Thanks for your input, John.  I see, so from what you say, anything installed 
via pip in the virtual environment then exists in the module/class include 
namespace within galaxy python command line tool code.  Good to know.

I'll note that this approach is compatible with toolshed tools (I'm testing it 
via one) because it relies on a galaxy admin managed .loc file to list the 
generic and customized reporting modules.  The (toolshed) reporting tool ships 
with a .loc file that doesn't reference any customized reports, e.g. 
blast_reporting_templates.loc.sample is

   #value       name    description
   # Add list of html templates here 
   templates.html_report        Standard Report Provides report with sections 
and table sections

And then a galaxy admin adds an entry:
  # Customized templates listed below
  templates_custom.html_report  Customized report       Test customized report

Task for getting a customized report in place does require manual steps though: 
customized module, addition of the .pth file, and editing of the above .loc 


Message: 4
Date: Wed, 16 Apr 2014 06:47:14 -0500
From: John Chilton <>
To: "Dooley, Damion" <>
Cc: "" <>
Subject: Re: [galaxy-dev] Can a tool upload a .loc file that is then
        ... RENAME: custom galaxy tool python modules
Content-Type: text/plain; charset=UTF-8

If this is working it sounds reasonable. I think my approach might be
to setup Galaxy inside a virtualenv (as recommended here
and just install your extra dependencies inside that virtualenv using

$ . <path_to_virtualenv>/bin/activate
$ pip install dependency1
$ pip install dependency2

After that you should be able to just do a normal Python import.

I think you have another open question about the next steps of this -
but just to make it explicit - everything is going to work better in
"the Galaxy ecosystem" if you can avoid calling code from tools like
this and just use the sort of stock options. For instance - neither of
these approaches will work with the tool shed. Sometimes that is not
possible - I understand that - but I just thought I would put the
disclaimer out there.

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