Hello ...

I've installed a Galaxy server on one of our local machines (X86_64 linux running CentOS 5). When I go to modules that have a "Select a reference genome:" option, the dropboxes are empty.

I did find this thread:

But it's still not making sense to me. To test things out, I've downloaded the chr*.fa.gz files for hg18 from UCSC. Based on the advice in this thread, I've used faToTwoBit on each of the .fa files. These files are all sitting in /home/galaxy/local/galaxy/genomes/hg18/

This poster says to add the location to tool-data/alignseq.loc, but this file's comments says that it uses axt files for alignment data and nib files for seqs - these are clearly neither.

I added the following entry to my faseq.loc file:
hg18    /home/galaxy/local/genomes/hg18

and to my twobit.loc:
hg18 /home/galaxy/local/galaxy/genomes/hg18

But even after restarting the server hg18 isn't showing up in the reference genome. Clearly I'm doing something very wrong here, can anyone help me out here?

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