diff options
Diffstat (limited to 'var/spack/repos/builtin/packages/blasr/package.py')
| -rw-r--r-- | var/spack/repos/builtin/packages/blasr/package.py | 83 |
1 files changed, 39 insertions, 44 deletions
diff --git a/var/spack/repos/builtin/packages/blasr/package.py b/var/spack/repos/builtin/packages/blasr/package.py index bc3ae0933f..79ae59cd55 100644 --- a/var/spack/repos/builtin/packages/blasr/package.py +++ b/var/spack/repos/builtin/packages/blasr/package.py @@ -13,71 +13,66 @@ class Blasr(Package): """The PacBio long read aligner.""" homepage = "https://github.com/PacificBiosciences/blasr/wiki" - url = "https://github.com/PacificBiosciences/blasr/archive/5.3.1.tar.gz" + url = "https://github.com/PacificBiosciences/blasr/archive/5.3.1.tar.gz" - version('5.3.1', sha256='ff7da5a03096294572e6c64340354da5c5ee1c86c277e7b899f2c170c1ac4049') + version("5.3.1", sha256="ff7da5a03096294572e6c64340354da5c5ee1c86c277e7b899f2c170c1ac4049") - depends_on('ncurses') - depends_on('hdf5+cxx@1.8.12:1.8') - depends_on('htslib') - depends_on('zlib') + depends_on("ncurses") + depends_on("hdf5+cxx@1.8.12:1.8") + depends_on("htslib") + depends_on("zlib") # 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('pbbam') - depends_on('blasr-libcpp') - depends_on('python', type='build') + depends_on("pbbam") + depends_on("blasr-libcpp") + depends_on("python", type="build") def setup_build_environment(self, env): - env.prepend_path('CPATH', self.spec['blasr-libcpp'].prefix) - env.prepend_path('CPATH', self.spec['blasr-libcpp'].prefix.pbdata) - env.prepend_path('CPATH', self.spec['blasr-libcpp'].prefix.alignment) - env.prepend_path('CPATH', self.spec['blasr-libcpp'].prefix.hdf) + env.prepend_path("CPATH", self.spec["blasr-libcpp"].prefix) + env.prepend_path("CPATH", self.spec["blasr-libcpp"].prefix.pbdata) + env.prepend_path("CPATH", self.spec["blasr-libcpp"].prefix.alignment) + env.prepend_path("CPATH", self.spec["blasr-libcpp"].prefix.hdf) # hdf has +mpi by default, so handle that possibility - if ('+mpi' in self.spec['hdf5']): - env.set('CC', self.spec['mpi'].mpicc) - env.set('CXX', self.spec['mpi'].mpicxx) + if "+mpi" in self.spec["hdf5"]: + env.set("CC", self.spec["mpi"].mpicc) + env.set("CXX", self.spec["mpi"].mpicxx) def setup_run_environment(self, env): - env.prepend_path('PATH', self.spec.prefix.utils) + env.prepend_path("PATH", self.spec.prefix.utils) - @run_before('install') + @run_before("install") def configure(self, spec, prefix): configure_args = [ - 'LIBPBDATA_INC={0}'.format( - self.spec['blasr-libcpp'].prefix), - 'LIBPBDATA_LIB={0}'.format( - self.spec['blasr-libcpp'].prefix.pbdata), - 'LIBBLASR_LIB={0}'.format( - self.spec['blasr-libcpp'].prefix.alignment), - 'LIBBLASR_INC={0}'.format( - self.spec['blasr-libcpp'].prefix), - 'LIBPBIHDF_INC={0}'.format(self.spec['blasr-libcpp'].prefix), - 'LIBPBIHDF_LIB={0}'.format(self.spec['blasr-libcpp'].prefix.hdf), - 'HDF5_INC={0}'.format(self.spec['hdf5'].prefix.include), - 'HDF5_LIB={0}'.format(self.spec['hdf5'].prefix.lib), - '--shared' + "LIBPBDATA_INC={0}".format(self.spec["blasr-libcpp"].prefix), + "LIBPBDATA_LIB={0}".format(self.spec["blasr-libcpp"].prefix.pbdata), + "LIBBLASR_LIB={0}".format(self.spec["blasr-libcpp"].prefix.alignment), + "LIBBLASR_INC={0}".format(self.spec["blasr-libcpp"].prefix), + "LIBPBIHDF_INC={0}".format(self.spec["blasr-libcpp"].prefix), + "LIBPBIHDF_LIB={0}".format(self.spec["blasr-libcpp"].prefix.hdf), + "HDF5_INC={0}".format(self.spec["hdf5"].prefix.include), + "HDF5_LIB={0}".format(self.spec["hdf5"].prefix.lib), + "--shared", ] - python('configure.py', *configure_args) + python("configure.py", *configure_args) - @run_before('install') + @run_before("install") def build(self, spec, prefix): - os.environ['CPLUS_INCLUDE_PATH'] = join_path( - self.stage.source_path, 'include') + os.environ["CPLUS_INCLUDE_PATH"] = join_path(self.stage.source_path, "include") make() def install(self, spec, prefix): mkdir(prefix.utils) mkdir(prefix.bin) - install('blasr', prefix.bin.blasr) - install('utils/loadPulses', prefix.utils) - install('utils/pls2fasta', prefix.utils) - install('utils/samFilter', prefix.utils) - install('utils/samtoh5', prefix.utils) - install('utils/samtom4', prefix.utils) - install('utils/sawriter', prefix.utils) - install('utils/sdpMatcher', prefix.utils) - install('utils/toAfg', prefix.utils) + install("blasr", prefix.bin.blasr) + install("utils/loadPulses", prefix.utils) + install("utils/pls2fasta", prefix.utils) + install("utils/samFilter", prefix.utils) + install("utils/samtoh5", prefix.utils) + install("utils/samtom4", prefix.utils) + install("utils/sawriter", prefix.utils) + install("utils/sdpMatcher", prefix.utils) + install("utils/toAfg", prefix.utils) |