Hello,
I am trying to fix something that I see in my paster.log file. At the end of the file, after everything has been loaded and the server is running, I get an error message saying that bz2 cannot be imported. When I start a python interpreter session and type in "import bz2" it runs without incident. I can even get the doc info.
I am also getting the error
when I run an "add column" to a basic data set from the text manipulation tools file. I'm wondering if they are related.
We are currently trying to check our queueing system to make sure it can correctly deliver
these back from the execution hosts to our filesystem.
-Robert Chase
Similar bugs appears here:
http://gmod.827538.n3.nabble.com/Job-output-not-returned-from-cluster-td3420173.html
http://osdir.com/ml/galaxy-source-control/2009-03/msg00015.html
Python 2.7.1 (r271:86832, Mar 13 2012, 17:18:00)
[GCC 4.1.2 20080704 (Red Hat 4.1.2-52)] on linux2
Type "help", "copyright", "credits" or "license" for more information.
>>> import bz2
>>> print bz2.__doc__
The python bz2 module provides a comprehensive interface for
the bz2 compression library. It implements a complete file
interface, one shot (de)compression functions, and types for
sequential (de)compression.
7.0.0.1:8080
Traceback (most recent call last):
File "./scripts/paster.py", line 34, in <module>
command.run()
File "/share/shared/galaxy-dist/eggs/PasteScript-1.7.3-py2.7.egg/paste/script/command.py", line 84, in run
invoke(command, command_name, options, args[1:])
File "/share/shared/galaxy-dist/eggs/PasteScript-1.7.3-py2.7.egg/paste/script/command.py", line 123, in invoke
exit_code = runner.run(args)
File "/share/shared/galaxy-dist/eggs/PasteScript-1.7.3-py2.7.egg/paste/script/command.py", line 218, in run
result = self.command()
File "/share/shared/galaxy-dist/eggs/PasteScript-1.7.3-py2.7.egg/paste/script/serve.py", line 276, in command
relative_to=base, global_conf=vars)
File "/share/shared/galaxy-dist/eggs/PasteScript-1.7.3-py2.7.egg/paste/script/serve.py", line 313, in loadapp
**kw)
File "/share/shared/galaxy-dist/eggs/PasteDeploy-1.3.3-py2.7.egg/paste/deploy/loadwsgi.py", line 204, in loadapp
return loadobj(APP, uri, name=name, **kw)
File "/share/shared/galaxy-dist/eggs/PasteDeploy-1.3.3-py2.7.egg/paste/deploy/loadwsgi.py", line 224, in loadobj
global_conf=global_conf)
File "/share/shared/galaxy-dist/eggs/PasteDeploy-1.3.3-py2.7.egg/paste/deploy/loadwsgi.py", line 248, in loadcontext
global_conf=global_conf)
File "/share/shared/galaxy-dist/eggs/PasteDeploy-1.3.3-py2.7.egg/paste/deploy/loadwsgi.py", line 278, in _loadconfig
return loader.get_context(object_type, name, global_conf)
File "/share/shared/galaxy-dist/eggs/PasteDeploy-1.3.3-py2.7.egg/paste/deploy/loadwsgi.py", line 413, in get_context
section)
File "/share/shared/galaxy-dist/eggs/PasteDeploy-1.3.3-py2.7.egg/paste/deploy/loadwsgi.py", line 458, in _context_from_explicit
value = import_string(found_expr)
File "/share/shared/galaxy-dist/eggs/PasteDeploy-1.3.3-py2.7.egg/paste/deploy/loadwsgi.py", line 18, in import_string
return pkg_resources.EntryPoint.parse("x="+s).load(False)
File "/share/shared/galaxy-dist/lib/pkg_resources.py", line 1954, in load
entry = __import__(self.module_name, globals(),globals(), ['__name__'])
File "/share/shared/galaxy-dist/lib/galaxy/web/buildapp.py", line 19, in <module>
from galaxy import config, jobs, util, tools
File "/share/shared/galaxy-dist/lib/galaxy/jobs/__init__.py", line 4, in <module>
from galaxy import util, model
File "/share/shared/galaxy-dist/lib/galaxy/model/__init__.py", line 13, in <module>
import galaxy.datatypes.registry
File "/share/shared/galaxy-dist/lib/galaxy/datatypes/registry.py", line 5, in <module>
import data, tabular, interval, images, sequence, qualityscore, genetics, xml, coverage, tracks, chrominfo, binary, assembly, ngsindex, wsf
File "/share/shared/galaxy-dist/lib/galaxy/datatypes/tabular.py", line 15, in <module>
from sniff import *
File "/share/shared/galaxy-dist/lib/galaxy/datatypes/sniff.py", line 7, in <module>
from galaxy.datatypes.checkers import *
File "/share/shared/galaxy-dist/lib/galaxy/datatypes/checkers.py", line 1, in <module>
import os, gzip, re, gzip, zipfile, binascii, bz2, imghdr
ImportError: No module named bz2