angsd: adding package angsd (#4620)

var/spack/repos/builtin/packages/angsd/package.py

@@ -0,0 +1,50 @@
+##############################################################################
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
+# Produced at the Lawrence Livermore National Laboratory.
+#
+# This file is part of Spack.
+# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# LLNL-CODE-647188
+#
+# For details, see https://github.com/llnl/spack
+# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
+#
+# This program is free software; you can redistribute it and/or modify
+# it under the terms of the GNU Lesser General Public License (as
+# published by the Free Software Foundation) version 2.1, February 1999.
+#
+# This program is distributed in the hope that it will be useful, but
+# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
+# conditions of the GNU Lesser General Public License for more details.
+#
+# You should have received a copy of the GNU Lesser General Public
+# License along with this program; if not, write to the Free Software
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+##############################################################################
+from spack import *
+
+
+class Angsd(MakefilePackage):
+    """Angsd is a program for analysing NGS data. The software can handle a
+       number of different input types from mapped reads to imputed genotype
+       probabilities. Most methods take genotype uncertainty into account
+       instead of basing the analysis on called genotypes. This is especially
+       useful for low and medium depth data."""
+
+    homepage = "https://github.com/ANGSD/angsd"
+    url      = "https://github.com/ANGSD/angsd/archive/0.919.tar.gz"
+
+    version('0.919', '79d342f49c24ac00d35934f2617048d4')
+
+    depends_on('htslib')
+
+    def setup_environment(self, spack_env, run_env):
+        run_env.set('R_LIBS', prefix.R)
+
+    def install(self, spec, prefix):
+        mkdirp(prefix.bin)
+        install('angsd', join_path(prefix.bin))
+        install_tree('R', prefix.R)
+        install_tree('RES', prefix.RES)
+        install_tree('scripts', prefix.scripts)