InstallationΒΆ

If you are working on a shared system it is best to install MERCluster into a new virtual environment. MERCluster requires python 3.6 or above.

To create a virtual environment with conda (if you are on a system without conda, consider installing Miniconda first):

conda create -n mercluster python=3.6

Activate the environment:

conda activate mercluster

Install MERCluster within the environment you just created and activated:

git clone https://github.com/seichhorn/MERCluster.git
pip install -e MERCluster

If you plan to use MERCluster to interface directly with MERlin analyses, install MERlin as follows:

conda install rtree pytables
git clone https://github.com/ZhuangLab/MERlin.git
pip install -e MERlin

If you wish to use this environment in a jupyter notebook, add it as a kernel:

conda install -c anaconda ipykernel
python -m ipykernel install --user --name=mercluster

You can now deactivate the environment:

conda deactivate

Note

For versions of conda prior to 4.6, conda activate and conda deactivate will need to be replaced with platform-specific commands:

  • Windows: activate or deactivate
  • Linux and macOS: source activate or source deactivate