From 5110a9af92103e28cf092a646a4a6b870537cbff Mon Sep 17 00:00:00 2001
From: Bruno Vieira <mail@bmpvieira.com>
Date: Wed, 9 Jan 2019 03:17:18 +0000
Subject: [PATCH] Add arioc

---
 .../science/biology/arioc/default.nix         | 43 +++++++++++++++++++
 pkgs/top-level/all-packages.nix               |  1 +
 2 files changed, 44 insertions(+)
 create mode 100644 pkgs/applications/science/biology/arioc/default.nix

diff --git a/pkgs/applications/science/biology/arioc/default.nix b/pkgs/applications/science/biology/arioc/default.nix
new file mode 100644
index 0000000..b1d94c0
--- /dev/null
+++ b/pkgs/applications/science/biology/arioc/default.nix
@@ -0,0 +1,43 @@
+{ stdenv, fetchzip, cudatoolkit, linuxPackages, makeWrapper }:
+
+stdenv.mkDerivation rec {
+  name = "${pname}-${version}";
+  pname = "arioc";
+  version = "1.30";
+
+  src = fetchzip {
+    url = "https://github.com/RWilton/Arioc/releases/download/v${version}/Arioc.x.130.zip";
+    sha256 = "015qw8k1i512xrvhpd5rdcjq32yfmqsv6a3ggw7f0bwjm0fig1z7";
+  };
+
+  buildInputs = [ cudatoolkit linuxPackages.nvidia_x11 makeWrapper ];
+
+  preBuild = ''
+    export CUDA_PATH="${cudatoolkit}"
+  '';
+
+  buildPhase = ''
+    sed -ie 's|/software/apps/cuda/9.2/bin/nvcc|${cudatoolkit}/bin/nvcc|' makefile
+    make AriocE
+    make AriocU
+    make AriocP
+  '';
+
+  installPhase = ''
+    mkdir -p $out/bin
+    cp ../bin/AriocE $out/bin
+    cp ../bin/AriocU $out/bin
+    cp ../bin/AriocP $out/bin
+    wrapProgram "$out/bin/AriocE" --prefix LD_LIBRARY_PATH ":" "${linuxPackages.nvidia_x11}/lib"
+    wrapProgram "$out/bin/AriocU" --prefix LD_LIBRARY_PATH ":" "${linuxPackages.nvidia_x11}/lib"
+    wrapProgram "$out/bin/AriocP" --prefix LD_LIBRARY_PATH ":" "${linuxPackages.nvidia_x11}/lib"
+  '';
+
+  meta = with stdenv.lib; {
+    description = "High-throughput read alignment with GPU-accelerated exploration of the seed-and-extend search space";
+    license = licenses.bsd2;
+    homepage = https://github.com/RWilton/Arioc;
+    platforms = platforms.unix;
+    maintainers = [ maintainers.bmpvieira ];
+  };
+}
diff --git a/pkgs/top-level/all-packages.nix b/pkgs/top-level/all-packages.nix
index 7156756..cbb7d05 100644
--- a/pkgs/top-level/all-packages.nix
+++ b/pkgs/top-level/all-packages.nix
@@ -41,6 +41,7 @@ let
 
   customPkgs = {
     nextflow = callPackage ../applications/science/misc/nextflow {};
+    arioc = callPackage ../applications/science/biology/arioc {};
     # aspera = callPackage ../tools/networking/aspera {};
     # bbcp = callPackage ../tools/networking/bbcp {};
     # ncbi-vdb = callPackage ../applications/science/biology/ncbi-vdb {};