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# Copyright 2013-2019 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 glob import glob
from spack import *
class NcbiToolkit(AutotoolsPackage):
"""NCBI C++ Toolkit"""
homepage = "https://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/"
url = "ftp://ftp.ncbi.nih.gov/toolbox/ncbi_tools++/CURRENT/ncbi_cxx--22_0_0.tar.gz"
version('22_0_0', 'e352d25b24c3a2d087c2cf3cedf6ea95',
url='ftp://ftp.ncbi.nih.gov/toolbox/ncbi_tools++/ARCHIVE/2019/Mar_28_2019/ncbi_cxx--22_0_0.tar.gz')
version('21_0_0', '14e021e08b1a78ac9cde98d0cab92098',
url='ftp://ftp.ncbi.nih.gov/toolbox/ncbi_tools++/ARCHIVE/2018/Apr_2_2018/ncbi_cxx--21_0_0.tar.gz')
variant('debug', default=False,
description='Build debug versions of libs and apps')
depends_on('boost@1.35.0:')
depends_on('bzip2')
depends_on('jpeg')
depends_on('libpng')
depends_on('libtiff')
depends_on('libxml2')
depends_on('libxslt@1.1.14:')
depends_on('lzo')
depends_on('pcre')
depends_on('giflib')
depends_on('sqlite@3.6.6:')
depends_on('zlib')
depends_on('samtools')
depends_on('bamtools')
def configure_args(self):
args = ['--without-sybase', '--without-fastcgi']
if '+debug' not in self.spec:
args += ['--without-debug']
return args
def patch(self):
with working_dir(join_path('src', 'util', 'image')):
filter_file(r'jpeg_start_compress(&cinfo, true)',
'jpeg_start_compress(&cinfo, TRUE)',
'image_io_jpeg.cpp', string=True)
# TODO: Convert these substitutions into BOOST_VERSION preprocessor
# patches to send upstream.
if self.spec.satisfies('^boost@1.69:'):
with working_dir(join_path('include', 'corelib')):
filter_file(r'(boost::unit_test::decorator::collector)',
r'\1_t', 'test_boost.hpp')
if self.spec.satisfies('^boost@1.70:'):
with working_dir(join_path('include', 'corelib')):
filter_file(('unit_test::ut_detail::'
'ignore_unused_variable_warning'),
'ignore_unused', 'test_boost.hpp', string=True)
with working_dir(join_path('src', 'corelib')):
for file_ in ['test_boost.cpp', 'teamcity_boost.cpp']:
filter_file(
r'(void log_build_info\s*\(.*ostream&[^)]*)\);',
r'\1, bool log_build_info = true);', file_)
filter_file(r'(::log_build_info\(.*ostream.*&[^)]+)\)',
r'\1, bool log_build_info)', file_)
filter_file(r'(log_build_info\(ostr)\)', r'\1, true)',
file_)
def build(self, spec, prefix):
with working_dir(join_path(glob(
'*MT64')[0], 'build')):
make('all_r')
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