Greetings,
I attempted to install Galaxy on a ROCKS 5.3 cluster. I checked out Galaxy to a location commonly accessible by all analysis nodes. I then set the path to Python 2.7 like so:
export PATH=/opt/galaxy-python/python:$PATH
However, executing run.sh gives me the error at the end of this message. The strange thing is that Galaxy runs fine on a CentOS 5.6 virtual machine.
Any help would be much appreciated. Thanks!
-----
Traceback (most recent call last): File "./scripts/paster.py", line 34, in ? command.run() File "/opt/galaxy-dist/eggs/PasteScript-1.7.3-py2.4.egg/paste/script/command.py", line 84, in run invoke(command, command_name, options, args[1:]) File "/opt/galaxy-dist/eggs/PasteScript-1.7.3-py2.4.egg/paste/script/command.py", line 123, in invoke exit_code = runner.run(args) File "/opt/galaxy-dist/eggs/PasteScript-1.7.3-py2.4.egg/paste/script/command.py", line 218, in run result = self.command() File "/opt/galaxy-dist/eggs/PasteScript-1.7.3-py2.4.egg/paste/script/serve.py", line 276, in command relative_to=base, global_conf=vars) File "/opt/galaxy-dist/eggs/PasteScript-1.7.3-py2.4.egg/paste/script/serve.py", line 311, in loadapp return loadapp( File "/opt/galaxy-dist/eggs/PasteDeploy-1.3.3-py2.4.egg/paste/deploy/loadwsgi.py", line 204, in loadapp return loadobj(APP, uri, name=name, **kw) File "/opt/galaxy-dist/eggs/PasteDeploy-1.3.3-py2.4.egg/paste/deploy/loadwsgi.py", line 225, in loadobj return context.create() File "/opt/galaxy-dist/eggs/PasteDeploy-1.3.3-py2.4.egg/paste/deploy/loadwsgi.py", line 625, in create return self.object_type.invoke(self) File "/opt/galaxy-dist/eggs/PasteDeploy-1.3.3-py2.4.egg/paste/deploy/loadwsgi.py", line 110, in invoke return fix_call(context.object, context.global_conf, **context.local_conf) File "/opt/galaxy-dist/eggs/PasteDeploy-1.3.3-py2.4.egg/paste/deploy/util/fixtypeerror.py", line 57, in fix_call val = callable(*args, **kw) File "/opt/galaxy-dist/lib/galaxy/web/buildapp.py", line 90, in app_factory add_controllers( webapp, app ) File "/opt/galaxy-dist/lib/galaxy/web/buildapp.py", line 39, in add_controllers module = __import__( module_name ) File "/opt/galaxy-dist/lib/galaxy/web/controllers/admin.py", line 310 link=( lambda item: (dict( operation="Manage users and groups", id=item.id, webapp="galaxy" ) if not item.default else dict( operation="Change amount", id=item.id, webapp="galaxy" )) ),
-----
IT Support wrote:
Greetings,
I attempted to install Galaxy on a ROCKS 5.3 cluster. I checked out Galaxy to a location commonly accessible by all analysis nodes. I then set the path to Python 2.7 like so:
export PATH=/opt/galaxy-python/python:$PATH
However, executing run.sh gives me the error at the end of this message. The strange thing is that Galaxy runs fine on a CentOS 5.6 virtual machine.
Any help would be much appreciated. Thanks!
Hi,
It looks despite adjusting $PATH, you're still getting Python 2.4. $PATH should point to the directory which contains the `python` binary, could this be:
/opt/galaxy-python/python/bin ?
