You should be able to use a custom genome with this tool by selecting "History" from the "Source for Genomic Data" parameter.

The bug you're describing has, to the best of my knowledge, been fixed in Galaxy and should not be present anymore. On which Galaxy instance are you seeing this issue? If this is not the main Galaxy server ( http://main.g2.bx.psu.edu/ ), you'll want to contact the maintainers of the instance that you're using and ask them to update the instance.

Best,

On Dec 14, 2011, at 1:31 PM, Rebecca C Mueller wrote:

Hi all,
Does anyone know if you can use the "Extract Genomic DNA" command with a genome not in the database? I am working with an algal genome (C. merolae) that isn't currently in the pulldown Database/Build menu. I keep getting the "Unspecified genome build" error, and am assuming that's the problem, as my other files appear to be formatted correctly (tab delimited without spaces for the intervals, same names for chromosomes in interval and fasta file, etc).
Thanks!
Rebecca
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