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# Copyright 2013-2018 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 import *
import os.path
import glob
class Express(CMakePackage):
"""eXpress is a streaming tool for quantifying the abundances of a set of
target sequences from sampled subsequences."""
homepage = "http://bio.math.berkeley.edu/eXpress/"
git = "https://github.com/adarob/eXpress.git"
version('2015-11-29', commit='f845cab2c7f2d9247b35143e4aa05869cfb10e79')
depends_on('boost')
depends_on('bamtools')
depends_on('zlib')
conflicts('%gcc@6.0.0:', when='@2015-11-29')
def patch(self):
with working_dir('src'):
files = glob.iglob('*.*')
for file in files:
if os.path.isfile(file):
edit = FileFilter(file)
edit.filter('#include <api', '#include <%s' % self.spec[
'bamtools'].prefix.include.bamtools.api)
edit = FileFilter('CMakeLists.txt')
edit.filter('\${CMAKE_CURRENT_SOURCE_DIR}/../bamtools/lib/'
'libbamtools.a', '%s' % self.spec['bamtools'].libs)
def setup_environment(self, spack_env, run_env):
spack_env.prepend_path('CPATH', self.spec[
'bamtools'].prefix.include.bamtools)
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