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Improve README docker instructions
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johnbradley committed Aug 11, 2022
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Expand Up @@ -258,9 +258,8 @@ There are 4 containers of interest (Crop_image and Morphology function are conta
## Running using docker
The pipeline can be run using docker to provide the required snakemake and singularity environment.
After cloning the repo from within the BGNN_Snakemake directory.
The pipeline can be run using [docker](https://docs.docker.com/get-docker/) to provide the required snakemake and singularity environment.
After installing docker clone this repo and cd into the BGNN_Snakemake directory.
To process the images in `List/list_test.csv` using the pipeline run (on macOS or Linux):
```
docker run --privileged -it -v $(pwd):/src -w /src snakemake/snakemake:v7.12.1 \
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