# 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](cli)


## Docker 

1. Install Docker following the [official instructions](https://docs.docker.com/engine/install/)
2. Pull the Docker image and run TreeFlow
    * To run Jupyter Lab:
        1. `docker run -p 8888:8888 ghcr.io/christiaanjs/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](cli):
        * `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`
        
### With local Docker image

To run with a locally-built Docker container:
1. Clone and navigate to the repository: `git clone https://github.com/christiaanjs/treeflow.git` then `cd treeflow` 
2. Build the container: `docker build -t treeflow .`
3. Follow the above steps tbut replace `ghcr.io/christiaanjs/treeflow` with just the local tag `treeflow`