Threads

This software implements the Threads algorithm, described in

Á. F. Gunnarsson, J. Zhu, B. C. Zhang, Z. Tsangalidou, A. Allmont, P. Palamara. A scalable approach for genome-wide inference of ancestral recombination graphs. bioRxiv, 2024.

The user manual for threads can be found here.

Rescomp user installation instructions

Clone the threads-arg repo:

git clone https://github.com/PalamaraLab/threads.git
cd threads

Load development modules:

module load Python/3.11.3-GCCcore-12.3.0
module load Boost/1.82.0-GCC-12.3.0
module load HDF5/1.14.0-gompi-2023a

Create a new venv, activate and pip install to build:

python -m venv venv
. venv/bin/activate
pip install --upgrade pip setuptools wheel
pip install .

For active development use -e and [dev] to for additional dependencies:

pip install -e .[dev]

For developers: making a release

• Bump the version number in pyproject.toml, CMakeLists.txt
• Update RELEASE_NOTES.md
• Push changes and check that all GitHub workflows pass
• Tag the commit in Git using syntax vX.Y.Z
• Make a release on GitHub, which should trigger a new build that will upload Python wheels to PyPI
• If building wheels for a new Python version:
  • Update classifiers in pyproject.toml
  • Check whether version of pypa/cibuildwheel needs updating in build-wheels.yml