diff options
Diffstat (limited to 'nixpkgs/pkgs/applications/science/biology/astral/default.nix')
-rw-r--r-- | nixpkgs/pkgs/applications/science/biology/astral/default.nix | 60 |
1 files changed, 60 insertions, 0 deletions
diff --git a/nixpkgs/pkgs/applications/science/biology/astral/default.nix b/nixpkgs/pkgs/applications/science/biology/astral/default.nix new file mode 100644 index 000000000000..6a9513c6b817 --- /dev/null +++ b/nixpkgs/pkgs/applications/science/biology/astral/default.nix @@ -0,0 +1,60 @@ +{ lib +, stdenvNoCC +, fetchFromGitHub +, jdk8 +, makeWrapper +, jre8 +, zip +}: +let + jdk = jdk8; + jre = jre8; +in +stdenvNoCC.mkDerivation rec { + pname = "astral"; + version = "5.7.1"; + + src = fetchFromGitHub { + owner = "smirarab"; + repo = "ASTRAL"; + rev = "v${version}"; + sha256 = "043w2z6gbrisqirdid022f4b8jps1pp5syi344krv2bis1gjq5sn"; + }; + + nativeBuildInputs = [ jdk makeWrapper jre zip ]; + + buildPhase = '' + patchShebangs ./make.sh + ./make.sh + ''; + + doCheck = true; + + checkPhase = '' + runHook preCheck + java -jar astral.${version}.jar -i main/test_data/song_primates.424.gene.tre + runHook postCheck + ''; + + installPhase = '' + mkdir -p $out/share/lib + mkdir -p $out/bin + mv astral.${version}.jar $out/share/ + mv lib/*.jar $out/share/lib + mv Astral.${version}.zip $out/share/ + cp -a main/test_data $out/share/ + makeWrapper ${jre}/bin/java $out/bin/astral \ + --add-flags "-jar $out/share/astral.${version}.jar" + ''; + + meta = with lib; { + homepage = "https://github.com/smirarab/ASTRAL"; + description = "Tool for estimating an unrooted species tree given a set of unrooted gene trees"; + sourceProvenance = with sourceTypes; [ + fromSource + binaryBytecode # source bundles dependencies as jars + ]; + license = licenses.asl20; + maintainers = with maintainers; [ bzizou ]; + }; +} |