Problems running reporting app with reports.yml using --daemon

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Problems running reporting app with reports.yml using --daemon

Peter Briggs
Dear devs

I'm trying to update my ansible playbooks for deploying Galaxy and I'm having problems when trying to run the reporting app in release_17.09 using a 'reports.yml' file (rather than 'reports.ini'), when specifying the --daemon option.

Running without any arguments, the application appears to start okay - but if I do

sh ./ --daemon

then it exits with the error:

/XXXXX/galaxy/.venv/bin/python: unrecognized option '--safe-pidfile'
getopt_long() error

This seems to be coming from the invocation of uwsgi within the script, and looks like an issue with Galaxy's version of uWSGI: version 2.0.15 (as specified in the requirements.txt file) doesn't support the '--safe-pidfile' option (that needs uWSGI 2.0.16). Editing requirements.txt to use 2.0.16 seems to address this issue (as in, --daemon no longer fails on startup).

Has anyone else encountered this issue? My ultimate goal is to be able to serve the uwsgi-based reports app via an nginx proxy (which used to work with the old i.e. non-uwsgi reports.ini-configured version).

Thanks for your help,


Peter Briggs [hidden email]
Bioinformatics Core Facility University of Manchester
B.1083 Michael Smith Bldg Tel: (0161) 2751482

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