From 6480e382173e689ea734525827c683c57596ebf9 Mon Sep 17 00:00:00 2001 From: Audrey Thoma Date: Wed, 28 Jun 2017 10:15:00 -0500 Subject: angsd: adding package angsd (#4620) --- var/spack/repos/builtin/packages/angsd/package.py | 50 +++++++++++++++++++++++ 1 file changed, 50 insertions(+) create mode 100644 var/spack/repos/builtin/packages/angsd/package.py diff --git a/var/spack/repos/builtin/packages/angsd/package.py b/var/spack/repos/builtin/packages/angsd/package.py new file mode 100644 index 0000000000..21ad31c957 --- /dev/null +++ b/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) -- cgit v1.2.3-70-g09d2