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luntergroup / smcsmc

Demographic inference from whole genomes
GNU General Public License v3.0
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feat: entry-point CLI, docker image, circle and release-please, functional tests #72

Closed Chris1221 closed 2 years ago

Chris1221 commented 2 years ago

Run SMCSMC using a Docker image. Working on how to mount data and run from there.

Chris1221 commented 2 years ago

A simple idea would be to make a template run_smcsmc.sh script and give instructions for mounting a directory of VCF files. Something like:

docker exec -it chris1221/smcsmc:latest < run_smcsmc.sh

The biggest issue that I see is that we don't have any logic for running on any other back-end than qsub, so if this were to be run on GCP or AWS it would run in serial which is not really very realistic. Even the current logic wouldn't extend to the case of remote files. We may want to use a task manager to run the iterations like Cromwell or Snakemake/Nextflow but we can cross that bridge when we come to it.