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brainvisa / casa-distro

Unified development environment for BrainVISA projects.
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Capsul soma-workflow variables are not set without manual config editing #335

Closed denisri closed 1 year ago

denisri commented 1 year ago

Is your feature request related to a problem? Please describe.

Capsul run command relies on Soma-Workflow env variables SOMAWF_INPUT_PARAMS and SOMAWF_OUTPUT_PARAMS. But in a remote batch system, these variables do not pass from the job shell to the casa-distro container without a manual config specifying their definition in /casa/host/conf/casa_distro.json. Moreover users usually don't know how to edit this config (and what to set in it). Plus, in site install the config file can only be personalized in (host) ~/.config/casa-distro/casa_distro3.json which is still harder to find, and cannot be edited uing the bv GUI.

Describe the solution you'd like Maybe define these 2 variables in the default config of Casa-Distro, even if it's not his matter ?

ylep commented 1 year ago

I agree that these variables can be passed by default, they are safe and casa-distro’s matter is to make things work ;-)

denisri commented 1 year ago

I'll do that during environment setup since it's the simplest solution.