Update: July 26, 2019
This section of the forum is now closed; we are working on a new support model for WDL that we will share here shortly. For Cromwell-specific issues, see the Cromwell docs and post questions on Github.

LSF support in Cromwell

Hello,
We would like to configure Cromwell to work with LSF. Initially I was not even sure the support for LSF is still there in the recent versions of Cromwell but was told that it is but it is merged with other backends.
How does one go about configuring LSF support? Is there a template for defining LSF backend?

To be honest, even the description of the SGE backend here
https://github.com/broadinstitute/cromwell#sun-gridengine-backend
is not very clear to me. It is too fragmented. If someone can share a simple full working example for SGE that would be a good start. Then perhaps it can be adapted to LSF.

Thanks

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Answers

  • KateNKateN admin Cambridge, MAMember, Broadie, Moderator admin

    Initially, LSF was its own backend, developed by a user who needed it. You can find that pull request here if you are interested in seeing how they implemented it.

    As of version 0.20, I believe, we merged LSF, SGE, and local into a single backend, as they were functionally similar. So it does still exist, just in a merged state.

  • inkink Member

    Thank you, yes I saw that pull request which went into 0.19 hotfix and which confused me a lot because I could not find the traces of it in the current development branch.

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