1 files changed, 84 insertions, 0 deletions
diff --git a/nixpkgs/pkgs/by-name/sa/salmon/package.nix b/nixpkgs/pkgs/by-name/sa/salmon/package.nix
new file mode 100644
index 000000000000..e4442e96fd6f
--- /dev/null
+++ b/nixpkgs/pkgs/by-name/sa/salmon/package.nix
@@ -0,0 +1,84 @@
+{ lib
+, stdenv
+, autoreconfHook
+, bash
+, boost
+, bzip2
+, cereal_1_3_2
+, cmake
+, curl
+, fetchFromGitHub
+, jemalloc
+, libgff
+, libiconv
+, libstaden-read
+, pkg-config
+, tbb_2021_8
+, xz
+, zlib
+}:
+
+stdenv.mkDerivation (finalAttrs: {
+  pname = "salmon";
+  version = "1.10.2";
+
+  pufferFishSrc = fetchFromGitHub {
+    owner = "COMBINE-lab";
+    repo = "pufferfish";
+    rev = "salmon-v${finalAttrs.version}";
+    hash = "sha256-JKbUFBEsqnENl4vFqve1FCd4TI3n9bRi2RNHC8QGQGc=";
+  };
+
+  src = fetchFromGitHub {
+    owner = "COMBINE-lab";
+    repo = "salmon";
+    rev = "v${finalAttrs.version}";
+    hash = "sha256-kwqoUmVCqjr/xRxJjQKaFjjCQW+MFASHJ2f9OiAumNU=";
+  };
+
+  patches = [
+    # Use pufferfish source fetched by nix
+    ./fetch-pufferfish.patch
+  ];
+
+  postPatch = "patchShebangs .";
+
+  buildInputs = [
+    (boost.override { enableShared = false; enabledStatic = true; })
+    bzip2
+    cereal_1_3_2
+    curl
+    jemalloc
+    libgff
+    libstaden-read
+    tbb_2021_8
+    xz
+    zlib
+  ] ++ lib.optionals stdenv.isDarwin [ libiconv ];
+
+  nativeBuildInputs = [ cmake pkg-config ];
+
+  strictDeps = true;
+
+  meta = {
+    description =
+      "Tool for quantifying the expression of transcripts using RNA-seq data";
+    longDescription = ''
+      Salmon is a tool for quantifying the expression of transcripts
+      using RNA-seq data. Salmon uses new algorithms (specifically,
+      coupling the concept of quasi-mapping with a two-phase inference
+      procedure) to provide accurate expression estimates very quickly
+      and while using little memory. Salmon performs its inference using
+      an expressive and realistic model of RNA-seq data that takes into
+      account experimental attributes and biases commonly observed in
+      real RNA-seq data.
+    '';
+    homepage = "https://combine-lab.github.io/salmon";
+    downloadPage = "https://github.com/COMBINE-lab/salmon/releases";
+    changelog = "https://github.com/COMBINE-lab/salmon/releases/tag/" +
+                "v${finalAttrs.version}";
+    license = lib.licenses.gpl3Only;
+    platforms = lib.platforms.all;
+    maintainers = [ lib.maintainers.kupac ];
+  };
+})