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)
