Importing data from Sierra LIMS

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This section will guide you through generating external links to your data stored in the Sierra LIMS system to be downloaded directly into Galaxy.

Go to the Sierra portal and login to your account.
Click on the Sample ID of the sample you want to download data from.
Click on the Edit Sample Details button.
At the bottom of the page there will be an input box for creating a link, enter a description for the link in the Reason for link section, and click Create link. This will reload the page and add a new link to the sample under Authorised links to this sample.
Go back to the sample page or click on the hyperlink called link to take you back.
In the Results section select the lane you want to access your data from.
The bottom of the page, under the Links section, will now contain a list of wget commands with links for accessing all the files within that sample/lane.
Since this list is for wget commands, you need to extract out the links from the command. You can copy the link in the first set of double quotes for each line and galaxy-wf-edit Paste/Fetch Data them directly into Galaxy to download the files.