Thanks Jeremy,
I did what you suggested and now it no longer complains!
Not sure if I had edited datatypes_conf.xml but just copying the sample worked and let's just hope I did not break any of my changes
Regards,
Thon
Thon deBoer Ph.D., Bioinformatics Guru California, USA |p: +1 (650) 799-6839 |m: mailto:thondeboer@me.com thondeboer@me.com
Public profile on http://www.linkedin.com/pub/thon-de-boer/1/1ba/a5b/ LinkedIn
From: Jeremy Goecks [mailto:jeremy.goecks@emory.edu] Sent: Thursday, August 22, 2013 11:11 AM To: Anthonius deBoer Cc: sam guerler; Galaxy-dev Galaxy-dev Subject: Re: [galaxy-dev] Why does my trackster complain about not being able to display BED files?
Am I missing a converter?
Yes, you are missing the bed_to_bigwig converter.
If you haven't made changes to your datatypes_conf.xml file, you can just copy datatypes_conf.xml.sample to datatypes_conf.xml to get the needed converters.
If you've made changes to datatypes_conf.xml, you'll need to manually add the needed converters. We recently transitioned all the *_to_summary_tree converters to *_to_bigwig, so you'll want to remove the summary_tree converters and replace them with the bigwig converters.
And why would a BED file even needed to be converted?
Converter = indexer for visualizations. Datasets are indexed so that (a) aggregate (coverage) data is readily available when viewing a large region and (b) finding features in a small region (when zoomed in) is fast.
J.