Galaxy / Alveo Data Importer

The Alveo Data Importer is part of the Alveo package which is integrated into Galaxy / Alveo. It uses the Alveo HTTP API to pull data from Alveo into Galaxy.

Launching the Data Importer

There are two ways to launch the Alveo Data Importer.

Launching from Alveo

As described in Transferring Data to Galaxy for Processing, when you display the Items in an Item List and select Run in Galaxy, Alveo launches Galaxy in a new tab and also launches the Alveo Data Importer parameter screen. It also populates the parameter fields with the correct values in order to import all of the Items in the selected Item List.

The Alveo data is not imported until you click on the Galaxy screen.

This is the recommended method, because the parameters are pre-filled with correct values which will import your selected Item List.

Launching from Galaxy / Alveo

If you are already running Galax / Alveo, you can launch the Alveo Data Importer directly and import any of your Item Lists, provided you know the details to enter into the parameters.

To Launch the Alveo Data Importer from Galaxy / Alveo...
  • Click on Analyze Data in the Navigation Bar, unless the Analyze Data screen is already being displayed.
  • Click on Get Data in the Tools Panel on the left of the screen. The Tools in this group will be listed.
  • Click on Alveo Data Importer in the Get Data Tool Group. The Data Importer Parameters will be displayed in the central operation panel.

Data Importer Parameters

AlveoDataImporterParameters

  •  The URL Is constructed from the URL for the Alveo instance, followed by the directory "item_list" and then the sequence number of the Item List you wish to import. The sequence number can be difficult to determine. For example, https://app.alveo.edu.au/item_lists/490
  • See What’s an API Key? for more information. In order to use the Alveo HTTP API, the Data Importer needs to know your API Key, which gives it the authority to access your Alveo Item Lists.
  • When you are uploading multiple Items, Galaxy / Alveo will construct unique Dataset names by appending the Item Name to this string.
  • All file types can be uploaded, but exotic file types may not be readable by Galaxy / Alveo.