On Feb 4, 2013, at 6:03 PM, James Boocock wrote:

> 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.

Hi James,

You'll probably need to make the changes to the command line after the command 
line has been assembled in prepare().  Can you do this later in prepare()?

--nate

> 
> 
> Cheers James.
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