On Thu, Dec 4, 2014 at 11:53 AM, David Matthews <padam@bristol.ac.uk mailto:padam@bristol.ac.uk > wrote:
HI,
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:
https://wiki.galaxyproject.org/Admin/Config/Performance/ProductionServer#Use...
--nate
David,
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 - http://blogs.cardiff.ac.uk/arcca/2014/10/24/portal-to-a-new-galaxy/
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,
Tom
-- Thomas Green Senior Programmer ARCCA, Redwood Building (Tower), King Edward VII Avenue, Cardiff, Wales, CF10 3NB, UK Tel: +44 (0)29 208 79269 Fax: +44 (0)29 208 70734 Email: greent10@cardiff.ac.uk Web: http://www.cardiff.ac.uk