ex1-reports.md

GATC - 2017 - Melbourne

Runing the Reports Application - Exercise

Authors: Nate Coraor. 2017

Section 1 - Configure reports

Begin by making a copy of the reports config file to your config directory, and editing it:

$ sudo -u galaxy cp /srv/galaxy/server/config/reports.ini.sample /srv/galaxy/config/reports.ini
$ sudo -u galaxy -e /srv/galaxy/config/reports.ini

Since we serve Galaxy at the root of our webserver, we'll need to serve Reports from a subdirectory: /reports. This is the default if we enable the proxy-prefix filter, all we need to do is uncomment the proxy-prefix setting. We also need to point the reports application at Galaxy's PostgreSQL database:

filter-with = proxy-prefix
cookie_path = /reports
database_connection = postgresql:///galaxy?host=/var/run/postgresql
file_path = /srv/galaxy/data

Section 2 - Configure nginx

We now have to configure nginx to serve the reports app at /reports. This is done in /etc/nginx/sites-available/galaxy. Add the following upstream:

upstream reports {
    server localhost:9001;
}

And in addition, add this new section to the existing server { ... } block:

    location /reports {
        proxy_pass           http://reports;
        proxy_set_header     X-Forwarded-Host $host;
        proxy_set_header     X-Forwarded-For  $proxy_add_x_forwarded_for;
    }

Then, restart nginx with:

$ sudo systemctl restart nginx

Section 3 - Start reports

We need a way to start and stop the reports application. This can be done with supervisor. Add the following to /etc/supervisor/conf.d/galaxy.conf:

[program:reports]
command         = /srv/galaxy/venv/bin/python ./scripts/paster.py serve /srv/galaxy/config/reports.ini --log-file=/srv/galaxy/log/reports.log
directory       = /srv/galaxy/server
autostart       = true
autorestart     = true
startsecs       = 10
user            = galaxy