V-Pipe Installation

V-pipe is a workflow designed for the analysis of next-generation sequencing (NGS) data from viral pathogens. It produces a number of results in a curated format (e.g., consensus sequences, SNV calls, local/global haplotypes). V-pipe is written using the Snakemake workflow management system.

The present tutorial will show you how to install V-pipe and the dependencies required to start using it - bioconda, conda-froge mamba and snakemake - before continuing with other tutorials and analysing virus data.

Requirements

V-pipe is optimized for Linux or Mac OS systems, and bioconda isn't supported on Windows. Therefore, we recommend users with a Windows system to install WSL2 - this is not a full virtual machine but rather a way to run Windows and Linux cooperatively at the same time.

Organizing Software

We will organise our software in the following tree structure, which will be reused in all subsequent tutorials:

📁 [HOME]
└───📁vp-analysis
    ├───📁V-pipe      # V-pipe checked out from Github
    ├───📁Miniforge3  # bioconda + conda-forge + mamba + Snakemake
    ├───📁work        # work directories
    ├───📁work-tests  #  …
    └───📁 …          #  …

• vp-analysis is the main directory where we will store everything.
• Miniforge3 is the directory where conda will be installed including the dependencies to start using V-pipe.
• V-pipe is the directory where V-pipe's code will be downloaded from GitHub
• finally, each analysis of virus data will be performed in a directory like work…, which holds the configuration and the sequencing data for that particular analysis.

Install V-pipe and conda from scratch

V-pipe uses the Bioconda bioinformatics software repository for all its pipeline components. The pipeline itself is implemented using Snakemake.

For advanced users: If your are fluent with these tools, see below

In this short tutorial, you will learn how to setup a workflow for the various examples in the analysis tutorials.

To deploy V-pipe, you can use the installation script with the following parameters:

curl -O 'https://raw.githubusercontent.com/cbg-ethz/V-pipe/master/utils/quick_install.sh'
bash quick_install.sh -p vp-analysis -w work

Note:

• using -p specifies the subdirectory where to download and install snakemake and V-pipe
• using -w will create a working directory and populate it. It will colloquial the references and the default config/config.yaml, and create a handy vpipe short-cut script to invoke snakemake.
• an additional option -b (not demonstrated above) allows to install a spefic branch or tagged version. If nothing is specified, the master branch will be installed.

If you get zsh: permission denied: ./quick_install.sh, run chmod +x quick_install.sh this gives the necessary permissions.

Tip: To create and populate other new working directories, you can call init_project.sh from within the new directory:

cd vp-analysis/

mkdir -p working_2
cd working_2
../V-pipe/init_project.sh

# now edit config.yaml, samples.tsv, run your analysis etc.

cd -

Analyse data

Now that you have setup the software necessary to start using V-pipe, you can follow with one of the tutorials showing you the analysis of viral sequencing data:

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

Fluent users

For advanced users: If your are fluent with these tools, you can:

• directly download and install Miniforge3, setup bioconda and install snakemake,
• specifiy your V-pipe configuration, and start using V-pipe

Use --use-conda to automatically download and install any further pipeline dependencies. Please refer to the documentation for additional instructions.

Reusing an existing conda installation

[TO BE CONTINUED]