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Tool credentials fail on containerized (singularity?) destinations #21715

@bernt-matthias

Description

@bernt-matthias

Describe the bug

For tool credentials the job script contains

SECRET="yadayada"; export secret

but these variables are not used in containerized destinations (eg #16666).

Guess we need to call the container with

SINGULARITYENV_SECRET="$SECRET" ... singularity, which means adding them to the env here:

command_parts.extend([f'SINGULARITYENV_{key}="{value}"'])

Galaxy Version and/or server at which you observed the bug
Galaxy Version: 25.1

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