I'm running a cufflinks pipeline on the public server, and I'm having trouble using the locally cached sequence as a reference when building my cuffmerge file of cufflinks assembled transcripts for further cuffdiff analysis.
When I set up the job with my cufflinks outputs (produced either with or without using sequence and/or annotation information) Galaxy gives me "no options available" for the locally cached sequence (it actually does briefly flash mm10 before ultimately deciding there are no options). All my files in my history have the correct dbkey ("mm10"). I have the same problem with cuffcompare.
It can detect and find the right locally cached sequence when running cufflinks or cuffquant though.
Thanks for any help,