search

Mouse-Imaging-Centre / pydpiper

Python code for flexible pipeline control
Other
24 stars 10 forks source link

pydpiper 2.0.12 pipeline_executor.py fails if PYDPIPER_CONFIG_FILE is undefined in environment #394

Closed gdevenyi closed 5 years ago

gdevenyi commented 5 years ago 
Traceback (most recent call last):
      File "/opt/quarantine/pydpiper/2.0.12/install/bin/pipeline_executor.py", line 4, in <module>
        __import__('pkg_resources').run_script('pydpiper==2.0.12', 'pipeline_executor.py')
      File "/opt/quarantine/anaconda/5.1.0-python3/install/lib/python3.6/site-packages/pkg_resources/__init__.py", line 750, in run_script
        self.require(requires)[0].run_script(script_name, ns)
      File "/opt/quarantine/anaconda/5.1.0-python3/install/lib/python3.6/site-packages/pkg_resources/__init__.py", line 1527, in run_script
        exec(code, namespace, namespace)
      File "/opt/quarantine/pydpiper/2.0.12/install/lib/python3.6/site-packages/pydpiper-2.0.12-py3.6.egg/EGG-INFO/scripts/pipeline_executor.py", line 675, in <module>
        main()
      File "/opt/quarantine/pydpiper/2.0.12/install/lib/python3.6/site-packages/pydpiper-2.0.12-py3.6.egg/EGG-INFO/scripts/pipeline_executor.py", line 631, in main
        raise ValueError("PYDPIPER_CONFIG_FILE does not exist in your bash environment!")
    ValueError: PYDPIPER_CONFIG_FILE does not exist in your bash environment!
gdevenyi commented 5 years ago

Overly aggressive solution to #372 ?

bcdarwin commented 5 years ago

Yep, I thought I'd fixed that but maybe it didn't get merged properly or something. One sec ...

gdevenyi commented 5 years ago

Works okay if I export an empty variable.

bcdarwin commented 5 years ago

Fixed in develop.