Visual Studio code

Web: https://code.visualstudio.com/.

Installation

Download and extract a copy for Linux x64, e.g., for the latest version 1.58.0,

cd ${HPC_WORK}
tar xvfz code-stable-x64-1625728370.tar.gz
ln -sf ${HPC_WORK}/VSCode-linux-x64/bin/code ${HPC_WORK}/bin/code

By default it requires chrome-sandbox is owned by root and has mode 4755 which could be achieved at CSD3 by

sudo chown root:root chrome-sandbox
sudo chmod 4755 chrome-sandbox

Unfortunately, as ordinary users this is impossible and we use without this option.

Execution

Start for reasons above,

code --no-sandbox

Jupyter notebook

We could start our virtual environment as described in hail, e.g.,

cd ~/rds/results/public/gwas/ukb_exomes/tutorials
code --no-sandbox 01-genome-wide-association-study.ipynb &

which greatly simplifies the procedure as described for genebass. MAKE sure various extensions/options suggesed from the session.