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pangenome / pggb

the pangenome graph builder
https://doi.org/10.1038/s41592-024-02430-3
MIT License
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pggb versioning info causing git dubious ownership problems #288

Open colindaven opened 1 year ago

colindaven commented 1 year ago

Hi,

I'm getting this error when building pulling the pggb container and making additional local changes.

PGGB version: 

fatal: detected dubious ownership in repository at '/usr/local/bin'
To add an exception for this directory, call:

        git config --global --add safe.directory /usr/local/bin

This error has been discussed at length on the net, eg

https://github.com/actions/runner-images/issues/6775

I may be wrong, but I think it is due to the versioning code here (see also the error above, where the PGGB version is listed just before the error):

https://github.com/pangenome/pggb/blob/master/Dockerfile#L148

Potentially, a workaround might be to add this prior to the version request in the Dockerfile.

RUN git config --system --add safe.directory /usr/local/bin

Thanks