--nate
Traceback (most recent call last): File "./scripts/paster.py", line 34, in ? command.run() File "/opt/galaxy-dist/eggs/PasteScript-1.7.3-py2.4.egg/paste/script/command.py", line 84, in run invoke(command, command_name, options, args[1:]) File "/opt/galaxy-dist/eggs/PasteScript-1.7.3-py2.4.egg/paste/script/command.py", line 123, in invoke exit_code = runner.run(args) File "/opt/galaxy-dist/eggs/PasteScript-1.7.3-py2.4.egg/paste/script/command.py", line 218, in run result = self.command() File "/opt/galaxy-dist/eggs/PasteScript-1.7.3-py2.4.egg/paste/script/serve.py", line 276, in command relative_to=base, global_conf=vars) File "/opt/galaxy-dist/eggs/PasteScript-1.7.3-py2.4.egg/paste/script/serve.py", line 311, in loadapp return loadapp( File "/opt/galaxy-dist/eggs/PasteDeploy-1.3.3-py2.4.egg/paste/deploy/loadwsgi.py", line 204, in loadapp return loadobj(APP, uri, name=name, **kw) File "/opt/galaxy-dist/eggs/PasteDeploy-1.3.3-py2.4.egg/paste/deploy/loadwsgi.py", line 225, in loadobj return context.create() File "/opt/galaxy-dist/eggs/PasteDeploy-1.3.3-py2.4.egg/paste/deploy/loadwsgi.py", line 625, in create return self.object_type.invoke(self) File "/opt/galaxy-dist/eggs/PasteDeploy-1.3.3-py2.4.egg/paste/deploy/loadwsgi.py", line 110, in invoke return fix_call(context.object, context.global_conf, **context.local_conf) File "/opt/galaxy-dist/eggs/PasteDeploy-1.3.3-py2.4.egg/paste/deploy/util/fixtypeerror.py", line 57, in fix_call val = callable(*args, **kw) File "/opt/galaxy-dist/lib/galaxy/web/buildapp.py", line 90, in app_factory add_controllers( webapp, app ) File "/opt/galaxy-dist/lib/galaxy/web/buildapp.py", line 39, in add_controllers module = __import__( module_name ) File "/opt/galaxy-dist/lib/galaxy/web/controllers/admin.py", line 310 link=( lambda item: (dict( operation="Manage users and groups", id=item.id, webapp="galaxy" ) if not item.default else dict( operation="Change amount", id=item.id, webapp="galaxy" )) ),
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:
Nate,
You were right: I was using Python 2.4; should have checked.
I changed the symlink in /opt/galaxy-python to point at a compiled version of Python 2.7. I then ran the run.sh script, only to get the same errors again.
I've even tried Python 3.2. Any clues? I run ROCKS 5.3.
Thanks! Nikhil
On Sep 2, 2011, at 12:43 PM, Nate Coraor wrote:
IT Support wrote:
Greetings,
I attempted to install Galaxy on a ROCKS 5.3 cluster. I checked out Galaxy to a location commonly accessible by all analysis nodes. I then set the path to Python 2.7 like so:
export PATH=/opt/galaxy-python/python:$PATH
However, executing run.sh gives me the error at the end of this message. The strange thing is that Galaxy runs fine on a CentOS 5.6 virtual machine.
Any help would be much appreciated. Thanks!
Hi,
It looks despite adjusting $PATH, you're still getting Python 2.4. $PATH should point to the directory which contains the `python` binary, could this be:
/opt/galaxy-python/python/bin ?
--nate
Traceback (most recent call last): File "./scripts/paster.py", line 34, in ? command.run() File "/opt/galaxy-dist/eggs/PasteScript-1.7.3-py2.4.egg/paste/script/command.py", line 84, in run invoke(command, command_name, options, args[1:]) File "/opt/galaxy-dist/eggs/PasteScript-1.7.3-py2.4.egg/paste/script/command.py", line 123, in invoke exit_code = runner.run(args) File "/opt/galaxy-dist/eggs/PasteScript-1.7.3-py2.4.egg/paste/script/command.py", line 218, in run result = self.command() File "/opt/galaxy-dist/eggs/PasteScript-1.7.3-py2.4.egg/paste/script/serve.py", line 276, in command relative_to=base, global_conf=vars) File "/opt/galaxy-dist/eggs/PasteScript-1.7.3-py2.4.egg/paste/script/serve.py", line 311, in loadapp return loadapp( File "/opt/galaxy-dist/eggs/PasteDeploy-1.3.3-py2.4.egg/paste/deploy/loadwsgi.py", line 204, in loadapp return loadobj(APP, uri, name=name, **kw) File "/opt/galaxy-dist/eggs/PasteDeploy-1.3.3-py2.4.egg/paste/deploy/loadwsgi.py", line 225, in loadobj return context.create() File "/opt/galaxy-dist/eggs/PasteDeploy-1.3.3-py2.4.egg/paste/deploy/loadwsgi.py", line 625, in create return self.object_type.invoke(self) File "/opt/galaxy-dist/eggs/PasteDeploy-1.3.3-py2.4.egg/paste/deploy/loadwsgi.py", line 110, in invoke return fix_call(context.object, context.global_conf, **context.local_conf) File "/opt/galaxy-dist/eggs/PasteDeploy-1.3.3-py2.4.egg/paste/deploy/util/fixtypeerror.py", line 57, in fix_call val = callable(*args, **kw) File "/opt/galaxy-dist/lib/galaxy/web/buildapp.py", line 90, in app_factory add_controllers( webapp, app ) File "/opt/galaxy-dist/lib/galaxy/web/buildapp.py", line 39, in add_controllers module = __import__( module_name ) File "/opt/galaxy-dist/lib/galaxy/web/controllers/admin.py", line 310 link=( lambda item: (dict( operation="Manage users and groups", id=item.id, webapp="galaxy" ) if not item.default else dict( operation="Change amount", id=item.id, webapp="galaxy" )) ),
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:
Nikhil,
As the user who is running galaxy type $which python Something to remember is in $PATH the first folder that points to python wins.
