Symbolic links are followed during Singularity user image creation

brainvisa / casa-distro

Unified development environment for BrainVISA projects.

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Symbolic links are followed during Singularity user image creation #284

Closed ylep closed 2 years ago

ylep commented 2 years ago

casa-distro uses the %files directive to copy installed files from the install directory into the user image. I just realized that %files follows symbolic links in this case, see https://sylabs.io/guides/3.8/user-guide/definition_files.html#files.

This is especially problematic for the /casa/install/bin/python symlink, which is copied from the host... :fearful:

We may switch to using %setup to control the copy, or maybe a cleaner alternative is to do a multi-stage build.

denisri commented 2 years ago

From the host ? 8O I thought it was copying the python from the container, which is not needed, but at least harmless. Gasp, we need something else, that's for sure...

denisri commented 2 years ago

Moreover some symlinks are here for a reason, and end up with many duplicated files in the installed packages (such as libraries in lib/)