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:nate@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. ___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: