On Thu, Dec 4, 2014 at 11:53 AM, David Matthews <pa...@bristol.ac.uk
<mailto:pa...@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_a_clean_environment
--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: green...@cardiff.ac.uk Web: http://www.cardiff.ac.uk
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