Nate,

I have been trying to figure out how to make the changes you suggested (i.e. write output files to the job_working_directory) and then move them over to files but I am having a difficult time navigating the code.  If you could point me in the right direction, that would be helpful.  I know the lib/galaxy/models/__init__.py initializes the output files but I don’t think that is the right place to make the change. This change probably needs to be done in the Job_Wrapper but most of the code is very cryptic to me. Any guidance would be greatly appreciated. These changes should not take very long to implement once I get a handle on the code.

Thanks,

Ilya

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