Thank you, Jennifer, your reply is much appreciated.  I'll try out your 
instructions and see how this goes today.

Best,
Eric
________________________________________
From: Jennifer Jackson [j...@bx.psu.edu]
Sent: Tuesday, January 17, 2012 6:28 PM
To: Paniagua, Eric
Cc: galaxy-user@lists.bx.psu.edu
Subject: Re: [galaxy-user] Data files for FunDO tool in Human Genome Variation?

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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--
Jennifer Jackson
http://usegalaxy.org
http://galaxyproject.org/wiki/Support

___________________________________________________________
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