Hi PT,
What exactly do you mean by Galaxy on the Cloud appears to expect that the
imported and converted fastq files are in the same S3 bucket where the
fastq.gz files were? Once imported from S3, you're correct in that
everything will be on the local EBS volume.
-Dannon
On Sun, Oct 6, 2013 at 4:43 AM, p Vedell ptved...@hotmail.com wrote:
Hi,
** **
I had fastq.gz files in an Amazon S3 bucket. I created a Galaxy on the
Cloud instance using CloudMan. I used GetData and pasted in the url’s of
the fastq.gz files into Galaxy on the Cloud. They were successfully
imported into the session and converted to fastq’s, it seems. However, at
the next step (fastq groomer), Galaxy on the Cloud appears to expect that
the imported and converted fastq files are in the same S3 bucket where the
fastq.gz files were. But, they are not there. I read somewhere in
documentation or notes that the data is actually in /mnt/galaxyData folder.
However, I am not sure how to point fastq groomer to this place in the web
interface or alternatively, I am not sure how to move the fastq’s back to
the s3 bucket (w/o downloading and re-uploading which would be very
time-consuming). Thanks for any help you can provide.
** **
PT
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