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:
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