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