Hi All --

I'm a novice when it comes to all things programming, but I recently
installed my own instance of Galaxy because I'm working with very large
datasets. Everything seems to be running OK, but when I attempt to run
Cuffdiff (w/ ref. annotation and bias correction from UCSC genome) on
output from Tophat2, I get the following error: "*Error: sort order of
reads in BAMs must be the same*." I'm perplexed, because I downloaded this
output from Tophat2 that I ran on the public server, before putting it
through Cuffdiff on my local instance. When I tried running the same files
(prior to download) in Cuffdiff on the public server, they ran just fine.

So, why do the files run properly when I run them publicly, but not
locally? Am I missing some metadata? Is my install not complete? Does the
ordering of bam files change when you download them? I've had a hard time
finding solutions, so any tips are greatly appreciated.

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