Hello,

Sorry for the delay in response. The annotation profiler requires a set of index files created from a UCSC database dump. A script was added to Galaxy in rev 3683:742fa2afcad9 (currently available in the galaxy-central repository, but, as of this moment, not yet in galaxy-dist), located at scripts/tools/annotation_profiler/build_profile_indexes.py that will create these indexes and the corresponding xml configuration for the specified genome. See scripts/tools/annotation_profiler/README.txt for more specifics on this process. Let us know if the provided readme is unclear on the required steps.

Thanks for using Galaxy,

Dan

On Mar 11, 2010, at 9:06 PM, CHAN Chee Seng wrote:

Hi,

I have configured and built my own galaxy server. I have set up most of the genome databases but I have a problem with the getting the “Tables to Use” to be displayed on the web interface.

I have looked at the following files.

1.   annotation_profiler_options.xml
   

2.   annotation_profiler_valid_builds.txt
   
   

I did not change the annotation_profiler_options.xml file (used as is) and annotation_profiler_valid_builds.txt contains just one line, hg18

which is fine since I am starting with human.

Where do I specify the location of my hg18?

Please let me know if you need more information.

Thanks for your help.

Best regards, Chee Seng, Chan Genome Institute of Singapore 60 Biopolis Street, Genome #02-01 Singapore 138672 DID 64788065

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