Install using Docker

The GW docker is currently out of date (v0.3), but we will hopefully be realeasing a v1.0 update soon.

To use the the Docker container interactively (i.e. not just from the command line) you must first install a screen-sharing on your system - we recommend using Xpra (https://xpra.org/) for this. This allows a screen to be shared between the container and host.

• Grab the gw docker image:

docker pull kcleal/gw

• Run the docker container using:

sudo docker run -it -p 9876:9876 \
--mount src=/path/genome,target=/home/genome,type=bind,readonly \
--mount src=/path/bams,target=/home/bams,type=bind,readonly \
kcleal/gw

The -p option binds the port 9876 between host and container. The –mount options are used to share the folders containing your reference genome and bam files - modify the src=… path as needed.

Now open a web-browser and type in the address 0.0.0.0:9876. A window into the container will be shown, with an xterm terminal open. You can then run gw using:

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

If you want to get data out of the container, you will need a setup another mount point when starting the container e.g.:

sudo docker run -it -p 9876:9876 \
--mount src=/path/genome,target=/home/genome,type=bind,readonly \
--mount src=/path/bams,target=/home/bams,type=bind,readonly \
--mount src=${PWD},target=/home/out,type=bind \
kcleal/gw

Anything saved in /home/out when in the container will be saved in the present-working-directory on your host machine.

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