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.