Installation and usage

The MetaPUF pipeline is built using Snakemake, a workflow tool to create reproducible and scalable data analyses. Below you can find tutorials on what are the pre-requisites and how to use some of the MetaPUF pipelines and standalones.

Pre-requisites

Installation

  • Create a conda environment

We recommend to create a snakemake environment for the MetaPUF project, you can find more details about how to install from here, after installation, please active the snakemake environment or you can rename it.

conda activate snakemake

  • From Github source code

You will need to install metapuf locally from Github

git clone https://github.com/PRIDE-reanalysis/MetaPUF.git

  • Options

  1. Please install (if you are using Linux/Mac OS) Mono for converting proteomics raw files. (install mono-complete if you encounter “assembly not found” errors).

  2. Please add your project path to PYTHONPATH in your .bashrc file: (i.e. export PYTHONPATH="/Users/your path/MetaPUF:$PYTHONPATH")

  3. Please download the Proteomics tools (ThermoRawFileParser, SearchGUI, PeptideShaker, please find details in README in the project github page) and locate them in the correct folder (MetaPUF/workflow/bin/)

Usage

Start running your own analysis with one line of code:

snakemake --cores 4

This is an example of running the workflow with Snakemake, we used 4 cores, you should change it based on your own machine.

Also, it is recommended to test your pipeline before a real run, use a snakemake dry run command:

snakemake -np