How to use V-pipe

Table of Contents

Table of Contents

• Hardware requirements
• Software requirements
  • OS
  • Software

Hardware requirements

The actual space usage depends on datasets size. Recommendation:

• RAM >= 16GiB

• Storage >= 40 GiB

• x86 CPU recommended (Apple silicon users see OS requirements below)
• cores >= 4

Software requirements

OS

• Linux and Mac OS X currently supported.
• Windows 10 users can install Windows Subsystem for Linux for compatibility with Linux as bioconda does not support Windows directly.
• Mac OS X users with Apple Silicon should use the arch -x86_64 … command (e.g.: env /usr/bin/arch -x86_64 /bin/zsh --login) to run through Rosetta as bioconda support isn’t stable yet.

Software

• mamba (e.g.: from miniforge) and snakemake are required
  • we strongly encourage our users to deploy the pipeline using the quick install script
  • the first tutorial, V-pipe Installation, demonstrates how to use it
• All dependencies of V-pipe are automatically downloaded and installed by snakemake from bioconda.