spacetrees

Code to estimate dispersal rates and locate genetic ancestors from genome-wide genealogies. Associated with the paper, Osmond & Coop 2024: https://elifesciences.org/articles/72177.

Formerly referred to as sparg, but that name is now reserved for inferring spatial histories from full ancestral recombination graphs (https://github.com/osmond-lab/sparg).

set up

Here is how to get set up and run spacetrees, from the command-line:

• Clone this directory, git clone https://github.com/osmond-lab/spacetrees.git.
• Move into this directory, cd spacetrees.
• Install Python v3.11.5 (https://www.python.org/downloads/release/python-3115/). On my server we can do this with module load NiaEnv/2022a python/3.11.5. May also work with similar versions.
• Create virtual environment, python -m venv venv. Make sure you are using the correct version of Python to do this.
• Activate virtual environment, source venv/bin/activate.
• Install Python packages, pip install -r requirements.txt.
• Install tsconvert, which isn't available via pip.
  • git clone https://github.com/tskit-dev/tsconvert.git. This was v0.1.dev57+g057435c for me, June 7, 2024.
  • cd tsconvert
  • pip install .
  • move back to the main working directory, cd -
• Install Relate. I used v1.2.1. See https://myersgroup.github.io/relate/index.html for more info and options.
  • On my server I downloaded the source code with git clone https://github.com/MyersGroup/relate.git on June 7, 2024. This is roughly version 1.2.1.
  • Move into the Relate directory, cd relate/build.
    • On my server I had to load these tools to build relate, module load cmake/3.22.5 gcc/11.3.0.
    • cmake ..
    • make
  • move back to the main working directory, cd -
• Run spacetrees via snakemake
  • you should now be able to estimate dispersal and locate genetic ancestors with spacetrees via snakemake! simply write snakemake all -c1 in the command line (-c1 indicates 1 thread, use more if you have them, but this example should run in less than a minute or two with -c1)
  • TODO: lots more detail needed about how to customize your options within Snakefile
  • TODO: show how to do this when you have multiple chromosomes
• Plot
  • make virtual environment accessible in Jupyter notebook with python -m ipykernel install --name $myenv --user and venv2jup
  • TODO: some may need to install Jupyter?
  • open the Jupyter notebook plots.ipynb. I do this through my server's JupyterHub, https://jupyter.scinet.utoronto.ca/
  • run the code (command+enter to execute a cell)
• Get in touch!
  • I'd love to hear if you are using this software, have any suggested improvements, or need any help: [email protected]