Installation

TiRank supports multiple installation methods. We recommend using a dedicated conda environment.

Method 1: Bioconda Installation (Recommended)

This is the simplest method. It installs the released TiRank package from Bioconda.

1. Clone the TiRank repository (recommended to access example scripts and the Snakemake workflow):

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 (and required graph dependencies):

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

Note

TiRank has been tested on Ubuntu 22.04 with Python 3.9.

Method 2: Docker

1. Install Docker.

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 TiRank inside the container:

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

5. (Optional) Mount a local directory for persistent storage:

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

Method 3: Interactive Web Tool (GUI)

This method runs the TiRank web application locally.

1. Set up the web server directory:

cd TiRank/Web
mkdir -p data

2. Download and extract the archived example datasets and pretrained model files from Zenodo:

   • Zenodo record (ExampleData.zip, ctranspath.pth, GUI tutorial video): https://doi.org/10.5281/zenodo.18275554

3. Ensure the following directory structure under Web/:

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

4. Run the web application:

python app.py

5. Open a browser at: http://localhost:8050

Method 4: Snakemake Workflow (Reproducible Execution)

For end-to-end workflow execution with automated environment provisioning, we recommend running the provided Snakemake workflow with integrated conda environment management.

1. Install a fixed Snakemake version:

conda create -n tirank_smk -c conda-forge -c bioconda python=3.9 snakemake=7.32.4
conda activate tirank_smk

2. From the TiRank repository root, run:

snakemake --snakefile workflow/Snakefile \
          --configfile workflow/config/config.yaml \
          --use-conda --cores 8

For details (including recommended folder layout and configuration), see: Snakemake Workflow