qiime info FileNotFoundError on 2024.10 amplicon Docker

[ebolyen (Evan Bolyen)]

Hi @Patg13,

@Patg13

The problem here is that this function is called each time the get_app_dir function is executed (during qiime info for exemple), but in Apptainer, every folders are only writable at build time. After that, the container is frozen in read-only. In Docker, that is not the case, the image is static, but the container in itself is not read only and can be written at any time (so no problem in that case).

That would explain why I can launch qiime info during build (which display the correct folder /opt/conda/envs/qiime2-amplicon-2024.10/var/q2cli, but cannot do so during runtime since it's frozen and it fallback on /home/qiime/q2cli and then crash because it cannot create the directory since it's also read-only in Apptainer.

Well that makes really great sense. Thanks for taking the deep dive on it @Patg13!

@Patg13

As a temporary fix, I copied the /opt/conda/envs/qiime2-amplicon-2024.10/var/q2cli to /home/qiime/q2cli, but I don't know if it could negatively affect qiime during runtime.

That should be totally fine for now. We'll see about modifying things on our end to avoid this behavior on a read-only system.

Tracking issue: CLI help cache lookup fails when conda environment goes to read-only. · Issue #356 · qiime2/q2cli · GitHub