Warning

This document is for an in-development version of Galaxy. You can alternatively view this page in the latest release if it exists or view the top of the latest release's documentation.

Galaxy Reports

Overview

For admins wishing to have more information on the usage of a Galaxy instance, one can configure and use the Galaxy Reports application. This is a separate application that can run beside Galaxy and must target the same database.

The Galaxy Reports application’s easy to use web interface will give you information on the following (and more):

  • Jobs

    • Today’s jobs

    • Jobs per day this month

    • Jobs in error per day this month

    • All unfinished jobs

    • Jobs per month

    • Jobs in error per month

    • Jobs per user

    • Jobs per tool

  • Workflows

    • Workflows per month

    • Workflows per user

  • Users

    • Registered users

    • Date of last login

    • User disk usage

  • System

    • Disk space maintenance

Configuration

  • Configure config/reports.yml in the same manner as your main galaxy instance (i.e., same database connection, but different web server port). This is a uWSGI YAML configuration file and should contain a reports section with app-specific configuration (options described below).

    • The default port for the reports application is 9001, and like Galaxy it only binds to localhost by default.

    • database_connection should match the value used in your Galaxy configuration

    • database_connection should point at a PostgreSQL database, experimental support for MySQL is available but SQLite is not supported at all.

  • Run reports in a uWSGI server with sh run_reports.sh

  • Use a web browser and go to the address you configured in reports.yml (defaults to http://localhost:9001/)

  • If you’d like the report tool to persist between sessions then use sh run_reports.sh --daemon to run it as a background process. As with Galaxy itself, use the --stop-daemon option to halt the background process. (The process output is written to reports_webapp.log if you have to debug a problem.)

  • To make your reports available from outside of the localhost using the NGINX proxy server, you can check out the documentation on how to protect Galaxy reports using authentication.

Configuration Options

log_level

Description

Verbosity of console log messages. Acceptable values can be found here: https://docs.python.org/library/logging.html#logging-levels

Default

DEBUG

Type

str

database_connection

Description

Database connection. Galaxy Reports are intended for production Galaxy instances, so sqlite (and the default value below) is not supported. An SQLAlchemy connection string should be used specify an external database.

Default

sqlite:///./database/universe.sqlite?isolation_level=IMMEDIATE

Type

str

file_path

Description

Where dataset files are stored.

Default

database/files

Type

str

new_file_path

Description

Where temporary files are stored.

Default

database/tmp

Type

str

template_cache_path

Description

Mako templates are compiled as needed and cached for reuse, this directory is used for the cache

Default

database/compiled_templates/reports

Type

str

debug

Description

Configuration for debugging middleware

Default

false

Type

bool

use_lint

Description

Check for WSGI compliance.

Default

false

Type

bool

use_heartbeat

Description

Write thread status periodically to ‘heartbeat.log’ (careful, uses disk space rapidly!)

Default

true

Type

bool

use_profile

Description

Profiling middleware (cProfile based)

Default

true

Type

bool

smtp_server

Description

Mail

Default

yourserver@yourfacility.edu

Type

str

error_email_to

Description

Mail

Default

your_bugs@bx.psu.edu

Type

str

enable_beta_gdpr

Description

Enables GDPR Compliance mode. This makes several changes to the way Galaxy logs and exposes data externally such as removing emails/usernames from logs and bug reports. You are responsible for removing personal data from backups. Please read the GDPR section under the special topics area of the admin documentation.

Default

false

Type

bool