Dear Jen.
Yes, that was my problem, I skipped some steps by relying too much on the 
screencast and ignoring the text.

Now I am reluctant to launch the AMI as I having trouble estimating my usage 
and costs on AWS - as a new user I have little
idea what to set many of the parameters in the usage calculator. Are there any 
examples of typical parameters and costs for running Galaxy on the cloud?
My first task is to map about 80 gbp of total paired end reads from genomic DNA 
from two accessions to a 900 mbp reference genome and
then find SNPs and INDELs. A ball-park figure would be reassuring!

From: Jennifer Jackson []
Sent: 09 April 2013 15:11
To: Thompson, Andrew
Cc: ''
Subject: Re: [galaxy-user] merging fastq files

Hi Andrew,

My first guess is that perhaps the region is not set correctly?

See " Step 1: One Time Amazon Setup", subsection 2, where region is " set your 
AWS Region to US East (Virginia)".
The image in the wiki for step 1.2 is slightly outdated, instead it will look 
like this:


Please give this a try and let us know if you continue to have issues.


Galaxy team

On 4/8/13 3:56 PM, Thompson, Andrew wrote:

Dear Jen
Thanks. I have merged the files and end up with 4 x 47 G fastq files for read 
mapping to the reference.
It seems this is too much data to analyse on the public main instance if the 
size limit is 250 G?
So I tried to set up the cloud option following the screencast 
(, but when I search for the current AMI 
name (861460482541/galaxy-cloudman-2011-03-22) it is not found in the list of 
community AMIs under Amazon's EC2 Management Console. Any ideas why this is not 

Jennifer Hillman-Jackson
Galaxy Support and Training

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