The problem is that you have an egg conflict with an existing Python 
installation. The recommended way to fix this is to set up a virtual 
environment as discussed here:

http://wiki.galaxyproject.org/Admin/Config/Performance/ProductionServer?action=show&redirect=Admin%2FConfig%2FPerformance%2FProduction+Server

Best,
J.

On Jan 14, 2013, at 3:10 PM, <mark.r...@syngenta.com> wrote:

> Ah, yes.  I forgot about the bug icon.  Sorry, still pretty new to galaxy.
>  
> Here is the error message:
>  
> /home/rosema1/Projects/galaxy-dist/lib/galaxy/__init__.py:79: UserWarning: 
> Module markupsafe was already imported from 
> /usr/lib/python2.7/dist-packages/markupsafe/__init__.pyc, but 
> /home/rosema1/Projects/galaxy-dist/eggs/MarkupSafe-0.12-py2.7-linux-x86_64-ucs4.egg
>  is being added to sys.path
>   self.check_version_conflict()
>  
> Stdout in the info link says:
>  
> Creating column 4 with expression c3-c2+1
> Kept 100.00% of 96 lines.
>  
>  
> Thanks
>  
> Mark
>  
> From: Jeremy Goecks [mailto:jeremy.goe...@emory.edu] 
> Sent: Monday, January 14, 2013 2:56 PM
> To: Rose Mark USRE
> Cc: galaxy-dev@lists.bx.psu.edu
> Subject: Re: [galaxy-dev] text manipulation Compute tool error
>  
> If you click on the bug icon for the failed dataset (click on the dataset 
> name to open the dataset and find the icon), what is the error listed? If you 
> click on the information icon, is there any additional output in the standard 
> output or error?
>  
> J.
>  
> On Jan 14, 2013, at 2:50 PM, <mark.r...@syngenta.com> wrote:
> 
> 
> No.  When I save the file I wish to manipulate from my local galaxy and 
> upload it to the public galaxy and run “Compute” it works (i.e. a 
> tab-delimited file is produced with the computed field occurring last, the 
> job listing in the history is green, and the result is available for input 
> into other tools).  When I run it on my local galaxy a file is produced that 
> has the computed field last ( which is accurately computed but it appears 
> that the white space between it and the other columns appears to be possibly 
> only a space and not a tab), no error is reported but the job listing in the 
> history is red, and the output is not available for input into other tools.  
> I’ve tried this on other tab-delimited files and it does the same thing.
>  
> Mark
>  
>  
>  
> From: Jeremy Goecks [mailto:jeremy.goe...@emory.edu] 
> Sent: Monday, January 14, 2013 12:58 PM
> To: Rose Mark USRE
> Cc: galaxy-dev@lists.bx.psu.edu
> Subject: Re: [galaxy-dev] text manipulation Compute tool error
>  
> Can you reproduce this behavior on our public server? If so, it'll be much 
> easier for us to take a look at the issue. 
>  
> If you can't reproduce on our public server, then providing as many details 
> as possible about the problem will provide the best chance for the list to 
> help you. For instance:
>  
> *what is the exact error that the tool is returning?
> *does it happen with all datasets or a particular dataset?
> *does it happen with all dataset types (e.g., interval, bed, gtf) or just 
> some?
>  
> Thanks,
> J.
>  
>  
> On Jan 14, 2013, at 11:46 AM, <mark.r...@syngenta.com> wrote:
> 
> 
> 
> I’ve received no replies to this post though clearly I must be doing 
> something wrong since the tool would be useless if this were its normal 
> behavior and judging from other posts people are using it.  Please help.
>  
> Thanks
>  
> Mark
>  
> From: galaxy-dev-boun...@lists.bx.psu.edu 
> [mailto:galaxy-dev-boun...@lists.bx.psu.edu] On Behalf Of 
> mark.r...@syngenta.com
> Sent: Sunday, January 06, 2013 4:32 PM
> To: galaxy-dev@lists.bx.psu.edu
> Subject: [galaxy-dev] text manipulation Compute tool error
>  
> Hello
>  
> On a local install of galaxy I am getting seemingly erroneous behavior from 
> the  text manipulation tool “Compute”.  It will compute the expression I set 
> (c3-c2+1) but will concatenate it to the last column rather that create a new 
> column. Also the job errors and is shown in red. I can get around the 
> concatenation problem by using the Add Column tool but subsequent use of 
> Compute also errors and its results are unavailable for further analysis 
> though the output appears correct.
>  
> Can you help?
>  
> Mark
>  
> 
> 
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