Hi Nate,

This is the confusing thing. I've check the python versions and python path of the vm running galaxy and where the jobs are run and it's 2.7 across the board. I submit the script that fetches the eggs to the cluster using the same environment as the jobs are submitted in. I was just wondering if I was missing something obvious. It seems to be fetching the eggs after the job is complete (otherwise I'd assume the first job ran would fail, rather than the second).

I'll have another poke about.

Cheers,

Joe

On Fri, Feb 28, 2014 at 3:14 PM, Nate Coraor nate@bx.psu.edu wrote:

Hi Joe,

Something is automatically re-fetching the Python 2.6 eggs? Is the Galaxy server itself using 2.6 perhaps?

--nate

On Fri, Feb 28, 2014 at 3:42 AM, Joseph Ward j.x.ward@dundee.ac.uk wrote:

...

Hi,

I've got a strange problem with python paths/eggs. When I run any tool

that

...

produces html/text output I get the error: WARNING:galaxy.eggs:Warning: MarkupSafe (a dependent egg of Mako) cannot

be

...

fetched.

So if I close galaxy, delete the eggs folder, run fetch_eggs.py (on the cluster, sourcing the same files as galaxy does so the python path

should be

...

identical) it gathers all the eggs it needs for python 2.7.

Running a job then ends with the proper results, no errors, but not with python 2.6 eggs present in the eggs folder alongside the 2.7 eggs. Re-running the same job, or running any other that produces html output,

not

...

throws up the error mentioned above.

I can't see anywhere where I've missed a python path or anywhere where python 2.6 is mentioned.

Any idea what I'm missing here?

Cheers, Joe

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