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. ___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
