Please install using the following commands:

conda create -n SWGA2 python=3.7

conda activate SWGA2

conda install -c janedwivedi -c conda-forge soapswga

conda install -c janedwivedi melt

conda install numpy openpyxl pandas h5py sortedcontainers scikit-learn=0.21.3

Additionally, you’ll have to download two files from: https://github.com/songlab-cal/soapswga/tree/master/src/models. Place these two files into a directory named “models”. In your params.json file, you’ll have to set the “src_dir” parameter as the path to this models folder.

An example params.json file and foreground/background fasta files can be found at: https://github.com/songlab-cal/soapswga/tree/master/examples/plasmid_example.

All documentation and source code can be found in the following repository: https://github.com/songlab-cal/soapswga.