Installation¶

RepliSage needs Python 3.10 or newer and is tested on Linux. The 3D stage uses OpenMM, which is much faster on a GPU, while the Monte Carlo runs on the CPU.

From PyPI¶

pip install pyRepliSage
replisage -h

This installs the replisage command. The package is imported as RepliSage.

If replisage -h shows old options (for example --region_start), an older installed copy is shadowing the repository. Reinstall with pip install -e . in the repository root, or run python -m src.run from there.

From source¶

git clone https://github.com/SFGLab/RepliSage
cd RepliSage
pip install -r requirements.txt     # dependencies
pip install -e .                    # the replisage command, editable

Without installing, you can also run it from the repository root: python -m src.run -h.

A clean environment (recommended)¶

conda create -n replisage python=3.11
conda activate replisage
pip install pyRepliSage

Optional parts¶

You want	Install
The pyvista movies (`movie_3d_sister.mp4`, `movie_3d_compartment.mp4`)	`pip install "pyRepliSage[viz]"` (the `ffmpeg` encoder comes with `imageio-ffmpeg`)
3D on a GPU	a CUDA or OpenCL OpenMM build, then `--platform CUDA` (or `OpenCL`)
To run the tests	`pip install "pyRepliSage[test]"`, then `pytest` (fast tests) or `python run_tests.py` (all checks with one summary)
To build these docs	`pip install "pyRepliSage[docs]"`, then `mkdocs serve`

The interactive viewer_3d.html needs nothing extra: it is one self-contained file that opens in any browser.

Check that it works¶

replisage -h                                   # lists every flag
replisage --bedpe-file loops.bedpe --region chr14:80835000-98674700 --n-steps 5000

The second command is a short loop-extrusion run. It writes a folder with report.html that you can open in a browser.

Docker¶

A Dockerfile is in the repository: docker build -t replisage .

Troubleshooting¶

Symptom	Cause and fix
The first Monte Carlo run pauses for a few seconds	numba compiles the energy functions once; later runs start at once
`No template found for residue` in the 3D stage	the force field file does not match the structure; keep the default `FORCEFIELD_PATH`
`pyBigWig` fails to install	install it from conda-forge: `conda install -c conda-forge pybigwig`
The movie is skipped	install `pyvista`; use `--skip-movies` to skip the movies
GPU not used	check `--platform`, and that your OpenMM sees the device: `python -m openmm.testInstallation`

Next: the command line and examples.