From a3d6e7b4b4585c5bc5bd8c7e6c8f305daecdd03b Mon Sep 17 00:00:00 2001
From: Justin Bedo <cu@cua0.org>
Date: Wed, 18 Dec 2019 09:37:39 +1100
Subject: [PATCH] lumpy: init 0.3.0

---
 .../science/biology/lumpy/default.nix         | 47 +++++++++++++++++++
 pkgs/top-level/all-packages.nix               |  2 +
 2 files changed, 49 insertions(+)
 create mode 100644 pkgs/applications/science/biology/lumpy/default.nix

diff --git a/pkgs/applications/science/biology/lumpy/default.nix b/pkgs/applications/science/biology/lumpy/default.nix
new file mode 100644
index 000000000000..04512e8e372e
--- /dev/null
+++ b/pkgs/applications/science/biology/lumpy/default.nix
@@ -0,0 +1,47 @@
+{ stdenv, fetchFromGitHub, htslib, zlib, curl, openssl, samblaster, sambamba
+, samtools, hexdump, python2Packages, which }:
+
+let
+  python =
+    python2Packages.python.withPackages (pkgs: with pkgs; [ pysam numpy ]);
+
+in stdenv.mkDerivation rec {
+  pname = "lumpy";
+  version = "0.3.0";
+
+  src = fetchFromGitHub {
+    owner = "arq5x";
+    repo = "lumpy-sv";
+    rev = version;
+    sha256 = "0azhzvmh9az9jcq0xprlzdz6w16azgszv4kshb903bwbnqirmk18";
+  };
+
+  nativeBuildInputs = [ which ];
+  buildInputs =
+    [ htslib zlib curl openssl python samblaster sambamba samtools hexdump ];
+
+  preConfigure = ''
+    patchShebangs ./.
+
+    # Use Nix htslib over bundled version
+    sed -i 's/lumpy_filter: htslib/lumpy_filter:/' Makefile
+    sed -i 's|../../lib/htslib/libhts.a|-lhts|' src/filter/Makefile
+  '';
+
+  # Upstream's makefile doesn't have an install target
+  installPhase = ''
+    mkdir -p $out
+    cp -r bin $out
+    cp -r scripts $out
+    sed -i 's|/build/source|'$out'|' $out/bin/lumpyexpress.config
+  '';
+
+  meta = with stdenv.lib; {
+    description = "Probabilistic structural variant caller";
+    homepage = "https://github.com/arq5x/lumpy-sv";
+    maintainers = with maintainers; [ jbedo ];
+    license = licenses.mit;
+    platforms = [ "x86_64-linux" ];
+  };
+
+}
diff --git a/pkgs/top-level/all-packages.nix b/pkgs/top-level/all-packages.nix
index d1a0d7d384ea..e0e54e1da956 100644
--- a/pkgs/top-level/all-packages.nix
+++ b/pkgs/top-level/all-packages.nix
@@ -24845,6 +24845,8 @@ in
 
   last = callPackage ../applications/science/biology/last { };
 
+  lumpy = callPackage ../applications/science/biology/lumpy { };
+
   macse = callPackage ../applications/science/biology/macse { };
 
   migrate = callPackage ../applications/science/biology/migrate { };