docker_usage_readme.md

Install Mykrobe predictor with docker

Download the docker toolbox https://www.docker.com/products/docker-toolbox or docker engine https://docs.docker.com/engine/installation/.

Pull mykrobe predictor impage

docker pull phelimb/mykrobe_predictor

Run the image

docker run phelimb/mykrobe_predictor mykrobe --help

Run mykrobe predictor

To run mykrobe predictor on data on your system you'll need to mount the directory where the data is located within your docker container.

e.g. if your data is located within /Users/phelimb/Documents/data then you can run mykrobe like this:

$ ls /Users/phelimb/Documents/data
test.fastq.gz

docker run -v /Users/phelimb/Documents/data:/data phelimb/mykrobe_predictor mykrobe predict sampleid tb -1 /data/tests.fastq.gz

You can pipe output locally

docker run -v /Users/phelimb/Documents/data:/data phelimb/mykrobe_predictor mykrobe predict sampleid tb -1 /data/tests.fastq.gz > out.json