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<mailto:icho...@illumina.com>
Website: www.illumina.com<http://www.illumina.com>

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