Installation and environment setup

As part of this protocol, all analysis steps are carried out using Python, an interpreted, high-level general-purpose programming language that can be used on a wide variety of operating systems, including LINUX, Windows, and macOS. Currently, the protocol is written in Python (v3.10.4) on a Linus-based Linux system (Red Hat Enterprise Linux version 7.9 (Maipo)). In addition to Python, R packages and tools are required for several analyses such as WGCNA, though those analyses are not part of this protocol. The protocol can be run on most UNIX and Linux distributions, however, Ubuntu 22 and Fedora 36, Red Hat 7, and macOS Monterey are recommended. Besides HPC devices, this protocol has been tested on other devices, with the following specifications:

OS!

Windows 11 (5.10.102.1-microsoft-standard-WSL2), and Fedora 36.

RAM!

16 GB

SDD!

256 GB

CPU!

Intel i7

Conda!

v4.12.0

A major requirement for POTFUL is RUST. The user must first install RUST on the OS of their choice.

Install Rust

Linux, WSL2 and mac OS

curl https://sh.rustup.rs -sSf | sh

Windows 11/10

run [vs_BuildTools.exe](https://aka.ms/vs/17/release/vs_BuildTools.exe) # `Microsoft C++ Build Tools`
run rustup-init.exe[https://win.rustup.rs/]

See also

You can learn a lot more at The Cargo Book.

[RUS]

Create conda environment

Fedora (36<) and Ubuntu (22<) and WSL2

POTFUL.yml

conda env create -n POTFUL --file POTFUL.yml

Mac OS

POTFUL_macPy39.yml

conda env create -n POTFUL --file POTFUL_macPy39.yml

Windows 11/10

POTFUL_WinPy39.yml

conda env create -n POTFUL --file POTFUL_WinPy39.yml

Clone git repository

Fork the POTFUL git repository and clone or download.

git clone https://github.com/<User Name>/POTFUL.git

Citations

RUS

Introduction - The Cargo Book. URL: https://doc.rust-lang.org/cargo/index.html (visited on 2022-09-21).