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{stdenv
,fetchurl
,fetchFromGitHub
,callPackage
,nettools
,rPackages
,rWrapper
,R
,jre
,python
,pythonPackages
,darwin
,gettext
,gfortran
,makeWrapper}:
let
buildRPackage = rPackages.buildRPackage;
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}
'';
}
|
