Installation

Please follow the guide below to install CGMega and its dependent software.

System Requirements

Operating system: Linux or are highly recommended. CGMega was developed and tested on Linux. Windows Subsystem for Linux (WSL) is not recommended.

Memory: Memory usage depends on the size of your Hi-C and PPI dataset and it may cost

CPU: Intel(R) Xeon(R) Silver 4210R CPU @ 2.40GHz. This is NOT the least requirement.

Software Requirements

CGMega was developed using python 3.8. The interpretation part adopted GNNExplainer.

  • python=3.8.12
  • pytorch=1.9.1
  • networkx=2.6.3
  • neoloop=0.4.3
  • transformers=4.19.4
  • wandb=0.12.18(optional)
  • pyg=2.0.3

Installation

We recommend installing CGMega using Git from our Github repository through the following command:

git clone https://github.com/NBStarry/CGMega.git
Note

The software package of CGMega is still under testing. We are going to release a stable version in the near future.

source: test_long/folder1-Installation/README.md