On Feb 3, 2011, at 11:58 AM, Peter Cock wrote:
On Thu, Feb 3, 2011 at 4:38 PM, Greg Von Kuster <greg@bx.psu.edu> wrote:
They run under a separate Galaxy webapp ...
Why? It seems to me it would be easier to have it under the admin pages of the main Galaxy webapp.
Running as a separate web application provides much more flexibility in many areas ( e.g., separate thread pools, user authentication, application settings, etc, etc, etc ).
... which you configure using the reports_wsgi.ini in the Galaxy install directory ( copy reports_wsgi.ini.sample and make appropriate changes for your local app ). This is where you'll set a port, and connect to the same database your Galaxy instance uses.
After setting the config, fire up the reports with:
%sh run_reports.sh
... and direct your browser to the port you've set in the config.
That didn't work on my development machine, no output at all. Having eventually found this Dev briefing apparently SQLite isn't supported:
https://bitbucket.org/galaxy/galaxy-central/wiki/Features/DevNewsBrief/2010_...
Is there any more documentation on this somewhere on the wiki that I've missed? It isn't working immediately on our production machine either - some relevant errors in reports_webapp.log include:
sqlalchemy.exc.ArgumentError: Invalid SQLite URL: sqlite://./database/universe.d?isolation_level=IMMEDIATE
Why would it use that connection string when I've recorded database_connection = postgres://... in reports_wsgi.ini?
There must be a problem with your config setting. The reports server will use the value defined in the "database_connection" setting.
[Errno 13] Permission denied: '/opt/galaxy-dist/database/compiled_templates/reports'
Is that a folder? When is it meant to be created?
Yes, this is a folder that should get created when you start the reports server. The config setting is named "template_cache_path" - see line 32 of ~/lib/galaxy/webapps/reports/config.py.
Thanks again,
Peter
Greg Von Kuster Galaxy Development Team greg@bx.psu.edu