Singularity/Docker

[alexcorm]

Hello,

Do you have any plan to release a Singularity/Docker version of Agnostos? It would be great as both are able to run with MPI and the portability will be better.

[genomewalker]

Hi
it is a good idea. We will need to investigate which is the best way on how to do it properly. We will try to implement it after we are finished with some improvements in the workflow.
Thanks
Antonio

[alexcorm]

As far I know, Singularity/Docker can be used with the latest Snakemake version using --use-singularity and adding something like that in each rule:

rule NAME:
    input:
        "table.txt"
    output:
        "plots/myplot.pdf"
    container:
        "docker://joseespinosa/docker-r-ggplot2"
    script:
        "scripts/plot-stuff.R"

And for Singularity/Docker, if MPI is installed in the image, it can be run as follow:

mpirun -n <NUMBER_OF_RANKS> singularity exec <PATH/TO/MY/IMAGE> </PATH/TO/BINARY/WITHIN/CONTAINER>

But I never tried to use run Docker image in MPI into a Snakemake Workflow!

[genomewalker]

I never tried it either. Will come back to you once we figure it out.

[rhernandvel]

Hi,
Is there any update on this?
Thanks