44 lines
1.5 KiB
Python
44 lines
1.5 KiB
Python
# 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 *
|
|
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"
|
|
|
|
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
|