> Indeed, following error occurs:
> 
> 157.193.10.150 - - [19/Mar/2013:08:30:06 +0200] "GET /visualization/trackster 
> HTTP/1.1" 200 - "http://galaxy.bits.vib.be/"; "Mozilla/5.0 (X11; Linux x86_64) 
> AppleWebKit/535.22+ (KHTML, like Gecko) Chromium/17.0.963.56 
> Chrome/17.0.963.56 Safari/535.22+"
> galaxy.webapps.galaxy.api.datasets ERROR 2013-03-19 08:30:13,722 Error in 
> dataset API at listing contents: :
> Traceback (most recent call last):
>  File "/home/galaxy/galaxy-dist/lib/galaxy/webapps/galaxy/api/datasets.py", 
> line 41, in show
>    is_true( kwd.get( 'retry', False ) ) )
>  File "/home/galaxy/galaxy-dist/lib/galaxy/webapps/galaxy/api/datasets.py", 
> line 96, in _converted_datasets_state
>    if not data_provider.has_data( chrom ):
>  File 
> "/home/galaxy/galaxy-dist/lib/galaxy/visualization/data_providers/genome.py", 
> line 814, in has_data
>    st = summary_tree_from_file( self.converted_dataset.file_name )
>  File "/home/galaxy/galaxy-dist/lib/galaxy/visualization/tracks/summary.py", 
> line 114, in summary_tree_from_file
>    st = cPickle.load( st_file )
> EOFError

This is the error that occurs when trying to read a dataset's index. What you 
want to look for is the error that occurs when creating this index; you'll need 
to look in the database to find this error. Here's a SQL command that will look 
for the most recent summary tree converter jobs:

--
select * from job where tool_id like 'CONVERTER%summary_tree%' order by id desc;
--

Is there anything in standard out/error that would explain why the summary tree 
is not created?


> I have found the root cause I believe:
> > when I visualize datasets from a data library, the data is not displayed.
> > Getting them from the source history gets displayed is OK
> > Importing them from a data library in a history, and displaying in 
> > trackster works

I cannot reproduce this on a clean version of galaxy-dist. One guess is library 
permissions may be causing a problem. Are the datasets that you want to 
visualize in a library (or they themselves) under restricted access?

Thanks,
J.
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