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-rw-r--r--var/spack/repos/builtin/packages/ncbi-toolkit/package.py43
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')