On Thu, Dec 4, 2014 at 11:53 AM, David Matthews <padam(a)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#...
--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(a)cardiff.ac.uk Web:
http://www.cardiff.ac.uk