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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 Postgres 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/)

Configuration Options

log_level

Description:Verbosity of console log messages. Acceptable values can be found here: https://docs.python.org/2/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_interactive

Description:NEVER enable this on a public site (even test or QA)
Default:true
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