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Add $SHELL Option to BEE ScriptRequirement #845

Closed rstyd closed 1 week ago

rstyd commented 1 month ago

We're currently making the unspoken assumption that BEE users will always prefer to use BASH for their sbatch scripts. That hasn't been an issue previously, but with the addition of the pre/post script support we have to ensure that the code within those scripts is interoperable with the sbatch script they will be embedded within.

For this issue, we should add an additional option to the beeflow:ScriptRequirement that specifies which $SHELL the user prefers. I think this option should be the path to the $SHELL e.g. /bin/bash, /bin/csh/, /bin/tcsh.

jtronge commented 1 month ago

I'm thinking we might want to have this per-workflow rather than in the config file. I can see where some workflows would have to use csh for some code while bash for another one, as an example. Maybe it could be a part of beeflow:ScriptRequirement?

pagrubel commented 1 month ago

That sounds good. We could have default defined in the config though so that those who don't change do not have to specify it.

kchilleri commented 2 weeks ago

@rstyd have you pushed your code for this issue anywhere?

kchilleri commented 1 week ago

PR#856 closes this issue