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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___________________________________________________________
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
use the Galaxy Development list:
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