GSForge¶

Welcome to the GSForge documentation!

Note

This is a pre-release version of GSForge, and some features and function names may not yet be stable.

GSForge is a Python software package that assists researchers in the selection of gene sets with potential association to an experimental condition or phenotypic trait, which offers new potential hypotheses for gene-trait causality.

GSForge and GEMmaker within the RNA-Seq Analysis Cycle

Note: This project is under active development.

Installation¶

GSForge works with Python 3.6+. It is currently only tested on Linux.

From Github¶

Clone the repository.

git clone git@github.com:SystemsGenetics/GSForge.git

Install via local pip:

pip install ./gsforge/

Using Docker¶

Update the image

docker pull systemsgenetics/gsforge_interactive:latest

To run GSForge using a jupyter notebook from a docker image:

Jupyter Lab

docker run --rm -p 10000:8888 -e JUPYTER_ENABLE_LAB=yes -v "$PWD":/home/jovyan/work systemsgenetics/gsforge_interactive:latest

Jupyter Notebook

docker run -p 8888:8888 -v "$PWD":/home/jovyan/work systemsgenetics/gsforge_interactive:latest

Both of the above commands mount the local directory to the "/home/jovyan/work" within the docker image. ("jovyan" is the default user name within the jupyter docker stack container.)