I wish to remove most of the mnt/galaxyIndices/genomes files so I can have a
smaller volume that contains those files and save money.
I am new to this system. I have set up a Galaxy Cloudman account and used the
tools on the web interface, and I can ssh the server using Ubuntu. So far, so
I tried the first approach here twice
https://wiki.galaxyproject.org/CloudMan/CustomizeGalaxyCloud but the system
hangs (>24h). I can't follow the "manual" instructions on this page and I'm
not sure it would result in a smaller volume anyway.
So, I was trying to follow Enis' steps from this thread to reduce the size of
the galaxyIndices volume:
His instructions are:
"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
8. Terminate & delete the cluster you created in step 1"
Here are my questions to help me to get through step 4:
1) Step 1: Is a "cluster" the same thing as an "instance"?
2) Step 2: I deleted the directories for individual genomes using rm -rf .
Is that the correct approach?
3) Step 3: Do I add the newly created EBS volume to the same instance
where I deleted the genomes? Or is it added the instance I want to keep?
4) Step 3: I can see how to attach this newly created volume using the AWS
EC2 management console, but how do I mount it? (and unmount it in Step 5?)
5) Step 4: what is the syntax for the rsync (or cp) command to copy
directories/files from one volume to another volume (within the same instance,
or in if they are in different instances)?
Any help would be gratefully received!
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