README.md

Tutorials

We strongly advise our users to start discovering V-pipe by looking at the tutorials

You can find several tutorials in this directory:

Getting V-pipe installed

• V-pipe Installation

Viruses

• V-Pipe HIV Tutorial: uses HIV test data
• SARS-CoV-2 Tutorial: uses SARS-CoV-2 data from a publication

Note about the tutorials

Due to automated testing, each copy-pastable block begins with a command entering the directory and ends with one 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