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profiles using drmaa? #19

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JPatrickPett opened this issue Apr 27, 2020 · 0 comments
Open

profiles using drmaa? #19

JPatrickPett opened this issue Apr 27, 2020 · 0 comments

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@JPatrickPett
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I am wondering what is the best way to combine Snakemake profiles with drmaa.
As the --cluster-config option is deprecated in favor of --profile, one would need to set cluster specific configurations via profiles also for drmaa.

If a profile sets the --cluster option, a command, possibly a Python script, can be added to the profile which collects all the cluster configuration information and is used by Snakemake to submit the jobs. However, when supplying the --drmaa option, no such command can be passed, as Snakemake uses the API to submit jobs.

Thus, to add a rule specific cluster configuration one would again need --cluster-config, which is deprecated.
Another option would be to write a cluster-submission command supplied via --cluster that uses drmaa. But I am wondering, whether that is the intended way to go?

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