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Analysis of inference methods on standard population models
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andrewkern Merge pull request #33 from jradrion/modified_chrm_list
changed chromosome list to allow for simulation of any focal chromoso…
Latest commit b61ce4c Jun 17, 2019


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
cd stdpopsim
python install
cd ..

Now clone the analysis repo, and install its dependencies

git clone
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
cat msmc_makefile_stdpopsim_patch > msmc/Makefile && cd msmc && make
cd ../../

Further instructions can be currently found in each task directory

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