I actually use python 2.5.1 and it works perfectly. I also set the user environment ~/bin to search first (beginning of export PATH=~/bin/:/usr/bin/:/usr/local/bin/ ). My symlink to the python 2.5.1 is within bin folder from my home shell.
Mykey
On 9/7/11 11:17 AM, "IT Support" support@eng.uiowa.edu wrote:
Nate,
You were right: I was using Python 2.4; should have checked.
I changed the symlink in /opt/galaxy-python to point at a compiled version of Python 2.7. I then ran the run.sh script, only to get the same errors again.
I've even tried Python 3.2. Any clues? I run ROCKS 5.3.
Thanks! Nikhil
On Sep 2, 2011, at 12:43 PM, Nate Coraor wrote:
IT Support wrote:
Greetings,
I attempted to install Galaxy on a ROCKS 5.3 cluster. I checked out Galaxy to a location commonly accessible by all analysis nodes. I then set the path to Python 2.7 like so:
export PATH=/opt/galaxy-python/python:$PATH
However, executing run.sh gives me the error at the end of this message. The strange thing is that Galaxy runs fine on a CentOS 5.6 virtual machine.
Any help would be much appreciated. Thanks!
Hi,
It looks despite adjusting $PATH, you're still getting Python 2.4. $PATH should point to the directory which contains the `python` binary, could this be:
/opt/galaxy-python/python/bin ?
--nate
Traceback (most recent call last): File "./scripts/paster.py", line 34, in ? command.run() File "/opt/galaxy-dist/eggs/PasteScript-1.7.3-py2.4.egg/paste/script/command. py", line 84, in run invoke(command, command_name, options, args[1:]) File "/opt/galaxy-dist/eggs/PasteScript-1.7.3-py2.4.egg/paste/script/command. py", line 123, in invoke exit_code = runner.run(args) File "/opt/galaxy-dist/eggs/PasteScript-1.7.3-py2.4.egg/paste/script/command. py", line 218, in run result = self.command() File "/opt/galaxy-dist/eggs/PasteScript-1.7.3-py2.4.egg/paste/script/serve.py ", line 276, in command relative_to=base, global_conf=vars) File "/opt/galaxy-dist/eggs/PasteScript-1.7.3-py2.4.egg/paste/script/serve.py ", line 311, in loadapp return loadapp( File "/opt/galaxy-dist/eggs/PasteDeploy-1.3.3-py2.4.egg/paste/deploy/loadwsgi .py", line 204, in loadapp return loadobj(APP, uri, name=name, **kw) File "/opt/galaxy-dist/eggs/PasteDeploy-1.3.3-py2.4.egg/paste/deploy/loadwsgi .py", line 225, in loadobj return context.create() File "/opt/galaxy-dist/eggs/PasteDeploy-1.3.3-py2.4.egg/paste/deploy/loadwsgi .py", line 625, in create return self.object_type.invoke(self) File "/opt/galaxy-dist/eggs/PasteDeploy-1.3.3-py2.4.egg/paste/deploy/loadwsgi .py", line 110, in invoke return fix_call(context.object, context.global_conf, **context.local_conf) File "/opt/galaxy-dist/eggs/PasteDeploy-1.3.3-py2.4.egg/paste/deploy/util/fix typeerror.py", line 57, in fix_call val = callable(*args, **kw) File "/opt/galaxy-dist/lib/galaxy/web/buildapp.py", line 90, in app_factory add_controllers( webapp, app ) File "/opt/galaxy-dist/lib/galaxy/web/buildapp.py", line 39, in add_controllers module = __import__( module_name ) File "/opt/galaxy-dist/lib/galaxy/web/controllers/admin.py", line 310 link=( lambda item: (dict( operation="Manage users and groups", id=item.id, webapp="galaxy" ) if not item.default else dict( operation="Change amount", id=item.id, webapp="galaxy" )) ),
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:
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:
My co-worker solved it. You were both right about the Python version. This was a very silly mistake.
