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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 *
class Augustus(MakefilePackage):
"""AUGUSTUS is a program that predicts genes in eukaryotic
genomic sequences"""
homepage = "http://bioinf.uni-greifswald.de/augustus/"
url = "http://bioinf.uni-greifswald.de/augustus/binaries/augustus-3.3.1.tar.gz"
list_url = "http://bioinf.uni-greifswald.de/augustus/binaries/old"
version('3.3.1', '8363ece221c799eb169f47e545efb951')
version('3.3', '93691d9aafc7d3d0e1adf31ec308507f')
version('3.2.3', 'b8c47ea8d0c45aa7bb9a82626c8ff830')
depends_on('bamtools')
depends_on('gsl')
depends_on('boost')
depends_on('zlib')
def edit(self, spec, prefix):
with working_dir(join_path('auxprogs', 'filterBam', 'src')):
makefile = FileFilter('Makefile')
makefile.filter('BAMTOOLS = .*', 'BAMTOOLS = %s' % self.spec[
'bamtools'].prefix)
makefile.filter('INCLUDES = *',
'INCLUDES = -I$(BAMTOOLS)/include/bamtools ')
if 'bamtools@2.5:' in spec:
makefile.filter('LIBS = -lbamtools -lz',
'LIBS = $(BAMTOOLS)/lib64/'
'/libbamtools.a -lz')
if 'bamtools@:2.4' in spec:
makefile.filter('LIBS = -lbamtools -lz',
'LIBS = $(BAMTOOLS)/lib/bamtools'
'/libbamtools.a -lz')
with working_dir(join_path('auxprogs', 'bam2hints')):
makefile = FileFilter('Makefile')
makefile.filter('# Variable definition',
'BAMTOOLS = %s' % self.spec['bamtools'].prefix)
makefile.filter('INCLUDES = /usr/include/bamtools',
'INCLUDES = $(BAMTOOLS)/include/bamtools')
if 'bamtools@2.5:' in spec:
makefile.filter('LIBS = -lbamtools -lz',
'LIBS = $(BAMTOOLS)/lib64/'
'/libbamtools.a -lz')
if 'bamtools@:2.4' in spec:
makefile.filter('LIBS = -lbamtools -lz',
'LIBS = $(BAMTOOLS)/lib/bamtools'
'/libbamtools.a -lz')
def install(self, spec, prefix):
install_tree('bin', join_path(self.spec.prefix, 'bin'))
install_tree('config', join_path(self.spec.prefix, 'config'))
install_tree('scripts', join_path(self.spec.prefix, 'scripts'))
def setup_environment(self, spack_env, run_env):
run_env.set('AUGUSTUS_CONFIG_PATH', join_path(
self.prefix, 'config'))
run_env.prepend_path('PATH', join_path(self.prefix, 'scripts'))
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