running AdmixPipe with apptainer?

[RvV1979]

Hi Steve,

Thanks for providing what seems a very useful pipeline. I have access to computing servers but without sudo permissions and therefore cannot run Docker. Therefore, I have tried running the docker instance with apptainer via the following commands:

apptainer pull docker://mussmann/admixpipe:3.2
apptainer run --bind ${dir}/data/:/app/data docker://mussmann/admixpipe:3.2

From within the docker container I can find the various binaries in /app/bin and scripts in /app/scripts/python/admixturePipeline/. However, none of these can be run directly. I therefore checked $PATH from within the container and it seems to be the $PATH from outside the container.

Do you know what may be going wrong and how I can ensure the locations of the pipeline software and scripts are in $PATH within the container?

Thanks

[RvV1979]

For anyone trying the same, for now this workaround seems to work for me:

> apptainer run --bind data/:/app/data --compat docker://mussmann/admixpipe:3.2
Apptainer> PATH=$PATH:/app/bin/:/app/scripts/python/admixturePipeline/ ; export PATH

[stevemussmann]

Good morning,

Thanks for bringing this to my attention. I've encountered a similar issue with Singularity and assume the underlying problem is similar here. Unfortunately I haven't had time to sit down and learn how exactly Singularity (or Apptainer) functions differently from Docker so that I can do a permanent fix.

Thanks for posting the workaround - glad that you got it working. I'll leave this issue open until I get a fix integrated.

-Steve

[RvV1979]

Thanks for the fast reply. I am for sure not an expert but perhaps some clues can be found here: https://apptainer.org/docs/user/main/docker_and_oci.html#best-practices-for-docker-apptainer-compatibility