diff options
| -rw-r--r-- | var/spack/repos/builtin/packages/ncbi-toolkit/package.py | 43 |
1 files changed, 36 insertions, 7 deletions
diff --git a/var/spack/repos/builtin/packages/ncbi-toolkit/package.py b/var/spack/repos/builtin/packages/ncbi-toolkit/package.py index 99fd7a7d94..b0a0bb3063 100644 --- a/var/spack/repos/builtin/packages/ncbi-toolkit/package.py +++ b/var/spack/repos/builtin/packages/ncbi-toolkit/package.py @@ -3,6 +3,8 @@ # # SPDX-License-Identifier: (Apache-2.0 OR MIT) +from glob import glob + from spack import * @@ -10,9 +12,15 @@ 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--21_0_0.tar.gz" + 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') - version('21_0_0', '14e021e08b1a78ac9cde98d0cab92098') + variant('debug', default=False, + description='Build debug versions of libs and apps') depends_on('boost@1.35.0:') depends_on('bzip2') @@ -30,17 +38,38 @@ class NcbiToolkit(AutotoolsPackage): depends_on('bamtools') def configure_args(self): - return ['--without-sybase', '--without-fastcgi'] + 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): - compiler_version = self.compiler.version.joined - - with working_dir(join_path( - 'GCC{0}-DebugMT64'.format(compiler_version), 'build')): + with working_dir(join_path(glob( + '*MT64')[0], 'build')): make('all_r') |