Hello Howard, To use this alternate as a reference genome: 1 - load the fasta version of the genome into your history 2 - when using tools, select the option "Use reference genome from history" (or similar), then select the fasta file There is no need to load the index files, only the fasta file and to make certain that Galaxy assigns the file type as "fasta" (using the pencil icon to access the "Edit Attributes" to set the datatype if necessary). Using FTP to load the data will be necessary. Instructions are on the tool form "Get Data -> Upload" and detailed help is also available at: http://galaxyproject.org/Learn/Upload%20via%20FTP http://galaxyproject.org/Learn/Screencasts see: Tool tutorials -> Using FTP Hopefully this helps! Best, Jen Galaxy team On 8/19/11 5:14 PM, Howard M. Goodman wrote:

I would like to use a "built in" Arabidopsis Landberg erecta (Ler) index instead of TAIR10 for example for all my analysis within Galaxy. I have such an index created by Mathew McCormack and have used it successfully doing a Bowtie test run on my home computer. It has the usual 6 Bowtie index files. Can you add this to the "built in" indexes or is there some way to add it to my history and use it in all the programs?

Thank you for you consideration.

Howard

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