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

Email: ichorny@illumina.com

Website: www.illumina.com