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# Copyright 2013-2024 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")
license("GPL-3.0-only")
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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