diff options
| -rw-r--r-- | pkgs/applications/science/biology/strelka/default.nix | 37 | ||||
| -rw-r--r-- | pkgs/top-level/all-packages.nix | 2 |
2 files changed, 39 insertions, 0 deletions
diff --git a/pkgs/applications/science/biology/strelka/default.nix b/pkgs/applications/science/biology/strelka/default.nix new file mode 100644 index 000000000000..1527f5d3ddad --- /dev/null +++ b/pkgs/applications/science/biology/strelka/default.nix @@ -0,0 +1,37 @@ +{stdenv, fetchFromGitHub, cmake, zlib, python2}: + +stdenv.mkDerivation rec { + name = "strelka-${version}"; + version = "2.9.5"; + + src = fetchFromGitHub { + owner = "Illumina"; + repo = "strelka"; + rev = "v${version}"; + sha256 = "0x4a6nkx1jnyag9svghsdjz1fz6q7qx5pn77wphdfnk81f9yspf8"; + }; + + buildInputs = [ cmake zlib python2 ]; + + preConfigure = '' + sed -i 's|/usr/bin/env python|${python2}/bin/python|' src/python/lib/makeRunScript.py + patchShebangs . + ''; + + postFixup = '' + pushd $out/lib/python/pyflow + sed -i 's|/bin/bash|${stdenv.shell}|' pyflowTaskWrapper.py + rm pyflowTaskWrapper.pyc + echo "import pyflowTaskWrapper" | python2 + popd + ''; + + meta = with stdenv.lib; { + description = "Germline and small variant caller"; + license = licenses.gpl3; + homepage = https://github.com/Illumina/strelka; + maintainers = with maintainers; [ jbedo ]; + platforms = [ "x86_64-linux" ]; + }; + +} diff --git a/pkgs/top-level/all-packages.nix b/pkgs/top-level/all-packages.nix index c81bf2922871..835a12a60952 100644 --- a/pkgs/top-level/all-packages.nix +++ b/pkgs/top-level/all-packages.nix @@ -20547,6 +20547,8 @@ with pkgs; star = callPackage ../applications/science/biology/star { }; + strelka = callPackage ../applications/science/biology/strelka { }; + varscan = callPackage ../applications/science/biology/varscan { }; hmmer = callPackage ../applications/science/biology/hmmer { }; |