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Obscure external packages from container interface #19

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Lestropie opened this issue Nov 11, 2020 · 0 comments
Open

Obscure external packages from container interface #19

Lestropie opened this issue Nov 11, 2020 · 0 comments

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@Lestropie
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While the set of commands from non-MRtrix3 neuroimaging software packages that will be present in the container has been reduced, they will still nevertheless be within PATH, and hence one could do e.g. MRtrix3.sif N4BiasFieldCorrection ...

What might be interesting is to have some form of gateway command / mechanism that only inserts the non-MRtrix3 contents of /opt/ into PATH following resolution of the requested command, such that the above example would not work but dwibiascorrect ants would be able to find that requested command.

It might be the case that this is fairly trivial to do for command invocations via the entrypoint but breaks down if SSHing into the container, but that would probably be an acceptable limitation.

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