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# Copyright 2013-2022 Lawrence Livermore National Security, LLC and other
# Spack Project Developers. See the top-level COPYRIGHT file for details.
#
# SPDX-License-Identifier: (Apache-2.0 OR MIT)
from spack.package import *
class Maq(AutotoolsPackage):
"""Maq is a software that builds mapping assemblies from short reads
generated by the next-generation sequencing machines."""
homepage = "http://maq.sourceforge.net/"
url = "https://downloads.sourceforge.net/project/maq/maq/0.7.1/maq-0.7.1.tar.bz2"
list_url = "https://sourceforge.net/projects/maq/files/maq/"
maintainers = ['snehring']
version('0.7.1', sha256='e1671e0408b0895f5ab943839ee8f28747cf5f55dc64032c7469b133202b6de2')
version('0.5.0', sha256='c292c19baf291b2415b460d687d43a71ece00a7d178cc5984bc8fc30cfce2dfb')
depends_on('perl', type='run')
def patch(self):
with working_dir('scripts'):
scripts = ['farm-run.pl', 'maq_eval.pl', 'maq.pl', 'maq_plot.pl']
for s in scripts:
filter_file('/usr/bin/perl', self.spec['perl'].prefix.bin.perl, s)
def flag_handler(self, name, flags):
if name.lower() == 'cxxflags':
flags.append('-fpermissive')
return (flags, None, None)
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