leanderd/single-cell-analysis repository overview

Generally, you have two option to use this container.

Option 1: Discard your container after your docker session and create a new, clean container on every session.

Run container with:

docker run --interactive --tty --rm --name sc_analysis_r_py_210114 --publish 8888-8892:8888-8892 --volume $HOME:/root/host_home --workdir /root leanderd/single-cell-analysis:210114 /bin/bash

Option 2: Create the container so that it persist between sessions so that any additional packages you install remain when you close docker.

Running the container for the first time:

docker run --interactive --tty --name sc_analysis_r_py_210114 --publish 8888-8892:8888-8892 --volume $HOME:/root/host_home --workdir /root leanderd/single-cell-analysis:210114 /bin/bash

For every following docker session, just start the existing container:

docker start -i sc_analysis_r_py_210114

Command shortcut to start jupyter lab inside the container:

jl

My name is Leander, I am a PhD student in Prof. Fabian Theis' lab at at Institute for Computational Biology, Helmholtz Munich and Prof. Elisabeth Binder's lab at the Max Planck Institute of Psychiatry, Munich.