Installation
You can install flexsweep and its dependencies using Conda or Pip. Both options will install library requirements automatically.
Conda
We recommend to use install conda from conda-forge which include mamba by default. In any other case, we recommend to install mamba to speep up conda packages installation.
mamba install -c bioconda flexsweep
Pip
Ensure you have python>=3.12 and pip installed and then simply run
pip install flexsweep
This will install stdpopsim into your local user Python packages (on some systems you will need to use python3 rather than python). Please see the Python package installation tutorial for more details on the various installation options. In particular, we recommend using a virtual environment to improve reproducibility.
It may also be necessary to update your PATH to run the command line interface. See here for details on what this means and how to do it.
Source
uv build uv pip install dist/flexsweep-2.0.tar.gz
Testing the Installation
You can easily test flexsweep by running the CLI in your terminal
flexsweep --help
Usage: flexsweep [OPTIONS] COMMAND [ARGS]...
CLI for Simulator and CNN.
Options:
--help Show this message and exit.
Commands:
cnn Run the Flex-sweep CNN for training or prediction.
dann Run the Flex-sweep DANN for training or prediction.
enrichment Gene-set sweep enrichment and FDR analysis.
fvs-discoal Estimate summary statistics from discoal...
fvs-vcf Estimate summary statistics from VCF files and...
polarize Polarize VCF using rust est-sfs refactor.
rank Rank genomic features by their maximum nearby sweep...
recombination-bins Output recombination bins from empirical...
scan Standalone outlier scan from a directory of...
scan-plot Visualize outlier scan results.
simulator Run the discoal simulator with user-specified...
You can also try to import the package into your python enviroment
python -c "import flexsweep"