def load(self): # read the pipeline's config file: self.read_conf() # set self.conf by evoque-ing the steps template: steps_basename = os.path.basename(self.steps_syml) self.globals.update(self.sample.attrs_dict()) self.globals["working_dir"] = self.sample.working_dir() self.globals["label"] = self.sample.label() self.globals["org"] = self.sample.org sy = superyaml({"config_file": steps_basename, "globals": self.globals, "domain": self.globals["domain"]}) sy.load() self.conf = sy.config # create and add steps (steps are specified by conf sections that have a 'name' key) (fixme) for k, v in self.conf.items(): try: if v.has_key("name"): v["rnaseq"] = self step = RnaseqStep(v) # step.rnaseq=self self.add_step(step) except AttributeError: pass except Exception: raise
import re from yaml import load, dump from superyaml import superyaml h = { "config_file": "/users/vcassen/software/starflow/Temp/rnaseq/rnaseq.yml.template", "globals_file": "/users/vcassen/software/starflow/Temp/rnaseq/globals.yml", } sy = superyaml(h) sy.load() print "sy is\n%s" % dump(sy.config)