Storage Management

Contributors

Nate Coraor Martin Čech Helena Rasche Saskia Hiltemann

Questions

• How does Galaxy locate data?

• How can I have Galaxy use multiple storage locations?

Objectives

• Setup Galaxy with both the Hierarachical and Distributed Object Storages

Data Libraries

• Provide a convenient way to share datasets with users
• Great for commonly used datasets (e.g. reference data, GTN tutorial data)

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Speaker Notes

• Data libraries provide a convenient way for Galaxy administrators to share datasets with users.
• This is ideal for commonly used datasets such as reference data, or data for GTN tutorials.

Data Libraries

• Access to library datasets:
  • Shared Data menu, browse data and import into history
  • Directly from tool form

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Speaker Notes

• Users can browse these data libraries and import datasets directly into their histories.
• Additionally, these datasets can also be selected directly from the tool form.

Advantages of data libraries

• Avoid duplication of data
• Does not count towards user’s quota
• Libraries can be shared with all users, or specific groups
• Manage permissions on library/dataset level using roles and groups.
  • Admins can create libraries.
  • Ordinary users can be granted permission to manage libraries

Speaker Notes

• Every dataset in the library is stored only once, no matter how many users are using it in their histories.
• The data in data libraries does not count against user quotas.
• Management of libraries can be delegated to users.
• And lastly, libraries can be public, restricted to individuals, or to groups.

Importing Data

• There are multiple ways to add data to libraries:
  • From history
  • From user directory
  • From import directory and/or path (admins only)
  • From remote source (via API/BioBlend/ephemeris)

Speaker Notes

• Galaxy provides many options for importing data.
• You can import data from a history, or from a server directory.
• Importing data from a server directory is convenient, as Galaxy can recreate the folder structure that is on disk.
• Additionally Galaxy can store library data as a symlink.
• This prevents needing to copy large shared datasets into Galaxy’s own data store.

Configuration

In galaxy.yml:

• user_library_import_dir
  • Allows authorized non-administrators to upload a directory of files.
  • Directory must contain sub-directories named the same as user’s email.
  • Works well in combination with ftp_upload_dir.
• library_import_dir
  • Allows administrators to upload a directory of files.
• allow_path_paste
  • Admin-only, allows importing from any path that the Galaxy’s user has access to.

Speaker Notes

• The path of the server directories that users and admins can use to import files can be configured in galaxy.yml .
• For admins, it is also possible to enable import from any server path.

Key Points

• The distributed object store configuration allows you to easily expand that storage that is attached to your Galaxy.
• You can move data around without affecting users.

Thank you!