def validate_program(self, programs):
# First we try to find the program in the local path
program_paths = [which(program) for program in programs]
program_paths = [path for path in program_paths if path is not None]
print programs
print program_paths
if program_paths:
return program_paths[0]
elif self.setup is None:
msg = 'No program from the set "%s" found in PATH and no SMRT Analysis supplied' % str(
programs)
log.error(msg)
raise IOError(msg)
# Fallback to the Setup Script if needed
setup_programs = [
os.path.join(self.setup, 'analysis/bin', p) for p in programs
]
setup_programs = [validate_file(p) for p in setup_programs]
setup_programs = [path for path in setup_programs if path is not None]
if setup_programs:
return setup_programs[0]
else:
msg = 'No program from the set "%s" found in either PATH or SMRT Analysis env' % str(
programs)
log.error(msg)
raise IOError(msg)
def test_setup(self):
"""Determine whether we need a setup script, and which environment to use"""
if self.setup and which(self.exe):
# TODO: Add validation that the setup script works
log.info('"%s" not detected, using supplied environment' % self.name)
return True
elif self.setup and which(self.exe) is None:
log.info('%s detected, but using supplied environment instead.' % self.name + \
'Do not pass a "setup" argument to use local environment')
return True
elif self.setup is None and which(self.exe):
log.info('"%s" detected, using local environment' % self.name)
return False
else:
msg = '"%s" requires EITHER a valid executable in the local ' % self.name + \
'path OR a virtualenv setup script'
log.error( msg )
raise Exception( msg )
def test_setup(self):
"""Determine whether we need a setup script, and which environment to use"""
if self.setup and which(self.exe):
# TODO: Add validation that the setup script works
log.info('"%s" not detected, using supplied environment' %
self.name)
return True
elif self.setup and which(self.exe) is None:
log.info('%s detected, but using supplied environment instead.' % self.name + \
'Do not pass a "setup" argument to use local environment')
return True
elif self.setup is None and which(self.exe):
log.info('"%s" detected, using local environment' % self.name)
return False
else:
msg = '"%s" requires EITHER a valid executable in the local ' % self.name + \
'path OR a virtualenv setup script'
log.error(msg)
raise Exception(msg)
def validate_program(self, programs):
# First we try to find the program in the local path
program_paths = [which(program) for program in programs]
program_paths = [path for path in program_paths if path is not None]
print programs
print program_paths
if program_paths:
return program_paths[0]
elif self.setup is None:
msg = 'No program from the set "%s" found in PATH and no SMRT Analysis supplied' % str(programs)
log.error(msg)
raise IOError(msg)
# Fallback to the Setup Script if needed
setup_programs = [os.path.join(self.setup, "analysis/bin", p) for p in programs]
setup_programs = [validate_file(p) for p in setup_programs]
setup_programs = [path for path in setup_programs if path is not None]
if setup_programs:
return setup_programs[0]
else:
msg = 'No program from the set "%s" found in either PATH or SMRT Analysis env' % str(programs)
log.error(msg)
raise IOError(msg)
