tutorial.md

layout	title	zenodo_link	questions	objectives	time_estimation	key_points	contributors	subtopic	tags	requirements
tutorial_hands_on	Galaxy Monitoring with Reports		How to monitor a Galaxy service with the Reports application?	Setup and start the Galaxy reports app.	30m	Galaxy supports pluggable monitoring extensions. The Reports webapp is one option to monitor your system.	natefoo bgruening slugger70 hexylena	features	monitoring	type topic_name tutorials internal admin ansible ansible-galaxy

Overview

{:.no_toc}

The reports application gives some pre-configured analytics screens.

Agenda

1. TOC {:toc}

{: .agenda}

Setting up Reports

The reports application is included with the Galaxy codebase and this tutorial assumes you've already done all of the setup required for Galaxy, systemd, uWSGI, and NGINX.

{% icon hands_on %} Hands-on: Setup Reports

1. First we add a basic configuration of the Reports app to the playbook templates. Create templates/galaxy/config/ folder, if it doesn't exist, and create templates/galaxy/config/reports.yml with the following contents:

   {% raw %}

   uwsgi:
       socket: 127.0.0.1:9001
       buffer-size: 16384
       processes: 1
       threads: 4
       offload-threads: 2
       static-map: /static/style={{ galaxy_server_dir }}/static/style/blue
       static-map: /static={{ galaxy_server_dir }}/static
       static-map: /favicon.ico=static/favicon.ico
       master: true
       virtualenv: {{ galaxy_venv_dir }}
       pythonpath: {{ galaxy_server_dir }}/lib
       mount: /reports=galaxy.webapps.reports.buildapp:uwsgi_app()
       manage-script-name: true
       thunder-lock: false
       die-on-term: true
       hook-master-start: unix_signal:2 gracefully_kill_them_all
       hook-master-start: unix_signal:15 gracefully_kill_them_all
       py-call-osafterfork: true
       enable-threads: true
   reports:
       cookie-path: /reports
       database_connection: "postgresql:///galaxy?host=/var/run/postgresql"
       file_path: /data
       filter-with: proxy-prefix
       template_cache_path: "{{ galaxy_mutable_data_dir }}/compiled_templates"

   {% endraw %}

2. In your galaxyservers group variables file, tell the playbook to deploy the reports configuration file:

   {% raw %}

   galaxy_config_templates:
   ...
     - src: templates/galaxy/config/reports.yml
       dest: "{{ galaxy_config_dir }}/reports.yml"

   {% endraw %}

3. Similar to Galaxy we will again use systemd to manage the Reports process.

   {% raw %}

   # systemd
   galaxy_systemd_reports: true
     ....

   {% endraw %}

4. Then we need to tell NGINX it should serve our Reports app under <server_url>/reports url. Edit your galaxyservers group variables file, and under the NGINX configuration, add a block for proxying the reports application. It should look like:

   location /reports/ {
       uwsgi_pass           127.0.0.1:9001;
       uwsgi_param          UWSGI_SCHEME $scheme;
       include              uwsgi_params;
   }

5. Run the playbook

6. The reports application should be available, under <server_url>/reports/.> {: .hands_on}