smoother_hg - Integrates hg and Smoother

This package allows opening smoother indices in HiGlass.

• Smoother's GitHub
• hg's GitHub

Quickstart:

prerequisites:

• conda should be installed
• build-essential should be installed

create & activate a new conda environment (optional)

conda create -y -n smoother_hg python=3.9
conda activate smoother_hg

install the proper compilers

conda install -y gcc=9.4.0 gxx=9.4.0 -c conda-forge

Install smoother_hg (and all requirements) from GitHub.

git clone https://github.com/Siegel-Lab/smoother_hg.git
cd smoother_hg
git checkout stable-latest
pip install -e . --no-binary libsps,libsmoother

# hg only works with numpy<=1.23.0 but does not declare this
pip install numpy==1.23.0

Download 2 example smoother indices.

wget https://syncandshare.lrz.de/dl/fi5sGd6q7mvegdzMfqjT4Y/radicl.smoother_index.zip
wget https://syncandshare.lrz.de/dl/fi8q6iroKx49azsZLHxeYB/micro-c.smoother_index.zip

conda install -y unzip
unzip radicl.smoother_index.zip
unzip micro-c.smoother_index.zip

Then open Example.ipynb in jupyter-lab or -notebook.