Section 2 The Docker Container

What is in the Workshop Docker environment

• A tarballed installation for three great apes, including genome sequences, genome features, gene homology and whole genome alignments between the species.
• git clones of the EnsemblLite and Cogent3 repositories
• Python dependencies, including support for Jupyter notebooks for interactive analyses.

But we need to finalise the container setup!

Updating the environment

We must do a few things within the container before using EnsembleLite. (These are workshop specific.)

So start your Docker engines. Within VS Code, navigate to the SMBE workshop directory and open it as a container.

We then get a terminal session going (Terminal > New Terminal).

Update a Jupyter Dependency

 pip install ipywidgets -U

Update EnsemblLite

cd ~/repos/EnsemblLite
git pull
pip uninstall ensembl_lite -y
pip install -e .

Update Cogent3

cd ~/repos/Cogent3
git pull
pip uninstall cogent3 -y
pip install -e .

Inflate the demo installation

As part of the installation, a tarball of an EnsemblLite installation for three great apes was downloaded. We are going to inflate that now.

Warning

Don't delete the apes_112.tar.gz file without editing the Dockerfile, otherwise it will be redownloaded again!

cd ~/workshop/data
tar zxf apes_112.tar.gz

This will take a couple of minutes.

Now we're ready to use the installation.