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,
On Mar 11, 2010, at 9:06 PM, CHAN Chee Seng wrote:
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
I have looked at the following files.
I did not change the annotation_profiler_options.xml file (used as is) and
annotation_profiler_valid_builds.txt contains just one line,
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.
Chee Seng, Chan
Genome Institute of Singapore
60 Biopolis Street, Genome
#02-01 Singapore 138672
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