analysis
Analysis of inference methods on standard population models
how to set up your environment to run the analysis
We recommend you start by creating a new conda environment for the analysis.
conda create -n popsim_env_test python=3.6.8 --yes
conda activate popsim_env_test
Next clone and install stdpopsim
git clone https://github.com/popgensims/stdpopsim.git
cd stdpopsim
python setup.py install
cd ..
Now clone the analysis repo, and install its dependencies
git clone https://github.com/popgensims/analysis.git
cd analysis/
for c in terhorst bioconda defaults conda-forge; do conda config --add channels $c; done
conda install --file requirements.txt --yes
For using msmc we need to download and compile it to play nice
with the conda environment that we have set up.
cd extern
git clone https://github.com/stschiff/msmc.git
cat msmc_makefile_stdpopsim_patch > msmc/Makefile && cd msmc && make
cd ../../
smcsmc can be installed manually or through conda on linux.
conda install -c luntergroup smcsmc Further instructions can be currently found in each task directory