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bartongroup / slivka

http://bartongroup.github.io/slivka/
Apache License 2.0
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Allow a service's runner configurations to customise of environment variables and command line parameters #145

Closed foreveremain closed 1 week ago

foreveremain commented 2 weeks ago

Slivka's service definition allows different parameters to be passed to runners according to input parameters (data and other arguments) for a job, but does not allow the constructed commandline executed by the runner to be reconfigured.

e.g. for the ClustalO service, the binary has an argument which specifies the number of threads to use. In v0.80 of slivka's slivka-bio, this parameter is hardcoded regardless of the number of cores allocated to it on the executable platform.

At the very least, different runner configurations should allow values of the thread parameter to be adjusted. Ideally there could also be a way that a runner is informed that a particular parameter should map to information such as the number of cores, allowing each runner to map this data to the runtime platform as needed.

foreveremain commented 1 week ago

need some updated docs, at least with a demo.