Server: Other

Contributors

Authors: Nate Coraor Björn Grüning Simon Gladman Helena Rasche

Questions

• How to monitor a Galaxy service?

Objectives

• Learn about different monitoring strategies.

• Setup and start the Galaxy reports app.

Data Types

• Galaxy’s method of understanding users’ files.
• Data types and converters are shipped with Galaxy.
• Admin UI displays all available data types.
  • Can be configured by modifying config/datatypes_conf.xml file.
• Use class inheritance (text:json is a super class of hivtrace, biom1, d3_hierarchy…)
  • Affects how tools consume datasets.

Speaker Notes Some datatypes can be installed from toolshed but this practice is deprecated and discouraged.

Data Providers

Provide efficient access to data for viz & API

Framework provides direct link to read the raw dataset or use data providers to adapt it

In config, assert that visualization requires a given type of data providers

Data providers process data before sending to browser - slice, filter, reformat, …

Admin UI

Has a lot of tools and lists that are useful for administrators of the Galaxy server.

• Data types
• Data tables
• Display applications
• Users, groups, roles, and quotas
• Running jobs
• Installed Tools
• Tool whitelist
• Tool errors

Tools

• Install new tools - Use to install tools from the configured toolsheds.

• Monitor installation - Shows tools currently being installed.

• Manage tools - To list, manage, repair, upgrade, check status, uninstall or disable currently installed tools.

• Manage metadata - Can help with certain types of tool problems, like incorrect lineage.

• Manage whitelist - Allows admins to selectively prevent tool outputs from being sanitized (allows for interactive javascript pages such as visualizations).

• View lineage - Shows the revision history and default versions of tools.

• View error logs - Will show tool problems during Galaxy startup.

Other links

• Quotas - Allows for control of user disk space.
• Local Data - Links to the Reference Data and Data Managers UI.
• Users, Groups, Roles - Used for quotas, libraries, sharing…
• Impersonate user - Allows to switch to a user account. Has to be enabled in configuration.

Key Points

• Galaxy supports pluggable monitoring extensions.
• Use grafana or the reports webapp to monitor your service.

Thank you!