Markup safe egg problem/fetching the wrong eggs?
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
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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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
Hi,
I've got a strange problem with python paths/eggs. When I run any tool
On Fri, Feb 28, 2014 at 3:42 AM, Joseph Ward <j.x.ward@dundee.ac.uk> wrote: 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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participants (2)
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Joseph Ward -
Nate Coraor