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wgsim: Create new package. (#7674)

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* wgsim: Create new package.

* fix flake8 error.

* wgsim: change cc compiler to spack_cc.

* add missing dependency.
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lingnanyuan 2018-04-09 14:23:11 -05:00 committed by Adam J. Stewart
parent c1e3e5de5c
commit dc8c8311c6
1 changed files with 47 additions and 0 deletions
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var/spack/repos/builtin/packages/wgsim/package.py Normal file
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##############################################################################
# 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)