From: Guruprasad Ananda <gua110@bx.psu.edu>

Date: February 1, 2010 11:01:00 AM EST

To: Iwe Muiser <e.c.muiser@gmail.com>

Subject: Re: [galaxy-dev] Installing data for Galaxy

Hello Iwe,

I apologise for not covering data integration in detail on our wiki.

Here's how you add a new sequence to your Galaxy instance. In your case, for hg18, please download hg18.2bit file from http://hgdownload.cse.ucsc.edu/goldenPath/hg18/bigZips/, and then update tool-data/alignseq.loc file with the following line:

seq hg18 PATH_TO_hg18.2bit

Also, in future if you want to find out which ".loc" file to use, you can check the validator tag under the input parameter in the tool's xml file. 

Please let us know if you need any more information.

Thanks,

Guru

Galaxy team.

On Feb 1, 2010, at 9:39 AM, Iwe Muiser wrote:

Hello,

I have some questions about installing data onto my Ubuntu linux box. Mainly genomic data that can be used by the extract_genomic_dna.py script. I have done some attempts to get this working but now I'm quite stuck. First I downloaded this data from the UCSC ftp site. (ftp://hgdownload.cse.ucsc.edu/goldenPath/hg18/chromosomes to be precise). Then I added the following line to "faseq.loc" as instructed: "hg18    /home/muiser/data/Human_data/HG18/chromosomes".
After this I restarted the galaxy deamon but nothing seems to have happened. I have the idea that I am missing certain steps.

The ultimate goal is to get a local galaxy install working like the one on "http://main.g2.bx.psu.edu/"

The wiki is helpful to install new tools and to get an idea of how stuff works but sparsely mentions data integration. Except for MAFs which I tried as well. I'm now building an index for these .maf files which I assume will take quite some time.

I hope you can help me out a bit.

Thanks in advance,

Iwe Muiser
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Guruprasad Ananda

Graduate Student

Bioinformatics and Genomics

The Pennsylvania State University