Dave;
The sample management system you built looks great. I patched a clean instance of galaxy, install PyYAML, and then ran into this error. Do I have to create the nglims_config_file first?
dsidote@ruw-172 ~/galaxy-dist > python scripts/nglims/add_ng_defaults.py universe_wsgi.ini Traceback (most recent call last): File "scripts/nglims/add_ng_defaults.py", line 336, in <module> main(*args) File "scripts/nglims/add_ng_defaults.py", line 51, in main with open(config["nglims_config_file"]) as in_handle: KeyError: 'nglims_config_file'
Thanks for giving it a try. As a first step, you might want to sanity check that the patch applied correctly: is there a tool-data/nglims.yaml file? If so, you'll want to make sure these values are in your [app:main] section of your universe_wsgi.ini file: use_nglims=True nglims_config_file=tool-data/nglims.yaml If all went well with the patch, the universe_wsgi.ini.sample should have these values. Let me know if you have any other problems, Brad