Documentation

Table of Contents

• Tutorials
  • Getting V-pipe installed
  • Viruses
  • Note about the tutorials
• General Information
• Configuration files
  • configuration manual
• How to benchmark
• Video tutorial

Tutorials

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

You can find several tutorials in the docs/ 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

General Information

You’ll find a short introduction to V-pipe in the README file at the root of V-pipe

Configuration files

In order to start using V-pipe, you need to provide three things:

1. Samples in a specific directory structure
2. (optional) TSV file listing the samples
3. Configuration file

To configure V-pipe refer to the documentation present in config/README.md.

configuration manual

More information about all the available configuration options and an exhaustive list can be found in the file config/config.html in your local installation of V-pipe (temporarily not available online).

How to benchmark

How to perform benchmarks is documented in resources/auxiliary_workflows/benchmark/README.md

Video tutorial

Comming soon