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Workflow shell wrappers #273

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wpbonelli opened this issue Jan 30, 2022 · 1 comment
Closed

Workflow shell wrappers #273

wpbonelli opened this issue Jan 30, 2022 · 1 comment
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bug Something isn't working priority Should be resolved first, if possible

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We need to allow plantit.yaml workflow definitions to specify a shell to optionally wrap the entry point, e.g. bash -c ... or sh -c ...

This seems to be necessary since Singularity shells run in a "special environment" which bypasses conda modifications etc. References:
@wpbonelli wpbonelli added bug Something isn't working priority Should be resolved first, if possible labels Jan 30, 2022
@wpbonelli wpbonelli self-assigned this Jan 30, 2022
wpbonelli added a commit that referenced this issue Feb 1, 2022
@wpbonelli
optionally wrap singularity entry point with shell (#273)
d64a8f3
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All in as of 2eb5568

@wpbonelli wpbonelli mentioned this issue Feb 1, 2022
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wpbonelli added a commit that referenced this issue Feb 2, 2022
@wpbonelli
fix #273 for config files with shell option, update docs
f3aa11b
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