export PATH=/opt/galaxy-python/python:$PATH
Should have been
export PATH=/opt/galaxy-python:$PATH
So I basically put the binary (and not the _path_ to the binary) in the $PATH variable. This led to the errors I posted.
Thank you for all your help! Nikhil
On Sep 7, 2011, at 10:16 AM, IT Support wrote:
Nate,
You were right: I was using Python 2.4; should have checked.
I changed the symlink in /opt/galaxy-python to point at a compiled version of Python 2.7. I then ran the run.sh script, only to get the same errors again.
I've even tried Python 3.2. Any clues? I run ROCKS 5.3.
Thanks! Nikhil
On Sep 2, 2011, at 12:43 PM, Nate Coraor wrote:
IT Support wrote:
Greetings,
I attempted to install Galaxy on a ROCKS 5.3 cluster. I checked out Galaxy to a location commonly accessible by all analysis nodes. I then set the path to Python 2.7 like so:
export PATH=/opt/galaxy-python/python:$PATH
However, executing run.sh gives me the error at the end of this message. The strange thing is that Galaxy runs fine on a CentOS 5.6 virtual machine.
Any help would be much appreciated. Thanks!
Hi,
It looks despite adjusting $PATH, you're still getting Python 2.4. $PATH should point to the directory which contains the `python` binary, could this be:
/opt/galaxy-python/python/bin ?
--nate
Traceback (most recent call last): File "./scripts/paster.py", line 34, in ? command.run() File "/opt/galaxy-dist/eggs/PasteScript-1.7.3-py2.4.egg/paste/script/command.py", line 84, in run invoke(command, command_name, options, args[1:]) File "/opt/galaxy-dist/eggs/PasteScript-1.7.3-py2.4.egg/paste/script/command.py", line 123, in invoke exit_code = runner.run(args) File "/opt/galaxy-dist/eggs/PasteScript-1.7.3-py2.4.egg/paste/script/command.py", line 218, in run result = self.command() File "/opt/galaxy-dist/eggs/PasteScript-1.7.3-py2.4.egg/paste/script/serve.py", line 276, in command relative_to=base, global_conf=vars) File "/opt/galaxy-dist/eggs/PasteScript-1.7.3-py2.4.egg/paste/script/serve.py", line 311, in loadapp return loadapp( File "/opt/galaxy-dist/eggs/PasteDeploy-1.3.3-py2.4.egg/paste/deploy/loadwsgi.py", line 204, in loadapp return loadobj(APP, uri, name=name, **kw) File "/opt/galaxy-dist/eggs/PasteDeploy-1.3.3-py2.4.egg/paste/deploy/loadwsgi.py", line 225, in loadobj return context.create() File "/opt/galaxy-dist/eggs/PasteDeploy-1.3.3-py2.4.egg/paste/deploy/loadwsgi.py", line 625, in create return self.object_type.invoke(self) File "/opt/galaxy-dist/eggs/PasteDeploy-1.3.3-py2.4.egg/paste/deploy/loadwsgi.py", line 110, in invoke return fix_call(context.object, context.global_conf, **context.local_conf) File "/opt/galaxy-dist/eggs/PasteDeploy-1.3.3-py2.4.egg/paste/deploy/util/fixtypeerror.py", line 57, in fix_call val = callable(*args, **kw) File "/opt/galaxy-dist/lib/galaxy/web/buildapp.py", line 90, in app_factory add_controllers( webapp, app ) File "/opt/galaxy-dist/lib/galaxy/web/buildapp.py", line 39, in add_controllers module = __import__( module_name ) File "/opt/galaxy-dist/lib/galaxy/web/controllers/admin.py", line 310 link=( lambda item: (dict( operation="Manage users and groups", id=item.id, webapp="galaxy" ) if not item.default else dict( operation="Change amount", id=item.id, webapp="galaxy" )) ),
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:
galaxy-dev@lists.galaxyproject.org
-
IT Support -
Malave, Michael -
Nate Coraor