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-t...).
How do I get the fixed code into my galaxy instance?
Thanks, -Raj
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