Hi Vipin,

On 8/28/13 1:34 PM, Vipin TS wrote:

Hello,

I am slightly confused with adding a new genome to my local Galaxy instance, I am using the recent default branch 10411:c42567f43aa7 (following the documentation at http://wiki.galaxyproject.org/Admin/Data%20Integration)

I have edited the ~/galaxy-dist/tool-data/all_fasta.loc to add new Arabidopsis genome and updated ~/galaxy-dist/tool-data/shared/ucsc/builds.txt, when I restarted my local instance, I am not finding the newly added genome in database.

Is it not showing up under the list of databases/genomes when you at these locations:

1 - Get Data -> Upload File -> Genome: (pull down menu)
or
2 - Click on the pencil icon for any dataset, first page of 'Edit Attributes' forms "Attributes -> Database/Build"

You mentioned restarting, which is good, because that is necessary. The next thing to double check is that the names are "exact" and that the files are tab delimited, not space delimited, and have no trailing or extra whitespace (this is easy to slip in by accident).

Or do you mean that it is not showing up as a target database/genome for a particular tool? Tools/groups of tools require additional set up, as explained on this page (also linked from the one you mention - which also has information about rsync of the indexes/loc files the public Main instance uses):
http://wiki.galaxyproject.org/Admin/NGS%20Local%20Setup

If this doesn't help solve the issue, pls send more details, perhaps a sample of files, and we can help.

Jen
Galaxy team

any idea what is going wrong here ?

thanks,

--/Vipin

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Jennifer Hillman-Jackson
http://galaxyproject.org