Hi Will, This should be fixed as of this commit: https://bitbucket.org/galaxy/galaxy-central/commits/3a154b52090316dee61f4299... Best, J. -- Jeremy Goecks Assistant Professor of Computational Biology George Washington University On Apr 9, 2014, at 10:03 PM, William Holtz <wholtz@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-genom... http://dev.list.galaxyproject.org/trackster-error-for-viewing-rat-data-rn5-t...
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/24893a84ce13a18815e3006...). 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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