From cc5ccabf31e4c605270afc9b271eb2cdaec4b4a2 Mon Sep 17 00:00:00 2001
From: Bruno Vieira <mail@bmpvieira.com>
Date: Thu, 10 Jan 2019 11:38:07 +0000
Subject: [PATCH] Add salmon

---
 .../science/biology/salmon/default.nix        | 46 +++++++++++++++++++
 pkgs/top-level/all-packages.nix               |  1 +
 2 files changed, 47 insertions(+)
 create mode 100644 pkgs/applications/science/biology/salmon/default.nix

diff --git a/pkgs/applications/science/biology/salmon/default.nix b/pkgs/applications/science/biology/salmon/default.nix
new file mode 100644
index 0000000..7d85036
--- /dev/null
+++ b/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 ];
+  };
+}
diff --git a/pkgs/top-level/all-packages.nix b/pkgs/top-level/all-packages.nix
index 2874c0e..5dd0b64 100644
--- a/pkgs/top-level/all-packages.nix
+++ b/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