On Wed, May 9, 2012 at 1:09 AM, Zeeshan Ali Shah <zashah@pdc.kth.se> wrote:

Hi, I was following screenshot and after adding workflow http://s3.amazonaws.com/heteroplasmy/heteroplasmy_information.html

Upon running it is mentioning that /mnt/galaxyIndices/hg19/bwa/base/hg19 which does not exist .. i have confirmed that after login to instance directly.

due to this reason it is unable to pick FASTQ file. any hint ?

The mentioned file does not exist but there should be a group of files that start with that particular name. The concept is described on the general Galaxy setup page: http://wiki.g2.bx.psu.edu/Admin/NGS%20Local%20Setup With that, could you describe you issue a bit better? I'm not sure what you mean by not being able to 'pick' a FASTQ file.

Also. When we newly create cloud man from AMI dated 22nd March 2011, Does it make sense to update Galxy via admin ? or just run it with out update..

At this point, this is actually no advisable because the process is likely to fail (there have been some structural changes to how Galaxy in installed that the automated process does not cover quite yet). However, a new image is being prepared with an updated Galaxy and should be available soon.

BR

Zeeshan

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