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# Copyright 2013-2023 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 *
from spack.pkg.builtin.boost import Boost
class Mira(AutotoolsPackage):
"""MIRA is a multi-pass DNA sequence data assembler/mapper for whole genome
and EST/RNASeq projects."""
homepage = "https://sourceforge.net/projects/mira-assembler/"
url = "https://downloads.sourceforge.net/project/mira-assembler/MIRA/stable/mira-4.0.2.tar.bz2"
license("GPL-2.0-or-later")
version("4.0.2", sha256="a32cb2b21e0968a5536446287c895fe9e03d11d78957554e355c1080b7b92a80")
depends_on("boost@1.46:")
# TODO: replace this with an explicit list of components of Boost,
# for instance depends_on('boost +filesystem')
# See https://github.com/spack/spack/pull/22303 for reference
depends_on(Boost.with_default_variants)
depends_on("expat@2.0.1:")
depends_on("gperftools")
conflicts("%gcc@6:", when="@:4.0.2")
def patch(self):
with working_dir(join_path("src", "progs")):
edit = FileFilter("quirks.C")
edit.filter(
"#include <boost/filesystem.hpp>",
"#include <boost/filesystem.hpp>\n#include <iostream>",
)
def configure_args(self):
args = [
"--with-boost=%s" % self.spec["boost"].prefix,
"--with-expat=%s" % self.spec["expat"].prefix,
]
return args
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