README.md

Tutorials

You can find two tutorials in this directory:

• tutorial_hiv.md: uses HIV test data
• tutorial_sarscov2.md: uses SARS-CoV-2 data from a publication

Note about the tutorials

Due to automated texting, each copy-pastable block begins with a command entering the directory and ends with on leaving the directory:

cd tutorial/work/
# do something
cd ../..

Of course you don't necessarily need to do that. You can simply remain in the working directory.

When editing files like config.yaml, you can use your favorite editor (vim, emacs, nano, butterflies, etc.). By default our tutorials use a heredoc to make it easier to copy-paste the blocks into bash:

cat > config.yaml <<EOF
general:
    virus_base_config: 'sars-cov-2'
EOF