Hi Raj,

Thanks for sharing your datasets. This issue should be fixed as of this commit 
in -central:

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

Best,
J.

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



On Mar 25, 2014, at 11:15 AM, Raj Ayyampalayam <ra...@uga.edu> wrote:

> Jeremy,
> 
> I uploaded my dataset to the main galaxy site and the visualization failed.
> Here is the link to the history: 
> https://usegalaxy.org/u/raj-a-n/h/amborella-viz-test
> I used the same genome and a cufflinks gtf file instead of the bam file (Bam 
> is too big to load).
> 
> I am seeing the same problem on both main and my local galaxy instances 
> (local is tracking latest galaxy-dist).
> 
> Thanks,
> -Raj
> 
> 
> On Wednesday, March 05, 2014 11:25:26 AM, Raj Ayyampalayam wrote:
>> I checked the version of bx-python egg and confirmed that it is
>> bx_python-0.7.1_7b95ff194725-py2.7-linux-x86_64-ucs2.egg.
>> 
>> I will upload the dataset to the public server and try it over there
>> and report.
>> 
>> Thanks,
>> -Raj
>> 
>> On Wednesday, March 05, 2014 11:21:56 AM, Jeremy Goecks wrote:
>>> 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 <ra...@uga.edu
>>> <mailto:ra...@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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>>> 
>> 
>> 
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> 
> 

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