Usage through a container

[3nrique0]

Hello, The installation through conda or pixie doesn't seem to cut it for the HPC I work on. I saw that there is a docker container.
However, for security reasons I cannot use docker. I created a .sif image with apptainer pull. The problem I find is that I need to activate the conda environment contained in the .sif. Conda activate only works on interactive sessions. Which limits how I can launch the harpy processes to the cluster. Do you have some advise on how to use the container in a more efficient way ?

[pdimens]

Thanks for writing. Here are two options to try to pursue:

1. Reach out to your HPC admins and ask them to install Harpy into the system.
2. If a pip-based installation would work, then I can try to come up with a script to do a local pip (user level) installation, or one in a virtualenv. Some of the immediate Harpy dependencies, like apptainer, samtools, etc. aren't available via pip, so they may require manual installation.

What do you think?

[pdimens]

linking with #194