Hi All,

I am currently working on a clustering interface for galaxy that will
hopefully enable users to pick the grid
in the tool form.

With tools that need access to files within the galaxy directory, I
have an idea to create a symlinked
fake galaxy root with all the files the tools needs for galaxy. This
is done currently in my own xml format
for each grid.

Problem is when parsing a tool_wrapper variable I need to prepare the
job and add my additional commands
to the command line so that the fake galaxy dir is created with the
symlinked databases.

Is it bad practice to disable preparation in each tool runner if the
job has come from my clustering module
or is there a better way to do this. Will the job runners
wrapper.prepare() overwrite any of my changes to the command-line
when the job makes its way to the runner say local.py.

Cheers James.
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