Connecting Galaxy to your institutional OwnCloud

OwnCloud logo

The import/export tools allow you to transfer files to and from selected institutional OwnCloud accounts directly.

This means you can browse your institutional OwnCloud drive and select files to import and analyze in Galaxy Australia. This is useful for large files, as they will transfer directly in the cloud without the need to download them to your own computer.

Is this service available to me?

You can use this service if your Australian institution's OwnCloud installation is configured in Galaxy.

Log into Galaxy and in the navigation bar, click on User > Preferences > Manage Information There should be an input for your organisation credentials.

If your institution isn't listed and you'd like it to be, please consider making a support request.

The following institutions are supported as of January 2023:

What is OwnCloud?

OwnCloud is an open-source framework that some organisations use to provision shareable cloud storage. Contact your research IT support to find out if your institution is using an OwnCloud instance. They may refer to their service by a different name.

Initial Setup

Before you can use this service, you must perform a one-off task where you provide Galaxy with credentials to access your OwnCloud account on your behalf. This uses the WebDAV protocol. There are two steps to setting up this connection.

  1. Getting an App Password

    Log into your institutional OwnCloud, and then and then click on Settings in the top right corner (not the bottom right) of the interface. Once in Settings you will see a menu on the left, click Security and you will see a section called App Passwords.

    App passwords simply require an "app name" which can be anything that helps you identify the password in the future, for example "Galaxy". Enter an "app name" and click Create new app password. You will then be presented with a username and password/token. Your username will be your institutional identifier (e.g. staff number or email address) and the password/token with be a randomly generated code. Please write this token down somewhere or copy it to your clipboard (CTRL + C). After clicking Done you will never be able to see this password/token again!

    Once the app password is created you will see it in the list of app passwords. You can also see when that password was last used. You also have the option to unlink your accounts (revoking access) by deleting the app password.

    You may see further examples of this process in the OwnCloud, AARNet, and Griffith university documentation.
  2. Letting Galaxy know your app password

    In Galaxy, go to your profile settings by clicking on User > Preferences > Manage Information, where you will need to set OwnCloud/CloudStor Credentials:
    OwnCloud credential entry in Galaxy user preferences
    Username: Your institutional login (may differ from your Galaxy Australia login)
    Password: The app password that you set above

    If the details above are configured properly, the next time you access the OwnCloud import/export functions in Galaxy (below) your folder/files will be visible.

warning Your OwnCloud credentials will be stored on this server. While reasonable efforts have been made to store these credentials safely, you must be aware and accept the risks of storing these credentials. In the event that the server is compromised, it may be possible for an attacker to gain access to your OwnCloud account. Access may be revoked via the OwnCloud interface.

Importing data

  1. File or files to be imported into your Galaxy history from your storage are accessed from the Upload Data > Choose Remote files:
    Importing files from OwnCloud into Galaxy
  2. From there, you can navigate to the files you need. Single or multiple files can be selected for Import. Selected folders will import all files as individual datasets (not a collection) into your Galaxy History.

Exporting data

  1. To export data to your OwnCloud, select Export datasets from the Galaxy tool panel:
    Export datasets Galaxy tool
  2. This tool will prompt you to navigate to a folder on your OwnCloud account.

    warning CAUTION: the export tool WILL overwrite existing OwnCloud files, so choose your target folder carefully!


When importing data:
Problem listing file source path FileSourcePath(file_source=, path='/')

This error message indicates that Galaxy can't connect to your OwnCloud.

If this is a newly configured connection this could be due to a typo in the password. To fix, try repeating the steps for “Getting an app password” (you can optionally delete your old app password), and using the new login.

Alternatively, check the configuration of your OwnCloud login username - remembering that this is different to your Galaxy login, and will be similar to colleagues at your organisation.