Add salmon

pkgs/applications/science/biology/salmon/default.nix

@@ -0,0 +1,46 @@
+{ stdenv, fetchTarball, makeWrapper,
+  cmake, autoconf, pkgconfig
+  cudatoolkit, linuxPackages,
+  bash, curl, unzip, bzip2, lzma
+  boost, tbb, jemalloc }:
+
+stdenv.mkDerivation rec {
+  name = "${pname}-${version}";
+  pname = "salmon";
+  version = "0.12.0";
+
+  src = fetchTarball {
+    url = "https://github.com/COMBINE-lab/salmon/archive/v${version}.tar.gz";
+    sha256 = "1dr8maifd6hv45812l4w244npxmd2v73fzqmngs12amb2lq1jzxm";
+  };
+
+  buildInputs = [
+    makeWrapper
+    cmake autoconf pkgconfig
+    cudatoolkit linuxPackages.nvidia_x11
+    bash curl unzip bzip2 lzma
+    boost tbb jemalloc
+  ];
+
+  CUDA_PATH = "${cudatoolkit}";
+
+  preConfigure = ''
+    for i in scripts/*.sh; do
+      substituteInPlace $i --replace /bin/bash ${bash}/bin/bash
+    done
+
+    substituteInPlace CMakeLists.txt --replace \
+      'set(Boost_USE_STATIC_LIBS ON)' \
+      'set(Boost_USE_STATIC_LIBS OFF)'
+  '';
+
+  installTargets = "install-bin install-doc";
+
+  meta = with stdenv.lib; {
+    description = "Highly-accurate & wicked fast transcript-level quantification from RNA-seq reads using lightweight alignments";
+    license = licenses.gpl3;
+    homepage = https://combine-lab.github.io/salmon;
+    platforms = platforms.unix;
+    maintainers = [ maintainers.bmpvieira ];
+  };
+}

pkgs/top-level/all-packages.nix

@@ -44,6 +44,7 @@ let
     nextflow = callPackage ../applications/science/misc/nextflow {};
     # Cuda aligners
     arioc = callPackage ../applications/science/biology/arioc {};
+    salmon = callPackage ../applications/science/biology/salmon {};
     # SRA
     sra-tools = callPackage ../applications/science/biology/sra-tools {};
     ncbi-vdb = callPackage ../applications/science/biology/ncbi-vdb {}; # sra-tools dep