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