GSEACompass 🧭

A minimalistic yet powerful app to run GSEA, pre-ranked GSEA and do post-analysis elaboration on the results.

To know more about how to use GSEACompass and its peculiar features, check out the offical user manual: gseacompass.gitbook.io

Outline

• Frameworks
• Build instructions
  • Download
  • Dependencies
  • Dependencies
  • Build and run

Frameworks

This tool is powered by:

• GSEApy on the python backend to run genomic analyses and graphical elaborations
• Electron.js on the desktop frontend
• Datatables.js as a view engine for post-analysis tables

Build instructions

Binaries

Download GSEACompass source code

Build from source

Make sure, before running GSEAWrap in a development enviroment, to fulfill these dependencies.

Rust

The Rust development environment has to be installed on your machine, since it's compulsory to install and run GSEApy. Follow this link for the official instructions to download and install it.

Python

Python3.12 and pip must be installed too, follow the official guides to install them (Python, pip).

System

The follow system dependencies are required, install only those regarding your operating system:

Ubuntu-based

Run the following command if your OS is Ubuntu or Ubuntu-based:

sudo apt install python3-devel

Fedora/RHEL

Run the following command if your OS is Fedora or similar:

sudo dnf install libquadmath libquadmath-devel

N.B. for Windows users:

Make sure Python and Rust are in the PATH environmental variable.

Python libraries

Once Python and pip are installed, open the directory in which you have unzipped the GSEACompass archive and run the command:

pip install -r requirements.txt

This will install all python-based dependencies needed to run the app.

Build dependencies

Node.js

Mind that Node.js is required to be installed on you system in order to build and run this application. Moreover, as suggested on the official Electron.js website:

Please install Node.js using pre-built installers for your platform. You may encounter incompatibility issues with different development tools otherwise.

Follow the official guide to install it.

Npm dependencies

Once installed Node.js, all npm-based dependencies can be installed with the following command, make sure to be in your local repository directory:

npm install

Build and run

To build and run the application just run the following command, make sure to be in the repository directory:

npm start run

In order to run the app, be sure to have installed the run dependencies too (see up above).