Ilya,

A search of the Galaxy codebase indicates that thirteen tools use symlinks 
(e.g. GATK, Sicer, Picard, Cuff*, Bowtie), so the changes required to support 
this new code are significant. (Changes would also likely be needed for tools 
in the tool shed.) Also, asking tool wrappers to delete symlinks would be an 
idiosyncratic requirement as tools assume they have a temporary working 
directory at their disposal.

For these reasons, it seems best to have the tool framework clean up symlinks 
as necessary to support the new code.

Best,
J.

On Sep 7, 2011, at 2:28 PM, Chorny, Ilya wrote:

> Ok, I figured out why you need the symlink.
>  
> Can you add an unlink after the process completes?
> i.e
>  
> for i, arg in enumerate( args ):
>             input_file_name = "./input%i" % ( i+1 )
>             os.unlink(input_file_name)
>  
> From: galaxy-dev-boun...@lists.bx.psu.edu 
> [mailto:galaxy-dev-boun...@lists.bx.psu.edu] On Behalf Of Chorny, Ilya
> Sent: Wednesday, September 07, 2011 9:18 AM
> To: galaxy-dev@lists.bx.psu.edu
> Subject: [galaxy-dev] cuffcompare wrapper
>  
> Hi Jeremy,
>  
> The symlink in the cuffcompare wrapper was causing galaxy to crash because I 
> run as the actual user and have to chmod the job_working directory at the end 
> so Galaxy can clean it up. Turns out is seems like the symlink is not needed. 
> Am I missing something. See below.
>  
> Your code:
> for i, arg in enumerate( args ):
>         input_file_name = "./input%i" % ( i+1 )
>         os.symlink( arg, input_file_name )
>         cmd += "%s " % input_file_name
>  
> My code:
> for i, arg in enumerate( args ):
>         cmd += arg
>  
>        
>  
> Ilya Chorny Ph.D.
> Bioinformatics Scientist I
> Illumina, Inc.
> 9885 Towne Centre Drive
> San Diego, CA 92121
> Work: 858.202.4582
> Email: icho...@illumina.com
> Website: www.illumina.com
>  
>  
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