On Thu, Aug 7, 2014 at 4:29 PM, Sajdak, Doris <dj...@buffalo.edu> wrote:
> 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?
>
> Thanks,
> Dori

That will cause you trouble with having to merge any future changes
to upload.py as well.

In this case, the sniffing should be handled via the Galaxy datatypes
mechanism (see datatypes_conf.xml for instance), so these hacks
may not be needed anymore?

Peter

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