Connecting to CloudStor

warning AARNet have announced that CloudStor will be decommissioned by the end of 2023. For long-term storage of your Galaxy data, we recommend archiving your histories to storage solutions provisioned by your institution. Find information on managing your Galaxy histories on the Galaxy Training Network. If you have any concerns about this transition, please make a support request.

The import/export tools allow you to transfer one or more files to a registered AARNet CloudStor account. Transfers to/from CloudStor are encrypted over HTTPS.

Before you can use this service, you must perform a one-off task where you must provide Galaxy with credentials to access your CloudStor account on your behalf. You must first setup an app specific password in CloudStor for Galaxy to use. You must then let Galaxy know what that app password is.

Setting up an app password in CloudStor

To create an app password:
Log into your CloudStor account and then click on Settings in the top right corner 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" this can be anything that helps you later identify the password in the future, for example "Galaxy". Fill in 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 email address and the password/token with be a randomly generated token. Please write this token down somewhere or copy it to your computer clipboard. When you click 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 by deleting the app password.

Click here for the most up to date instructions from AARNet.

Letting Galaxy know your app password

In Galaxy, go to your profile settings under the User menu > Preferences > Manage Information, where you will need to set OwnCloud/CloudStor Credentials.

Galaxy CloudStor screenshot

Server URL:

Username: The email your account is registered with

Password: Copied from the app password set up at CloudStor

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

warning WARNING: Your CloudStor 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 CloudStor account.

Data import from CloudStor

  1. File or files to be imported into your Galaxy history from Cloudstor are accessed from the Upload Data > Choose Remote Files tool:
    Choose remote files screenshot
  2. Single or multiple files can be selected for Import. Folders selected will import all files as individual files, not a Collection, into your History

Data export to CloudStor

  1. To export data to Cloudstor, use the Export datasets to files source tool
  2. If your Cloudstor account is configured inside Galaxy the Directory URI option will show your Cloudstor folder:
    CloudStor directory option screenshot

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