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
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 ptvedell@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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Dannon Baker -
p Vedell