> Indeed, following error occurs:
> - - [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?

Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:


Reply via email to