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 <raj76@uga.edu
<mailto: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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