A Dockerized version of Staphopia.
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README.md

README.md

staphopia-docker

A Dockerized version of Staphopia.

Download and Build Docker Image

cd ~/ 
git clone git@github.com:staphopia/staphopia-docker.git
cd staphopia-docker
docker build -t staphopia .

Run Staphopia on a sample

cd /path/to/your/sample
ls
YOURFASTQ_R1.fastq.gz YOURFASTQ_R2.fastq.gz

docker run --rm -it --user `id -u` -v $PWD:/data staphopia staphopia YOURFASTQ_R1.fastq.gz -f2 YOURFASTQ_R2.fastq.gz -p NUM_CPU --sample_tag SAMPLE_NAME