For a pilot I would just use our public instance at http://usegalaxy.org to polish up the exact workflow and settings that would give you satisfactory results on a subset of data. This way it would be much easier to figure out where you can "cut-corners" for performance. You will then have a "best-parctise" workflow that you'll be able to rerun on the cloud.

On Nov 23, 2010, at 3:17 PM, David Martin wrote:

Hello,

We are about to get about 200 GB of illumina reads(43 bp) from 20 samples, two groups of 10 animals. We are hoping to use Galaxy on the Cloud to compare gene expression between the two groups. First of all, do you think this is possible with the current state of Galaxy Cloud development? Secondly, we are currently practicing with small drosophila datasets (4 sets of 2 GB each), and over the course of a few days of doing relatively little besides grooming and filtering the data, we had already been charged $60 by Amazon, which we thought was a bit inefficient. What is the best way to proceed working from one day to the next? Should one terminate the cluster at Cloud Console and then stop(pause) the cluster at the AWS console, and then restart the instance the next day? Does one have to reattach all of the EBS volumes before restarting the cluster? We were just terminating the instance and then bringing it back up and all the data was still there, ie it worked fine, but when we looked after a couple days there were 45 EBS volumes there - much of it was surely redundant as our data wasn’t very large. Perhaps we need to take a snapshot and reboot the instance from this? Thank you for any hints regarding this matter, this is all very new to me. Let me know if you need clarification or more information.

David Martin
dmarti@lsuhsc.edu
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Anton Nekrutenko

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http://usegalaxy.org