Fix **kw passing and remove queue name based switch

bjpop / rubra

Infrastructure code to support DNA pipeline

MIT License

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Fix **kw passing and remove queue name based switch #11

Closed genomematt closed 11 years ago

genomematt commented 11 years ago

This will break some of our scripts that assume terry-smp will set smp. I am not passing _arg as we dont consume any at the moment so less chance of silencing errors. Also note this use of *_kw is one reason why we cant also use it to set arbitrary #PBS flags. Another is the overloading of flags like -l which means you can't use a simple key:value system as keys are not unique.

bjpop commented 11 years ago

I've merged these changes into my master which now has the script_literals feature.

However I have created a new branch for the merge: https://github.com/bjpop/rubra/tree/genomematt-master

Matt's changes treat the smp queue as being equivalent to #PBS -l procs=8,tpn=8, which I think is not true. So until this is resolved, I'll leave it in that branch.

bjpop commented 11 years ago

Not pulling this request, due to issues with SMP queue.

However, I did cherry pick "Pass extra keyword arguments to Runnable_Script", which is now pushed to master.

I'll close this request.