On Apr 2, 2012, at 1:43 PM, Robert Chase wrote:

> 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-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.

Could you also do:

>>> bz2

Which should show the path to the module.  Also, printing sys.path from the 
interactive interpreter and from within the file that fails 
(lib/galaxy/datatypes/checkers.py) would give a few more hints.

Thanks,
--nate

> 
> 
> 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 
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