Easy Installation

This guide helps you install PGT with basic features. We recommend building PGT with Docker to avoid dependency issues. We recommend compiling PGT(and possibly its requirements) from the source code using the latest compiler for the best performace. You can also deploy PGT without building by Docker . Please note that PGT only supports Linux; for Windows users, please consider using WSL or docker.

Prerequisites

To build PGT, please make sure that the following dependencies are present:

biopython==1.81
certifi==2023.7.22
cffi 
charset-normalizer==3.3.1
dgl
docopt==0.6.2
future 
h5py==3.8.0
idna==3.4
networkx==2.6.3
numpy 
psutil==5.9.6
pycparser 
requests==2.31.0
scipy==1.7.3
torch
tqdm==4.66.1
typing_extensions 
urllib3==2.0.7
yarg==0.1.9

Some of these packages can be installed with popular package management system, such as pip:

pip install -r requirements.txt

If you can install the above dependencies, you can go on . If not, you need to check if the versions of the relevant libraries are correct.

Install requirements

Some of these packages can be installed with popular package management system, such as pip:

pip install -r requirements.txt

Get PGT source code

Of course a copy of PGT source code is required, which can be obtained via one of the following choices:

  • Clone the whole repo with git: `git clone https://github.com/RUC-MIALAB/PGT.git

  • Clone the minimum required part of repo: git clone https://github.com/RUC-MIALAB/PGT.git --depth=1

  • Get the source code of a stable version from here

Update to latest release

Please check the release page for the release note of a new version.

It is OK to download the new source code from beginning following the previous step.

To update your cloned git repo in-place:

git remote -v
# Check if the output contains the line below
# origin https://github.com/RUC-MIALAB/PGT.git (fetch)
# The remote name is marked as "main" if you clone the repo from your own fork.

git fetch origin
git checkout v0.0.1 # Replace the tag with the latest version
git describe --tags # Verify if the tag has been successfully checked out

Container Deployment

We’ve built a ready-for-use version of PGT with docker. For a quick start: pull the image, prepare the data, run container. Instructions on using the image can be accessed in Dockerfile.