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nadeemlab / SPT

Spatial profiling toolbox for spatial characterization of tumor immune microenvironment in multiplex images
https://oncopathtk.org
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Expand workflow configure support for singularity #286

Closed CarlinLiao closed 9 months ago

CarlinLiao commented 9 months ago

Some HPCs (like ours) ban the use of Docker, but permit the use of Singularity.

Presently, spt workflow configure workflow='cg-gnn' requires the use of Docker. We'd like it to support using Singularity instead of Docker. Conveniently, Nextflow has been integrating more Singularity support and Singularity has been integrating more Docker support, so this shouldn't be too hard a lift.

While we're at it, we should also revisit other places where Singularity is used in spt workflow configure and integrate them into this new Singularity run option, if convenient.

CarlinLiao commented 9 months ago

Actually, if I understand correctly, in order to support containerized-Nextflow-without-Docker, we need still need to set it up such that we the Docker-image-to-Singularity conversion happens outside of the computer we want to use, since converting from Docker to Singularity images necessarily requires Docker to be installed. So this may not be as simple as a drop-in replacement.