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" )) ),
-----
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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" )) ),
-----
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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" )) ),
-----
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participants (3)
-
IT Support -
Malave, Michael -
Nate Coraor