Installation

1. Set up a Python environment (e.g. with virtualenv or conda) with Python 3.9 or later (3.12 recommended)

2. Clone and navigate to the repository: git clone https://github.com/christiaanjs/treeflow.git then cd treeflow

3. Install the Python package: pip install .

   • To run the example notebooks: pip install ".[examples]"

4. Run TreeFlow

   • To run Jupyter Lab

     1. jupyter lab

     2. Follow the link that appears to Jupyter (http://127.0.0.1:8888/lab?token=...)

   • Run one of TreeFlow’s command line applications

Docker

1. Install Docker following the official instructions

2. Clone and navigate to the repository: git clone https://github.com/christiaanjs/treeflow.git then cd treeflow

3. Build the container: docker build -t treeflow .

4. Run TreeFlow

   • To run Jupyter Lab:

     1. docker run -p 8888:8888 treeflow

        • To use a different port (e.g. 8999) use docker run -p 8999:8888 treeflow

        • If you need to access a local directory (e.g. for input and output files) mount it into the docker image: docker run -v /home/dev/repo/data:/app/data treeflow to mount the directory /home/dev/repo/data to the data directory in the notebook (both must be absolute paths, and /app is the working directory in the container)

        • If you need to save output to the mounted directory you’ll need to give the Docker user (ID 10001) permissions: mkdir /home/dev/repo/data/out then sudo chown -R 10001:10001 /home/dev/repo/data/out

     2. Follow the link that appears to Jupyter (http://127.0.0.1:8888/lab?token=...), changing the port if necessary

     3. To stop the process, use docker kill {container} (you can use docker ps to lookup the ID)

        • On Linux docker ps | grep treeflow | awk '{print $1}' | xargs docker kill will stop all TreeFlow containers

   • To run one of TreeFlow’s command line applications:

     • docker run treeflow {command}

     • You may want to mount a data directory for input/output e.g. docker run -v /home/dev/repo/data:/app/data treeflow_vi -i data/alignment.fasta -t data/topology.nwk --tree-samples-output data/tree-results.nexus