Configure BaseSpace connection from within Genomics Analysis Portal

  1. Log into Genomics Analysis Portal as root.
  2. Go to the Administration page, locate BaseSpace in the Configuration tile, and click on Configure.
  3. Fill in the Client Id and Client Secret from above and set the redirect URI to point to your Genomics Analysis Portal installation (for example Click on Save.
  4. Restart the CLC Genomics Server. If jobs are running, you may wish to put the server in Maintenance Mode first, as described in the administration manual at
When using the secure Genomics Analysis Portal link, Genomics Analysis Portal users will now see a button providing access to BaseSpace.

Note that when samples are selected for analysis in the Genomics Analysis Portal, the necessary files are downloaded from BaseSpace into the CLC Genomics Server temporary folder, and are deleted when they are no longer needed, i.e. when the Genomics Analysis Portal analysis is done. Due to the amount of space that can be taken up by these temporary files, it can be useful to specify an alternative, larger, disk area where temporary files created by the CLC Genomics Server can be written. Instructions to do this are provided in the server administration manual at