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