Hi Eric,

Yes, you would need the data files locally, sort of the same way that genomes need to be built locally from 3rd party sources. For this dataset, do the following:


1. Obtain the input source data. There are two files.

File A. From the downloads section of FunDo website:
http://django.nubic.northwestern.edu/fundo/media/data/do_lite.txt
The file is tab-separated text. Disease, Entrez gene acc., gene symbol

File B. From the UCSC Table browser using "Get Data -> UCSC Main (or from their Downloads website): Genes track including positions, gene acc., and gene symbol.

2. Create a file that is tab-separated text with these columns (correct order is important).

chromosome
start
end
strand
gene symbol
gene acc
disease

3. General path to get from 1 -> 2

Sort both of the files by gene accession.
Do a join on the accession.
Extract the columns used by the tool.

You could do #3 in Galaxy with the Text Manipulation tools or outside of Galaxy with unix shell commands or simple scripting, this is up to you.

Hopefully this helps! Thank you for you patience,

Best,

Jen
Galaxy team

On 1/12/12 9:00 AM, Paniagua, Eric wrote:
Hi,

I'm trying to get the HGV tools set up on our local instance, and I've hit a 
stumbling block.  I can't find where to get a copy of the data files that FunDO 
uses.  They must exist because the tool seems to work fine on the main PSU 
instance, but after scouring the project's web page and online supplementary 
material for the related publications, I'm still empty handed.

Anyone know where to obtain them?  Is it required to build them again locally?

Thanks,
Eric

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