Install using Docker

A GW docker file for x64 chips can be found in the GW repository: https://github.com/kcleal/gw/blob/master/deps/Dockerfile

• Build the container using:

  sudo docker build -t gw .

• Run using:

  sudo docker run -it –cpus=4 –memory=8g -p 9876:9876 –mount src=DATA_PATH,target=TARGET_PATH,type=bind gw

The -p option binds the port 9876 between host and container. The –mount option is used to share the folders containing your reference genome and bam files (DATA_PATH) The TARGET_PATH will be the location of these files in the docker container.

Now open a web-browser and type in the address 0.0.0.0:9876. A window into the container will be shown. You can now run gw using the CLI interface e.g.:

gw genome/ref.fasta -b bams/your.bam -r chr1:1-20000

Also of note, the container contains the micromamba package manager, so you can download and install new packages as needed.