Hi Nate,
Thanks for your reply,
I guess the idea is that the job is prepared in the interface which lets
a user select
the grid. This is currently located in my galaxy instance as a if
statement in the
default job dispatcher. Just before it sends it to the job runner and
all the preparation
is done there.
But regarding the command line you are probably right, it would just
mean that every job runner
on our instance will have to be patched to include this if statement as
to whether the command line
needs to be reassigned.
Another simple question regarding adding UI options to toolform.mako.
Could i parse them
to my module using javascript.
Although I feel the best approach would be to add these options to the
job model and then they would remain tracked in the database.
Cheers James.
On 2/14/2013 4:20 AM, Nate Coraor wrote:
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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