Wrap inferCNV

Resolves #8

1 files changed, 93 insertions, 0 deletions

diff --git a/tools/infercnv-app.nix b/tools/infercnv-app.nix
new file mode 100644
index 0000000..ad6a16f
--- /dev/null
+++ b/tools/infercnv-app.nix
@@ -0,0 +1,93 @@
+{stdenv
+  ,fetchurl
+  ,fetchFromGitHub
+  ,callPackage
+  ,nettools
+  ,rPackages
+  ,rWrapper
+  ,R
+  ,jre
+  ,python
+  ,pythonPackages
+  ,darwin
+  ,gettext
+  ,gfortran
+,makeWrapper}:
+
+let
+  buildRPackage = callPackage "${<nixpkgs>}/pkgs/development/r-modules/generic-builder.nix" {
+    inherit R gettext gfortran;
+    inherit (darwin.apple_sdk.frameworks) Cocoa Foundation;
+  };
+
+  GMD = buildRPackage rec {
+    name = "GMD-${version}";
+    version = "0.3.3";
+    src = fetchurl {
+      url = "https://cran.r-project.org/src/contrib/Archive/GMD/GMD_0.3.3.tar.gz";
+      sha256 = "0jshdcmqcr7lz4p5xb76qbaqavm2609r01lhi9hd0aqnnry18kmg";
+    };
+    buildInputs = with rPackages; [ R gplots ];
+  };
+
+  NGCHMR = buildRPackage rec {
+    name = "NGCHMR-${version}";
+    version = "git";
+    src = fetchFromGitHub {
+      owner = "bmbroom";
+      repo = "NGCHMR";
+      rev = "9f5f1fbf39339d21295b5056e469edcdcbaae142";
+      sha256 = "0paw3fz22kbk4ps4mfxzfchqvipspl7a60jsz46fsg10v6d3z7yv";
+    };
+    propagatedBuildInputs = with rPackages; [ R tsvio digest httr jsonlite nettools ];
+    patches = [ ./infercnv-ngchmr.patch ];
+  };
+
+  tsvio = buildRPackage rec {
+    name = "tsvio-${version}";
+    version = "git";
+    src = fetchFromGitHub {
+      owner = "bmbroom";
+      repo = "tsvio";
+      rev = "067b01ffc1491d50fc1e104b1fe36208a3997980";
+      sha256 = "05byfn2bim51wswffs9lm23p4i0bghyn63rny480dvagydn1a85c";
+    };
+  };
+
+  inferCNV = buildRPackage rec {
+    name = "inferCNV-${version}";
+    version = "git";
+    requireX = false;
+    src = fetchFromGitHub {
+      owner = "broadinstitute";
+      repo = "inferCNV";
+      rev = "cf442af0db6191fa8ba57c4921ac2d1f98c2c39d";
+        sha256 = "0cv8qiaqpd6b4152dplnzvgv77cmk961rmvzr27qgmlaazc5hblh";
+    };
+    propagatedBuildInputs = with rPackages; [ R GMD NGCHMR RColorBrewer gplots optparse logging ];
+  };
+
+  r = rWrapper.override {
+    packages = with rPackages; [ inferCNV ape ];
+  };
+
+  py = python.withPackages (pkgs: with pkgs; [ statistics ]);
+
+  shaidymapgen = fetchurl {
+    url = "http://tcga.ngchm.net/NGCHM/ShaidyMapGen.jar";
+    sha256 = "1pz710ig8nnydz329ry8fydccbrp3arp614dgba3bcyy9flm3gnw";
+  };
+
+in stdenv.mkDerivation rec {
+  name = inferCNV.name;
+  src = inferCNV.src;
+  buildInputs = [ r makeWrapper py ];
+  propagatedBuildInputs = [ jre ];
+  installPhase = ''
+    mkdir -p $out/bin
+    cp scripts/* $out/bin
+  '';
+  postFixup = ''
+    wrapProgram $out/bin/inferCNV.R --set SHAIDYMAPGEN=${shaidymapgen}
+  '';
+}