Markup safe egg problem/fetching the wrong eggs?

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Markup safe egg problem/fetching the wrong eggs?

Joseph Ward
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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Re: Markup safe egg problem/fetching the wrong eggs?

Nate Coraor (nate@bx.psu.edu)
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 <[hidden email]> 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
>
> ___________________________________________________________
> Please keep all replies on the list by using "reply all"
> in your mail client.  To manage your subscriptions to this
> and other Galaxy lists, please use the interface at:
>   http://lists.bx.psu.edu/
>
> To search Galaxy mailing lists use the unified search at:
>   http://galaxyproject.org/search/mailinglists/
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Re: Markup safe egg problem/fetching the wrong eggs?

Joseph Ward
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 <[hidden email]> 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 <[hidden email]> 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
>
> ___________________________________________________________
> Please keep all replies on the list by using "reply all"
> in your mail client.  To manage your subscriptions to this
> and other Galaxy lists, please use the interface at:
>   http://lists.bx.psu.edu/
>
> To search Galaxy mailing lists use the unified search at:
>   http://galaxyproject.org/search/mailinglists/

The University of Dundee is a registered Scottish Charity, No: SC015096


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