socker

Dockerised Jupyter (ipython) Notebook for statistical genetics and genomics

Built on cfljam/pyrat_genetics

For info about ipython scipystack see http://odewahn.github.io/docker-jumpstart/ipython-notebook.html

Provides

• VCFtools
• VCFLib
• Samtools/HTSLib
• BedTools
• R genetics tools

To Run

• On OSX or Windows, install docker toolbox
• Start up Docker-machine

docker-machine start <name-of-my-machine>
eval "$(docker-machine env <name-of-my-machine>)"

• Pull and run the image

docker run -rm -p 8888:8888 -v /my_local_dir:/vm_mount_point -it cfljam/socker

Note

On OSX or Windows using Boot2docker host you will likely need to open ports in VirtualBox by doing this manually

e.g. for port 8888

Settings->Network -> Port Forwarding