Server: Other

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# Server: Other

<div class="contributors-line">
		Authors: 
<a href="/training-material/hall-of-fame/natefoo/" class="contributor-badge contributor-natefoo"><img src="https://avatars.githubusercontent.com/natefoo?s=27" alt="Avatar">Nate Coraor</a>

<a href="/training-material/hall-of-fame/bgruening/" class="contributor-badge contributor-bgruening"><img src="/training-material/assets/images/orcid.png" alt="orcid logo"/><img src="https://avatars.githubusercontent.com/bgruening?s=27" alt="Avatar">Björn Grüning</a>

<a href="/training-material/hall-of-fame/slugger70/" class="contributor-badge contributor-slugger70"><img src="https://avatars.githubusercontent.com/slugger70?s=27" alt="Avatar">Simon Gladman</a>

<a href="/training-material/hall-of-fame/hexylena/" class="contributor-badge contributor-hexylena"><img src="/training-material/assets/images/orcid.png" alt="orcid logo"/><img src="https://avatars.githubusercontent.com/hexylena?s=27" alt="Avatar">Helena Rasche</a>

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<div class="footnote" style="bottom: 8em;"><i class="far fa-calendar" aria-hidden="true"></i><span class="visually-hidden">last_modification</span> Updated: Apr 6, 2021</div>

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Useful when presenting.

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### <i class="far fa-question-circle" aria-hidden="true"></i><span class="visually-hidden">question</span> Questions

- How to monitor a Galaxy service?

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### <i class="fas fa-bullseye" aria-hidden="true"></i><span class="visually-hidden">objectives</span> Objectives

- Learn about different monitoring strategies.

- Setup and start the Galaxy reports app.

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## 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.

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

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# 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, ...

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## 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

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## 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.

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## 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.

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### <i class="fas fa-key" aria-hidden="true"></i><span class="visually-hidden">keypoints</span> Key points

- Galaxy supports pluggable monitoring extensions.

- Use grafana or the reports webapp to monitor your service.

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## Thank You!

This material is the result of a collaborative work. Thanks to the [Galaxy Training Network](https://training.galaxyproject.org) and all the contributors!

<a href="/training-material/hall-of-fame/slugger70/" class="contributor-badge contributor-slugger70"><img src="https://avatars.githubusercontent.com/slugger70?s=27" alt="Avatar">Simon Gladman</a>

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<a rel="license" href="https://creativecommons.org/licenses/by/4.0/">
This material is licensed under the Creative Commons Attribution 4.0 International License</a>.