bushlab/polyfun_micromamba repository overview

⁠Introduction

This container is an installation of PolyFun (POLYgenic FUNctionally-informed fine-mapping), PolyLoc (POLYgenic LOCalization of complex trait heritability) and PolyPred (POLYgenic Prediction of complex traits).

⁠Running the container

Launch the container with the command:

docker run -it --rm -p 8888:8888 polyfun_micromamba:v1.0

Once in the container, the working directory will be /tmp/polyfun.

⁠Activating the polyfun environment

Activate the polyfun environment with the command:

micromamba activate polyfun

⁠Prerequisite Locations

PolyFun requires the following prerequisites:

• FINEMAP v1.4, which can be found at : /tmp/polyfun/finemap_v1.4.1_x86_64/finemap_v1.4.1_x86_64 in the container.

• LDstore 2.0, which can be found at: /tmp//polyfun/ldstore_v2.0_x86_64/ldstore_v2.0_x86_64 in the container.

• PLINK 1.9. This is not a prerequisite, but it is installed in the container within the /tmp/polyfun directory.

⁠Jupyter Notebook with the R Kernel

Launch a Jupyter Notebook server with the command:

jupyter notebook --ip=$(hostname -i) --port=8888

Navigate to the following:

<domain-name>:8888

⁠Testing the Container

Run the test_polyfun.py script to test the installation of PolyFun with the command:

python test_polyfun.py --finemap-exe finemap_v1.4.1_x86_64/finemap_v1.4.1_x86_64

⁠References

PolyFun can be found here.⁠