Dear Galaxy Team,

Two questions.

1) Is there a bare-bones version of Galaxy available somewhere?  That is, 
Galaxy with no tools pre-installed?  We are creating Ansible play books for 
configuring Docker/Galaxy instances with our NLP tools installed.  Currently we 
are using a fork of the Galaxy project with the bio tools removed, but this is 
less than ideal when we try to update to new versions of Galaxy.

Alternatively, does anyone have an automated process to delete unwanted tools 
that we could run immediately after cloning the main Galaxy repo?

2) Is is possible to either a) modify the existing upload tool, or b) implement 
a new upload tool?  Several options in the upload tool do not make sense in our 
domain (e.g. selecting a genome) and we would also like to do some 
post-processing to files after they have been uploaded.  I've looked at the 
code for the existing upload tool and it seems quite tightly coupled to the 
Galaxy code base.  I was hoping the "Downgrade upload tool" thread from a few 
weeks ago was going to help, but unfortunately for me (and good for the user) 
they found a solution that didn't involve installing a new upload tool.

However, could I follow the approach suggested in that thread?  I.E. go back in 
time and find an old upload.[py | xml] and use that as a starting point for my 
own custom upload tool?  How far back in time would I have to go to find an that was a standalone tool?


Research Associate
Department of Computer Science
Vassar College
Poughkeepsie, NY

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