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:thondeb...@me.com>
thondeb...@me.com

Public profile on  <http://www.linkedin.com/pub/thon-de-boer/1/1ba/a5b/>
LinkedIn

 

From: Jeremy Goecks [mailto:jeremy.goe...@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.

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