Hi Will,

This should be fixed as of this commit:

https://bitbucket.org/galaxy/galaxy-central/commits/3a154b52090316dee61f42993eaa5a1fa40116d3

Best,
J.

--
Jeremy Goecks
Assistant Professor of Computational Biology
George Washington University



On Apr 9, 2014, at 10:03 PM, William Holtz <who...@lygos.com> wrote:

> 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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