diff options
| author | Bruno Bzeznik <Bruno.Bzeznik@imag.fr> | 2022-05-30 14:53:28 +0200 |
|---|---|---|
| committer | Bruno Bzeznik <Bruno.Bzeznik@imag.fr> | 2022-05-31 09:03:24 +0200 |
| commit | 376897ced34becbfce58950225360c28e0a3ecf0 (patch) | |
| tree | 79f11c8d266483783d893f78682493d94bff0312 /pkgs | |
| parent | f6facfe59d1e6f891d456a93ac34ae60d7ab2813 (diff) | |
astral: init at 5.7.1
Diffstat (limited to 'pkgs')
| -rw-r--r-- | pkgs/applications/science/biology/astral/default.nix | 56 | ||||
| -rw-r--r-- | pkgs/top-level/all-packages.nix | 2 |
2 files changed, 58 insertions, 0 deletions
diff --git a/pkgs/applications/science/biology/astral/default.nix b/pkgs/applications/science/biology/astral/default.nix new file mode 100644 index 0000000000000..b092edc0e6029 --- /dev/null +++ b/pkgs/applications/science/biology/astral/default.nix @@ -0,0 +1,56 @@ +{ 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"; + license = licenses.asl20; + maintainers = with maintainers; [ bzizou ]; + }; +} diff --git a/pkgs/top-level/all-packages.nix b/pkgs/top-level/all-packages.nix index 97e824dbd0498..56277e326a1a5 100644 --- a/pkgs/top-level/all-packages.nix +++ b/pkgs/top-level/all-packages.nix @@ -32715,6 +32715,8 @@ with pkgs; aragorn = callPackage ../applications/science/biology/aragorn { }; + astral = callPackage ../applications/science/biology/astral { }; + archimedes = callPackage ../applications/science/electronics/archimedes { stdenv = gcc6Stdenv; }; |