On Thu, Dec 4, 2014 at 11:53 AM, David Matthews <pa...@bristol.ac.uk 
<mailto:pa...@bristol.ac.uk> > wrote:


        We have had a copy of Galaxy working on a login node on our cluster 
here for a few weeks. We have tried to get it to work with the queue but could 
not and so reverted back to the login node for now. However, when we try to 
upload data (via URL or from the desktop) we now get this error:

        Traceback (most recent call last):
          File "/isys/galaxy/galaxy-dist/tools/data_source/upload.py", line 10, 
in <module>
            import galaxy.model
          File "/isys/galaxy/galaxy-dist/lib/galaxy/model/__init__.py", line 
27, in <module>
            import galaxy.datatypes.registry
          File "/isys/galaxy/galaxy-dist/lib/galaxy/datatypes/registry.py", 
line 10, in <module>
            import data
          File "/isys/galaxy/galaxy-dist/lib/galaxy/datatypes/data.py", line 2, 
in <module>
            import metadata
          File "/isys/galaxy/galaxy-dist/lib/galaxy/datatypes/metadata.py", 
line 22, in <module>
            from galaxy.util import listify
          File "/isys/galaxy/galaxy-dist/lib/galaxy/util/__init__.py", line 38, 
in <module>
            eggs.require( 'docutils' )
          File "/isys/galaxy/galaxy-dist/lib/galaxy/eggs/__init__.py", line 
411, in require
            return c[req.project_name].require()
          File "/isys/galaxy/galaxy-dist/lib/galaxy/eggs/__init__.py", line 
239, in require
            dists = self.resolve()
          File "/isys/galaxy/galaxy-dist/lib/galaxy/eggs/__init__.py", line 
192, in resolve
            if e.args[1].key != e.args[0].key:
        IndexError: tuple index out of range

Hi David,

I believe this is a dependency conflict. The best option would be to create a 
Python virtualenv and start Galaxy from that:




I agree with Nate - I think I had a number of issues similar to these when my 
Python was not quite setup correctly.  This is made worse when you have a 
virtual machine infrastructure connecting to your HPC cluster. The virtual 
machine is where the Galaxy server will reside and making sure Python versions 
match between the 2 systems can be tricky.  I eventually used pyenv 
(https://github.com/yyuu/pyenv) to manage my Python installations but a number 
of options are available (originally used virtualenv but due to Python versions 
having to match on local and remote side I used pyenv instead to compile the 
same version of Python)

I placed a few notes (although not about my python errors - maybe another blog 
post is on its ways) on our teams blog - 

I have more detailed instructions I wrote whilst setting up the system from 
scratch if you would like some further pointers.   Since Cardiff and Bristol 
are now part of a wider scheme to collaborate (i.e. GW4) maybe we can learn 
from each other.

Good luck,


Thomas Green        Senior Programmer
ARCCA, Redwood Building (Tower), King Edward VII Avenue, Cardiff, Wales, CF10 
Tel: +44 (0)29 208 79269        Fax: +44 (0)29 208 70734
Email: green...@cardiff.ac.uk        Web: http://www.cardiff.ac.uk


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