New subject: bz2 error and An error occurred running this job: Job output not returned from cluster

2 Apr 2012


      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
An error occurred running this job: Job output not returned from cluster
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-td3420...
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