Installing Dependencies

This guide will cover how to install COMO's dependencies in a Conda environment

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Overview

We will be installing COMO’s dependencies in a Conda (or Mamba!) virtual environment. If you don’t know what a virtual environment is, here is a brief explanation:

A virtual environment is a self-contained and isolated workspace that allows you to manage and segregate dependencies for different projects. This means that you can have different sets of packages and libraries installed in separate virtual environments, preventing conflicts between projects that might require different versions of the same package. Virtual environments help keep your project dependencies organized, making it easier to maintain, share, and reproduce your software environments. When you work within a virtual environment, any packages you install or modify only affect that specific environment, leaving your system-wide configurations unchanged. This is especially useful when working on projects with specific version requirements or when collaborating with others, as it ensures consistent and controlled development environments.

Creating a virtual environment

The first step is to create the actual virtual environment. This command should done on the command line

conda create -n como

Activating the Environment

The environment has been created, but it hasn’t been activated yet. Activate the environment by executing the below line

conda activate como

Install Mamba

Mamba is much faster than Conda, due to it being written in C++. It is a drop-in replacement for Conda, so you can use it in place of Conda without any issues. To install Mamba, execute the following command:

conda install --channel conda-forge mamba

Once the environment has been created, we can install the dependencies required by COMO.

Warning: You must execute this in the root directory of the COMO folder that was downloaded in the previous step

# Change directories into the COMO folder
cd COMO/
mamba env update --file environment.yml

Once this is done, the final step is installing our customized version of zFPKM that allows for filtering insignificant local maxima during RNA-seq processing. During the “Installing Dependencies” step, R was installed. We can use that now to install zFPKM from our source

Important: Installing zFPKM from our source is an important step in the installation process. Failing to do so will result in errors when running COMO.

R -e "devtools::install_github('babessell1/zFPKM')"

Summary

Now that you’ve installed COMO’s dependencies, you’re ready to start using COMO!