singularity support?

[kkmann]

I was just wondering whether there are any plans to support running jobs within singularity containers?
My HPC experience is limited (slurm only) but if I am not completely off, one would only have to modify the sbatch command slightly, right? Would that go in the template file?

[HenrikBengtsson]

Yes, controlling which Rscript binary to run would be set in the batchtools template file. So, replace

## Launch R and evaluated the batchtools R job
Rscript -e 'batchtools::doJobCollection("<%= uri %>")'

with something like

## Launch R and evaluated the batchtools R job
singularity exec rocker_r-base.img Rscript -e 'batchtools::doJobCollection("<%= uri %>")'

where the image was built using something like:

$ singularity build rocker_r-base.img docker://rocker/r-base