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From: Kelly Vincent <kpvincent@bx.psu.edu> Date: July 26, 2010 11:23:47 AM EDT To: buiduyminh@gmail.com Cc: Galaxy Lab <galaxy-lab@bx.psu.edu> Subject: Re: [galaxy-lab] [galaxy-dev] How to add megablast database?

Hi,

See the wiki page http://bitbucket.org/galaxy/galaxy-central/wiki/NGSLocalSetup for information on getting the database files in place.

If you want to use blastn instead of megablast, you would just need to modify the wrapper slightly. You will at minimum need to modify tools/metag_tools/megablast_wrapper.py, by changing the command-line call (line 72) appropriately. If you need only the same parameters as megablast uses, you can just change the python file that is called in the command tag in tools/metag_tools/ megablast_wrapper.xml. Otherwise, you'll need to add relevant parameters to the XML and python files.

Let us know if you need any further assistance.

Regards, Kelly

On Jul 24, 2010, at 10:56 AM, Minh Bui wrote:

...

Hi,

I am using local Galaxy on my computer. I would like to use megablast but I don't know how to add wgs and nt database to local galaxy (I am new to galaxy).

1. Where can I download those databases (if you dont mind, can you give me the link?) ? 2. How can I add those databases to galaxy? 3. What if I want to do BLASTN instead of megablast, how can I do that?

Thank you very much, _______________________________________________ galaxy-dev mailing list galaxy-dev@lists.bx.psu.edu http://lists.bx.psu.edu/listinfo/galaxy-dev

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