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-bounces@lists.bx.psu.edu [mailto:galaxy-dev-bounces@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
 
 
___________________________________________________________
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/