2. The vast majority of the storage costs are fro the Gemome databases in the 700GB /mnt/galaxyIndices, which I don't need. Can this be reduced to the bare essentials ?

You can do this manually: 

1. Start a new Galaxy cluster (ie, one you can easily delete later)

2. ssh into the master instance and delete whatever genomes you don't need/want (these are all located under /mnt/galaxyIndices)

3. Create a new EBS volume of size that'll fit whatever's left on the original volume, attach it and mount it

4. Copy over the data from the original volume to the new one while keeping the directory structure the same (rsync is probably the best tool for this)

5. Unmount & detach the new volume; create a snapshot from it

6. For the cluster you want to keep around (while it is terminated), edit persistent_data.yaml in it's bucket on S3 and replace the existing snap ID for the galaxyIndices with the snapshot ID you got in the previous step

7. Start that cluster and you should have a file system from the new snapshot mounted.

8. Terminate & delete the cluster you created in step 1

If you don't want to have to do this the first time around on your custom cluster, you can first try it with another temporary cluster and make sure it all works as expected and then move on to the real cluster.

Best,

Enis