diff --git a/var/spack/repos/builtin/packages/wgsim/package.py b/var/spack/repos/builtin/packages/wgsim/package.py new file mode 100644 index 0000000000..fa3cc8c13e --- /dev/null +++ b/var/spack/repos/builtin/packages/wgsim/package.py @@ -0,0 +1,47 @@ +############################################################################## +# Copyright (c) 2013-2017, 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/spack/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 Wgsim(Package): + """Wgsim is a small tool for simulating sequence reads from a reference + genome. + + It is able to simulate diploid genomes with SNPs and insertion/deletion + (INDEL) polymorphisms, and simulate reads with uniform substitution + sequencing errors. It does not generate INDEL sequencing errors, but this + can be partly compensated by simulating INDEL polymorphisms.""" + + homepage = "https://github.com/lh3/wgsim" + + version('2011.10.17', git='https://github.com/lh3/wgsim.git', commit='a12da3375ff3b51a5594d4b6fa35591173ecc229') + + depends_on('zlib') + + def install(self, spec, prefix): + cc = Executable(spack_cc) + cc('-g', '-O2', '-Wall', '-o', 'wgsim', 'wgsim.c', '-lz', '-lm') + + install_tree(self.stage.source_path, prefix.bin)