Hello Howard,

http://www.arabidopsis.org/browse/Cereon/index.jsp

    Monsanto SNP and Ler Collections

This genome appears to be under specific user conditions. In particular, these would prohibit any data coping into the public Galaxy instance as a native genome, since Galaxy does not have any restrictions on use. However, you may be able to obtain a fasta genome from this source and use it in the public Galaxy instance.

Best wishes,

Jen
Galaxy team


On 8/22/11 9:17 AM, Howard M. Goodman wrote:
Hi Jen,

Thank you.

I have an index, but not a genomic fasta file. The genomic fasta does not seem to be 
available as far as I can tell. Is there a way to "unbuild" an index into a 
fasta file? Or would you reconsider adding this index?

Note, I am a very novice Galaxy user.

Thanks again
Howard

On Aug 19, 2011, at 5:29 PM, Jennifer Jackson wrote:

Hello Howard,

To use this alternate as a reference genome:

1 - load the fasta version of the genome into your history
2 - when using tools, select the option "Use reference genome from history" (or 
similar), then select the fasta file

There is no need to load the index files, only the fasta file and to make certain that Galaxy 
assigns the file type as "fasta" (using the pencil icon to access the "Edit 
Attributes" to set the datatype if necessary).

Using FTP to load the data will be necessary. Instructions are on the tool form "Get 
Data ->  Upload" and detailed help is also available at:

http://galaxyproject.org/Learn/Upload%20via%20FTP

http://galaxyproject.org/Learn/Screencasts
see: Tool tutorials ->  Using FTP

Hopefully this helps!

Best,

Jen
Galaxy team

On 8/19/11 5:14 PM, Howard M. Goodman wrote:
I would like to use a "built in" Arabidopsis Landberg erecta (Ler) index instead of 
TAIR10 for example for all my analysis within Galaxy. I have such an index created by Mathew 
McCormack and have used it successfully doing a Bowtie test run on my home computer. It has the 
usual 6 Bowtie index files. Can you add this to the "built in" indexes or is there some 
way to add it to my history and use it in all the programs?

Thank you for you consideration.

Howard


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



--
Jennifer Jackson
http://usegalaxy.org
http://galaxyproject.org/Support
___________________________________________________________
The Galaxy User list should be used for the discussion of
Galaxy analysis and other features on the public server
at usegalaxy.org.  Please keep all replies on the list by
using "reply all" in your mail client.  For discussion of
local Galaxy instances and the Galaxy source code, please
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