Installation

TiRank supports multiple installation methods. It is recommended to create a dedicated conda environment to ensure compatibility.

Method 1: Bioconda Installation (Recommended)

This is the easiest method. You can install the stable version of TiRank directly from the Bioconda channel.

1. Clone the TiRank repository (for access to example scripts):

   git clone https://github.com/LenisLin/TiRank.git
   cd TiRank
   

2. Create a clean python environment:

   conda create -n tirank python=3.9
   conda activate tirank
   

3. Install TiRank:

   conda install -c bioconda -c conda-forge tirank leidenalg python-igraph
   

Note

The TiRank framework has been tested on Ubuntu 22.04 with Python 3.9, using NVIDIA Driver 12.4 and RTX 3090 GPUs.

Method 2: Docker

1. Install Docker

   Ensure Docker is installed on your system.

2. Pull the TiRank Docker Image

   docker pull lenislin/tirank_v1:latest
   

3. Run the Docker Container

   docker run -p 8050:8050 lenislin/tirank_v1:latest /bin/bash
   

4. Verify Container Execution

   After running the above command, you should be inside the container’s terminal. Verify the setup by activating the environment and checking the TiRank version:

   conda activate TiRank
   
   python -c "import tirank; print(tirank.__version__)"
   

5. Persistent Data Storage (Optional)

   To mount a local directory to retain data inside the container:

   docker run -it -v /path/to/local/data:/container/data lenislin/tirank_v1:latest /bin/bash
   

6. Stop and Remove the Docker Container

   Use the following commands to manage containers:

   docker stop <container_id>
   docker rm <container_id>
   

Method 3: Interactive Web Tool (GUI)

This method is for running the TiRank web application locally.

1. Set Up the Web Server

   Navigate to the Web directory and create a data folder:

   cd TiRank/Web
   mkdir data
   

   Download the required datasets and pretrained models into the newly created data directory:

   • Example Data and Pretrained Models

2. Set Up Directory Structure

   Ensure the following directory structure is maintained within the Web folder:

   Web/
   ├── assets/
   ├── components/
   ├── img/
   ├── layout/
   ├── data/
   │   ├── pretrainModel/
   │   │   └── ctranspath.pth
   │   ├── ExampleData/
   │   │   ├── CRC_ST_Prog/
   │   │   └── SKCM_SC_Res/
   ├── tiRankWeb/
   └── app.py
   

3. Run the Web Application

   Execute the following command from within the Web directory:

   python app.py
   

4. Access the Web Interface

   Open a web browser and navigate to http://localhost:8050 to access the TiRank GUI.