
-      dmd
-      ldc
-      which
-      rdmd
-      zlib
-    ];
-
-    meta = with stdenv.lib; {
-      homepage = https://github.com/lomereiter/sambamba/wiki;
-      description = "Sambamba is a set of command-line tools for working with SAM/BAM file formats which are used for storing next generation sequencing (NGS) datasets.";
-      platforms = platforms.all;
-      license = licenses.gpl2;
-    };
-
-    enableParallelBuilding = true;
-  }
diff --git a/pkgs/sambamba/ldc.nix b/pkgs/sambamba/ldc.nix
deleted file mode 100644
index aaa123e..0000000
--- a/pkgs/sambamba/ldc.nix
+++ /dev/null
@@ -1,57 +0,0 @@
-{ stdenv, fetchFromGitHub
-, cmake, dmd, cacert, openssl, libconfig, libedit, zlib, libxml2, curl, llvm }:
-
-
-stdenv.mkDerivation rec {
-  version = "1.2.0";
-  name = "ldc-${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++"
-#  ];
-}