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
file.
Damion
------------------------------
Message: 4
Date: Wed, 16 Apr 2014 06:47:14 -0500
From: John Chilton <jmchil...@gmail.com>
To: "Dooley, Damion" <damion.doo...@bccdc.ca>
Cc: "galaxy-dev@lists.bx.psu.edu" <galaxy-dev@lists.bx.psu.edu>
Subject: Re: [galaxy-dev] Can a tool upload a .loc file that is then
... RENAME: custom galaxy tool python modules
Message-ID:
<CANwbokfAJCLWH7afNk-s7yZXKcz6pWYVq4Ttn0Q=uezvfxt...@mail.gmail.com>
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
https://wiki.galaxyproject.org/Admin/Config/Performance/ProductionServer)
and just install your extra dependencies inside that virtualenv using
pip.
$ . <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.
-John
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