pysrim-docker

Warning

This package has been replaced by https://github.com/agoose77/pysrim-executor

Docker executor for PySRIM

Getting Started

To use this package, simply replace your SR or TRIM imports with those from srim.docker, e.g.

from srim.docker import TRIM

trim = TRIM(...)

Out of the box, pysrim-docker uses the costrouc/srim Docker image, and writes the input and output files to a temporary directory.

How Does it Work?

pysrim-docker overrides the run() method of the SR and TRIM classes with one that executes a bash script in a particular Docker image. This script simply copies the inputs to the appropriate directory, runs the required binary, and returns the results.

Why?

Since using Docker, I have seen its utility in hiding obscure build steps behind a simple container image. However, I prefer to write code that might be part of an analysis pipeline, rather than standalone Python modules, and so it is prefereable to have the input file generation peformed on the host. An additional benefit of this is that the pysrim installation can be updated indepently of the Docker image.