Would it be possible that you have an old copy of the bx-python egg? You should have bx-python 0.7.1  

If you check your eggs directory and you see version 0.7.1, then there may be something wrong with bx-python. In this case, please upload your build and bam to our public server and try again; if it fails on our public server, share the datasets with me and I'll take a look. 

Thanks,
J.

--
Jeremy Goecks
Assistant Professor, Computational Biology Institute
George Washington University



On Mar 4, 2014, at 5:14 PM, Raj Ayyampalayam <raj76@uga.edu> wrote:

Hello,

I am trying to visualize a large genome (Large number of scaffolds) and a large (bam file) in trackster on our local galaxy instance (running release_2014.02.10).
When ever I try to do the above I see the following error in the logs:

  File "bbi_file.pyx", line 215, in bx.bbi.bbi_file.BBIFile.query (lib/bx/bbi/bbi_file.c:5596) 
  File "bbi_file.pyx", line 222, in bx.bbi.bbi_file.BBIFile.query (lib/bx/bbi/bbi_file.c:5210) 
  File "bbi_file.pyx", line 183, in bx.bbi.bbi_file.BBIFile.summarize (lib/bx/bbi/bbi_file.c:4475) 
  File "bbi_file.pyx", line 248, in bx.bbi.bbi_file.BBIFile._get_chrom_id_and_size (lib/bx/bbi/bbi_file.c:5656) 
  File "bpt_file.pyx", line 76, in bx.bbi.bpt_file.BPTFile.find (lib/bx/bbi/bpt_file.c:1388) 
  File "bpt_file.pyx", line 55, in bx.bbi.bpt_file.BPTFile.r_find (lib/bx/bbi/bpt_file.c:1154) 
AttributeError: 'BinaryFileReader' object has no attribute 'read_bits64' 

Trackster works OK when I load smaller data sets.

It seems that there was a fix for this in bx-python code, as per mail from Jeremy (http://dev.list.galaxyproject.org/trackster-error-for-viewing-rat-data-rn5-tp4662664p4662672.html).
How do I get the fixed code into my galaxy instance?

Thanks,
-Raj


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