Good Morning Nate,
Thanks for your information regarding the eggs, I now see how they work,
unfortunately our problems still persist (definitely not with the eggs this
time)and we are unable to get our much used and well like instance of galaxy to
start.
The trace below is what we see when attempting to start this instance, do you
have any suggestions or assistance as to how we can repair it and get it
running again?
Thanks in advance,
Michael.
===TRACE from run.sh===
File "./scripts/paster.py", line 34, in <module>
command.run()
File
"/home/home/galaxy/software/galaxy-central/eggs/PasteScript-1.7.3-py2.6.egg/paste/script/command.py",
line 84, in run
invoke(command, command_name, options, args[1:])
File
"/home/home/galaxy/software/galaxy-central/eggs/PasteScript-1.7.3-py2.6.egg/paste/script/command.py",
line 123, in invoke
exit_code = runner.run(args)
File
"/home/home/galaxy/software/galaxy-central/eggs/PasteScript-1.7.3-py2.6.egg/paste/script/command.py",
line 218, in run
result = self.command()
File
"/home/home/galaxy/software/galaxy-central/eggs/PasteScript-1.7.3-py2.6.egg/paste/script/serve.py",
line 276, in command
relative_to=base, global_conf=vars)
File
"/home/home/galaxy/software/galaxy-central/eggs/PasteScript-1.7.3-py2.6.egg/paste/script/serve.py",
line 313, in loadapp
**kw)
File
"/home/home/galaxy/software/galaxy-central/eggs/PasteDeploy-1.3.3-py2.6.egg/paste/deploy/loadwsgi.py",
line 204, in loadapp
return loadobj(APP, uri, name=name, **kw)
File
"/home/home/galaxy/software/galaxy-central/eggs/PasteDeploy-1.3.3-py2.6.egg/paste/deploy/loadwsgi.py",
line 224, in loadobj
global_conf=global_conf)
File
"/home/home/galaxy/software/galaxy-central/eggs/PasteDeploy-1.3.3-py2.6.egg/paste/deploy/loadwsgi.py",
line 248, in loadcontext
global_conf=global_conf)
File
"/home/home/galaxy/software/galaxy-central/eggs/PasteDeploy-1.3.3-py2.6.egg/paste/deploy/loadwsgi.py",
line 278, in _loadconfig
return loader.get_context(object_type, name, global_conf)
File
"/home/home/galaxy/software/galaxy-central/eggs/PasteDeploy-1.3.3-py2.6.egg/paste/deploy/loadwsgi.py",
line 413, in get_context
section)
File
"/home/home/galaxy/software/galaxy-central/eggs/PasteDeploy-1.3.3-py2.6.egg/paste/deploy/loadwsgi.py",
line 458, in _context_from_explicit
value = import_string(found_expr)
File
"/home/home/galaxy/software/galaxy-central/eggs/PasteDeploy-1.3.3-py2.6.egg/paste/deploy/loadwsgi.py",
line 18, in import_string
return pkg_resources.EntryPoint.parse("x="+s).load(False)
File "/home/home/galaxy/software/galaxy-central/lib/pkg_resources.py", line
1954, in load
entry = __import__(self.module_name, globals(),globals(), ['__name__'])
File "/home/home/galaxy/software/galaxy-central/lib/galaxy/web/buildapp.py",
line 19, in <module>
from galaxy import config, jobs, util, tools
File "/home/home/galaxy/software/galaxy-central/lib/galaxy/jobs/__init__.py",
line 4, in <module>
from galaxy import util, model
EOFError: EOF read where object expected
Removing PID file paster.pid
-----Original Message-----
From: Nate Coraor [mailto:n...@bx.psu.edu]
Sent: 06 March 2012 19:15
To: michael burrell (NBI)
Cc: galaxy-dev@lists.bx.psu.edu
Subject: Re: [galaxy-dev] Potential issue with eggs ?
