Prepare decoding quantities for ASMC
Project description
ASMC Prepare Decoding
Tool to compute decoding quantities.
Quickstart
Install the Python module from PyPI
Most functionality is available through a Python module which can be installed with:
pip install asmc_prepare_decoding
This Python module is available on Linux, macOS and Windows.
Some additional functionality, for creating CSFS, requires the additional dependency smcpp, which is not available via PyPI. If you require this functionality, you should additionally follow these instructions to install smcpp.
Examples for using the Python module can be found in the notebooks directory:
- creating decoding quantities from precomputed CSFS
- creating decoding quantities from scratch (requires smcpp)
Installing smcpp
The optional smcpp dependency is not available on PyPI, and itself requires a few additional dependencies.
On Linux, run
sudo apt install libgmp-dev libmpfr-dev libgsl0-dev
on macOS, run
brew install mpfr gmp gsl
Then, we recommend starting from a clean virtual environment. Switch to the source directory and run:
python3 -m venv venv
source venv/bin/activate
python -m pip install --upgrade pip setuptools wheel
python -m pip install asmc_prepare_decoding
python -m pip install git+https://github.com/popgenmethods/smcpp/@v1.15.3
License
This project is currently released under the GNU General Public License Version 3.
Project details
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