I have a set of galaxy generated bam and bigwig files containing over 600 
contigs. When I attempt to view any of these files with trackster (on a local 
server running current galaxy-dist) I get the following in my log file:

galaxy.webapps.galaxy.api.datasets ERROR 2014-04-09 17:41:16,063 Error in 
dataset API at listing contents: 'BinaryFileReader' object has no attribute 
'read_bits64': 'BinaryFileReader' object has no attribute 'read_bits64'
Traceback (most recent call last):
  File "/home/galaxy/galaxy-dist/lib/galaxy/webapps/galaxy/api/datasets.py", 
line 44, in show
    is_true( kwd.get( 'retry', False ) ) )
  File "/home/galaxy/galaxy-dist/lib/galaxy/webapps/galaxy/api/datasets.py", 
line 106, in _converted_datasets_state
    if not data_provider.has_data( chrom ):
  File 
"/home/galaxy/galaxy-dist/lib/galaxy/visualization/data_providers/genome.py", 
line 1078, in has_data
    all_dat = bbi.query( chrom, 0, 2147483647, 1 ) or \
  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'

Two people have previously reported similar errors to this list. I don't know 
how to reply to messages that predate me joining the list, so here are links to 
the threads:
http://dev.list.galaxyproject.org/read-bits64-error-when-loading-large-genomes-data-into-trackster-tp4663622.html
http://dev.list.galaxyproject.org/trackster-error-for-viewing-rat-data-rn5-tp4662664.html


Following the suggestion of Jeremy Goecks in one of those old threads, I 
checked my bx-python version. The directory name bx-python is installed in 
indicates that I have version 0.7.1. Version 0.7.1 is from 2011 and pre-dates 
the the bug Jeremy mentioned 
(https://bitbucket.org/james_taylor/bx-python/commits/24893a84ce13a18815e3006c9f89b3828022ac96).
 Additionally, I ran:
strings 
./galaxy-dist/eggs/bx_python-0.7.1_7b95ff194725-py2.7-linux-x86_64-ucs4.egg/bx/bbi/bpt_file.so
 | grep read_bits64
and found a match, thus confirming the installed version pre-dates the bug fix, 
as all references to read_bits64 were removed in that commit. Additionally I 
cloned and compiled the current version of bx-python and found that the above 
command did not find any matches.

The offending installation of bx-python is part of the base installation of 
galaxy and not an item I added from the toolshed. I am unsure of how to go 
about replacing this egg with the newer version of bx-python. If someone can 
update the bx-python egg on http://eggs.g2.bx.psu.edu/ or give me instructions 
on how to replace my copy of the egg, I would greatly appreciate it!

Additionally, I found that all three of the versions of bx-python in the 
galaxy-main toolshed still contain this bug. Of the three versions of bx-python 
int the galaxy-test toolshed, only 3:5457e32b427c (2013-12-14) contains the bug 
fix.

Thank you in advance for your assistance!

-Will
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