On Feb 29, 2012, at 11:50 AM, Michael Burrell (TOC) wrote:
> Good evening all,
>
> I am seeing the following issue when attempting to start galaxy.
>
> Traceback (most recent call last):
> File "./scripts/paster.py", line 34, in <module>
> command.run()
> File
> "/home/home/galaxy/software/galaxy-central/eggs/PasteScript-1.7.3-py2.6.egg/paste/script/command.py",
> line 84, in run
> invoke(command, command_name, options, args[1:])
> File
> "/home/home/galaxy/software/galaxy-central/eggs/PasteScript-1.7.3-py2.6.egg/paste/script/command.py",
> line 123, in invoke
> exit_code = runner.run(args)
> File
> "/home/home/galaxy/software/galaxy-central/eggs/PasteScript-1.7.3-py2.6.egg/paste/script/command.py",
> line 218, in run
> result = self.command()
> File
> "/home/home/galaxy/software/galaxy-central/eggs/PasteScript-1.7.3-py2.6.egg/paste/script/serve.py",
> line 276, in command
> relative_to=base, global_conf=vars)
> File
> "/home/home/galaxy/software/galaxy-central/eggs/PasteScript-1.7.3-py2.6.egg/paste/script/serve.py",
> line 313, in loadapp
> **kw)
> File
> "/home/home/galaxy/software/galaxy-central/eggs/PasteDeploy-1.3.3-py2.6.egg/paste/deploy/loadwsgi.py",
> line 204, in loadapp
> return loadobj(APP, uri, name=name, **kw)
> File
> "/home/home/galaxy/software/galaxy-central/eggs/PasteDeploy-1.3.3-py2.6.egg/paste/deploy/loadwsgi.py",
> line 224, in loadobj
> global_conf=global_conf)
> File
> "/home/home/galaxy/software/galaxy-central/eggs/PasteDeploy-1.3.3-py2.6.egg/paste/deploy/loadwsgi.py",
> line 248, in loadcontext
> global_conf=global_conf)
> File
> "/home/home/galaxy/software/galaxy-central/eggs/PasteDeploy-1.3.3-py2.6.egg/paste/deploy/loadwsgi.py",
> line 278, in _loadconfig
> return loader.get_context(object_type, name, global_conf)
> File
> "/home/home/galaxy/software/galaxy-central/eggs/PasteDeploy-1.3.3-py2.6.egg/paste/deploy/loadwsgi.py",
> line 413, in get_context
> section)
> File
> "/home/home/galaxy/software/galaxy-central/eggs/PasteDeploy-1.3.3-py2.6.egg/paste/deploy/loadwsgi.py",
> line 458, in _context_from_explicit
> value = import_string(found_expr)
> File
> "/home/home/galaxy/software/galaxy-central/eggs/PasteDeploy-1.3.3-py2.6.egg/paste/deploy/loadwsgi.py",
> line 18, in import_string
> return pkg_resources.EntryPoint.parse("x="+s).load(False)
> File "/home/home/galaxy/software/galaxy-central/lib/pkg_resources.py", line
> 1954, in load
> entry = __import__(self.module_name, globals(),globals(), ['__name__'])
> File
> "/home/home/galaxy/software/galaxy-central/lib/galaxy/web/buildapp.py", line
> 19, in <module>
> from galaxy import config, jobs, util, tools
> File
> "/home/home/galaxy/software/galaxy-central/lib/galaxy/jobs/__init__.py", line
> 4, in <module>
> from galaxy import util, model
> EOFError: EOF read where object expected Removing PID file paster.pid
>
> Would this suggest that the eggs are bad? What would be the best way
> to remedy the situation
Hi Michael,
I think your eggs are okay, the occurrence of "egg" in the traceback is simply
because the problem occurs beneath a call in the PasteDeploy egg. I think your
copy of the source may be corrupt. Could you verify that things are okay by
using 'hg status'? I'd also suggest finding and removing all .pyc files and
letting Python recreate them.
--nate
>
> Thanks
>
> Michael.
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