I'm trying to create a RNA-Seq Workflow with Bowtie/Tophat and Cufflinks using 
a newly assembled genome (not public).  I created the genome index files via 
Bowtie locally but Galaxy will not accept the .ebwt index files 
(n=4)--"Inappropriate content" error.

Second, for some reason, the Illumina fastq files will not load on the web 
version or my local version either.

(FYI, I successfully ran these same files through our local command line 
version of Tophat and Cufflinks without problems)

Please advise.


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