Sorry about miss-named message. I found a solution which makes me realize this
might have been a bit of a python newbie 'duh' issue.
For those who might need something similar, solution is to add a .pth file to
site-packages folder of python version that galaxy is running under, e.g.
contains 1 line of text:
And now if your code imports say:
HTMLReportModule = __import__('custom_templates.html_report')
It will look in the python2.6_galaxy_custom_modules folder as well as the
Now is this the best solution? I haven't seen any folder reserved for custom
client python method code within a galaxy install, right? I believe this
approach lets any number of updates happen to the tool or to galaxy while
preserving the customized code module(s).
Thanks for any input,
P.s If anyone wants an extra helpful detail on this dynamic replacement of a
standard tool module with a custom one - this tip lets one work with any module
folder depth "a.b.c.d.my_module". If you skip the "fromlist" part then you
have to bother with mentioning b.c.d.my_module expressly. E.g. for the
HTMLReport class defined in html_report.py,
# See http://stackoverflow.com/questions/769534
HTMLReportModule = __import__('custom_templates.foo.bar.html_report',
fromlist=['does not in fact matter what goes here!'])
lets one then simply say:
htmlManager = HTMLReportModule.HTMLReport(...)
> Message: 2
> Subject: Re: [galaxy-dev] Can a tool upload a .loc file that is then ...
> Python code in galaxy tools can import all sorts of modules. Is there a way
> to add an extra path to the sys.path so that I can include some other python
> modules that way? I.e. in some galaxy python config file?
> I'd like to say in my tool code
> HTMLReportModule = __import__(html_template)
> htmlManager = HTMLReportModule.HTMLReport(tagGroup, options, query_stats)
> htmlManager.render(out_tabular_file, out_html_file)
> and in this way provide a switch from a standard report template that my
> galaxy tool has in its folder, to a custom one that a client has fiddled
> with and is comfortably outside galaxy's codespace. The html_template
> variable would have 'templates.html_report' for the stock template, but
> 'custom_templates.html_report' would pull it from wherever was set in the
> path. Seems like a secure approach. (I don't want to pass the paths via
> the browser).
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