diff options
Diffstat (limited to 'var/spack/repos/builtin/packages/ncbi-toolkit/package.py')
| -rw-r--r-- | var/spack/repos/builtin/packages/ncbi-toolkit/package.py | 109 |
1 files changed, 61 insertions, 48 deletions
diff --git a/var/spack/repos/builtin/packages/ncbi-toolkit/package.py b/var/spack/repos/builtin/packages/ncbi-toolkit/package.py index ab53332331..d4525a0edd 100644 --- a/var/spack/repos/builtin/packages/ncbi-toolkit/package.py +++ b/var/spack/repos/builtin/packages/ncbi-toolkit/package.py @@ -13,69 +13,82 @@ 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" + url = "ftp://ftp.ncbi.nih.gov/toolbox/ncbi_tools++/CURRENT/ncbi_cxx--22_0_0.tar.gz" - version('22_0_0', sha256='ef39429bbc7f13c44c0d327432d9cfb430f9f20d10d825e6b2c4ddd7ccce457f', - 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', sha256='48cc3ae24ca63d1ab1be148e7525e8c5b9f4eaa5eb36d172800784b640a84a4f', - url='ftp://ftp.ncbi.nih.gov/toolbox/ncbi_tools++/ARCHIVE/2018/Apr_2_2018/ncbi_cxx--21_0_0.tar.gz') + version( + "22_0_0", + sha256="ef39429bbc7f13c44c0d327432d9cfb430f9f20d10d825e6b2c4ddd7ccce457f", + 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", + sha256="48cc3ae24ca63d1ab1be148e7525e8c5b9f4eaa5eb36d172800784b640a84a4f", + 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') + variant("debug", default=False, description="Build debug versions of libs and apps") - depends_on('boost@1.35.0:') + depends_on("boost@1.35.0:") # TODO: replace this with an explicit list of components of Boost, # for instance depends_on('boost +filesystem') # See https://github.com/spack/spack/pull/22303 for reference depends_on(Boost.with_default_variants) - 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') + 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'] + 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) + 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']: + 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_) + 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') + with working_dir(join_path(glob("*MT64")[0], "build")): + make("all_r") |