ampliconarchitect: init

1 files changed, 57 insertions, 0 deletions

diff --git a/tools/aa-app.nix b/tools/aa-app.nix
new file mode 100644
index 0000000..4b782b3
--- /dev/null
+++ b/tools/aa-app.nix
@@ -0,0 +1,57 @@
+{
+  stdenv,
+  fetchurl,
+  fetchFromGitHub,
+  python3,
+}: let
+  python = python3.withPackages (pkgs:
+    with pkgs; [
+      numpy
+      scipy
+      pysam
+      matplotlib
+      future
+      (mosek pkgs)
+    ]);
+
+  mosek = assert stdenv.system == "x86_64-linux";
+    pkgs:
+      pkgs.buildPythonPackage {
+        pname = "mosek";
+        version = "8.1.0.83";
+        src = fetchurl {
+          url = "https://download.mosek.com/stable/8.1.0.83/mosektoolslinux64x86.tar.bz2";
+          sha256 = "sha256-d/S/IalmQwizWYZ89ZskUoVAaXWYszuw7w+w0Vp+13k";
+        };
+        doCheck = false;
+        preBuild = ''
+          cd 8/tools/platform/linux64x86/python/3/
+        '';
+        propagatedBuildInputs = with pkgs; [numpy];
+        postInstall = ''
+          find $out -name lib\*.so\* -print0 | xargs -0 \
+            patchelf --add-rpath ${stdenv.cc.cc.lib}/lib
+        '';
+      };
+in
+  stdenv.mkDerivation rec {
+    pname = "AmpliconArchitect";
+    version = "1.3";
+
+    src = fetchFromGitHub {
+      owner = "virajbdeshpande";
+      repo = pname;
+      rev = "40da8520a953810ad43e5a6fdf4aba7449d7f5e0";
+      sha256 = "sha256-4SAOpdjXiZFTfpD6WpLfs2zDyGT2hcWabl+sUjboBpc=";
+    };
+
+    doBuild = false;
+    installPhase = ''
+      mkdir -p $out/libexec
+      cp -r src $out/libexec/aa
+      mkdir $out/bin
+      ln -s $out/libexec/aa/{AmpliconArchitect,amplified_intervals,ref_util,downsample}.py $out/bin
+    '';
+
+    buildInputs = [python];
+  }