I'm in an odd situation:  I was given an older version of Galaxy with 
additional tools built into it by a new faculty member.  He brought this from 
his former institutions and wanted us to run his Galaxy instance on our 
systems.  We don't want to support several instances so we agreed to put his 
tools into our Galaxy implementation.  However, we are running into all kinds 
of snags.  The latest issue is that we realized changes have been made to 
upload.py to allow for additional data types.  Here's an example of what I mean:

def check_bam( temp_name ):
    return Bam().sniff( temp_name )
def check_sff( temp_name ):
    return Sff().sniff( temp_name )
def check_celstgz( temp_name ):
    return CelsTgz().sniff( temp_name )

While this doesn't seem like a big deal to add those changes into our 
installation, I'm concerned that doing so will make us unable to update Galaxy 
in the future.  Can you either confirm or deny that changes to upload.py on our 
system will be overwritten with Galaxy updates?


Dori Sajdak
Senior Systems Administrator
State University of NY at Buffalo
Center for Computational Research
701 Ellicott St
Buffalo, NY 14203
Phone: (716) 881-8934
Fax: (716) 849-6656
Web: http://ccr.buffalo.edu

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