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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)
import glob
import os.path
from spack import *
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/"
url = "https://github.com/adarob/eXpress/archive/1.5.2.zip"
# 1.5.1 used to be known as 2015-11-29 (same commit), but they've
# added tags, so lets use 'em
version('1.5.2', sha256='25a63cca3dac6bd0daf04d2f0b2275e47d2190c90522bd231b1d7a875a59a52e')
version('1.5.1', sha256='fa3522de9cc25f1ede22fa196928912a6da2a2038681911115ec3e4da3d61293')
depends_on('boost+date_time+exception+filesystem+system+chrono+atomic+container+math+thread+program_options')
depends_on('bamtools')
depends_on('zlib')
# patch from the debian package repo:
# https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=811859
patch('gcc-6.patch', when='%gcc@6.0.0:')
patch('gcc-6.patch', when='%fj')
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(r'\${CMAKE_CURRENT_SOURCE_DIR}/../bamtools/lib/'
'libbamtools.a', '%s' % self.spec['bamtools'].libs)
def setup_build_environment(self, env):
env.prepend_path('CPATH',
self.spec['bamtools'].prefix.include.bamtools)
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