Is is possible for me to generate my own singularity images by changing install.smk?

[xguse]

I need a newer guppy install. I also want/need GPU. It SEEMS that I can alter the install.smk script to update these things. What I dont know how to do is to create a new singularity image using this updated install.smk.

Is this possible? Should I be worried about this approch?

[giesselmann]

Hi, yes, you can alter the install.smk and generate your own singularity based on that. Under test/build_singularity.sh you find the docker commands for the build (I'm only familiar with docker and the official images are hosted on dockerhub.com) e.g.: docker build -t basecalling --shm-size 4g -f singularity/basecalling/Dockerfile . You convert from docker daemon to singularity with: singularity build /path/to/local/basecalling.sif docker-daemon://basecalling:latest Afterwards you can add a config entry to either env.yaml or nanopype.yaml and overwrite the container for a specific module:

singularity_images:
     basecalling : '/path/to/local/basecalling.sif'

BUT: If I remember correctly, the guppy command line interface changed in 4.x, they split guppy_basecaller and the basecall server. Since we rely heavily on the serrver with the '--port xy' argument, I haven't upgraded to the latest guppy in the main branch. I'm happy to merge a pull request, if you find the latest guppy working and a fix for the cli!