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< Table Of Contents

Installation Instructions

System requirements

DiMSum is expected to work on all operating systems.

Installing MoCHI and its dependencies using Conda (recommended)

The easiest way to install MoCHI is by using the bioconda package.

Firstly, install the Conda package/environment management system (if you don't already have it).

On MacOS, run:

curl -L -O https://github.com/conda-forge/miniforge/releases/latest/download/Miniforge3-MacOSX-x86_64.sh
sh Miniforge3-MacOSX-x86_64.sh

On Linux, run:

curl -L -O https://github.com/conda-forge/miniforge/releases/latest/download/Miniforge3-Linux-x86_64.sh
sh Miniforge3-Linux-x86_64.sh

IMPORTANT: If in doubt, respond with "yes" to the following question during installation: "Do you wish the installer to initialize Miniforge3 by running conda init?". In this case Conda will modify your shell scripts (~/.bashrc or ~/.bash_profile) to initialize Miniforge3 on startup. Ensure that any future modifications to your $PATH variable in your shell scripts occur before this code to initialize Miniforge3.

After installing Conda you will need to add the bioconda channel as well as the other channels bioconda depends on. Start a new console session (e.g. by closing the current window and opening a new one) and run the following:

conda config --add channels bioconda
conda config --add channels conda-forge

Next, create a dedicated Conda environment to install the MoCHI bioconda package and it's dependencies:

conda create -n pymochi pymochi
conda activate pymochi

TIP: See here for more information about managing conda environments.

To check that you have a working installation of MoCHI, run the Demo

Installing MoCHI from source (GitHub)

Installing MoCHI from source is not recommended. The easiest way to install MoCHI (and its dependencies) is by using the MoCHI bioconda package. See Installing MoCHI and its dependencies using Conda.

This this yaml file can be used to create a dedicated Conda environment with all necessary dependencies (as explained below).

  1. Install the Conda package/environment management system (if you already have Conda skip to step 2):

On MacOS, run:

curl -L -O https://github.com/conda-forge/miniforge/releases/latest/download/Miniforge3-MacOSX-x86_64.sh
sh Miniforge3-MacOSX-x86_64.sh

On Linux, run:

curl -L -O https://github.com/conda-forge/miniforge/releases/latest/download/Miniforge3-Linux-x86_64.sh
sh Miniforge3-Linux-x86_64.sh

IMPORTANT: If in doubt, respond with "yes" to the following question during installation: "Do you wish the installer to initialize Miniforge3 by running conda init?". In this case Conda will modify your shell scripts (~/.bashrc or ~/.bash_profile) to initialize Miniforge3 on startup. Ensure that any future modifications to your $PATH variable in your shell scripts occur before this code to initialize Miniforge3.

  1. Clone the MoCHI GitHub repository:

    $ git clone https://github.com/lehner-lab/MoCHI.git

  2. Create the pymochi Conda environment:

    $ conda env create -f MoCHI/pymochi.yaml

  3. Install MoCHI:

    $ conda activate pymochi
$ cd MoCHI
$ pip install -e ./

Demo MoCHI

Run the demo to ensure that you have a working MoCHI installation (expected run time <10min):

$ demo_mochi.py