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