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 {};