Installation Guide#

This guide provides instructions for setting up InPheRNo-ChIP using a Conda environment, specifically tailored for Python 3.11.5 and PyMC 5.9.2.

Prerequisites#

Before installing InPheRNo-ChIP, ensure that Conda is installed on your system. Conda simplifies package management and deployment. If Conda is not installed, download it from Anaconda’s official website.

Creating a Conda Environment#

InPheRNo-ChIP requires specific versions of libraries, managed using a Conda environment.

To set up and activate the Conda environment, follow these steps:

  1. Clone the Repository:

    Clone the InPheRNo-ChIP repository and navigate to the project directory:

    git clone https://github.com/Emad-COMBINE-lab/InPheRNo-ChIP.git
cd InPheRNo-ChIP

  2. Create the Conda Environment:

    Use the inpheC_0820.yml file, which is pre-configured for Python 3.11.5 and PyMC 5.9.2, to create a new Conda environment:

    conda env create -f inpheC_0820.yml

    This command will create a new environment named inpheC and install all the required dependencies.

  3. Activate the Conda Environment:

    Activate the newly created environment:

    conda activate inpheC

Updating the Environment#

Should the inpheC_0820.yml file be updated, synchronize your environment with:

conda env update -f inpheC_0820.yml --prune

Troubleshooting#

If you encounter installation issues:

  • Update Conda: Ensure your Conda installation is up to date by running conda update conda.

  • Check the Environment File: Verify that the inpheC_0820.yml file you are using is the correct one from the InPheRNo-ChIP repository.

  • Consult the Issue Tracker: For specific errors, review the project’s issue tracker to see if others have encountered and resolved similar issues.

  • Recreate the Environment: Sometimes, issues can be resolved by removing the existing Conda environment and recreating it:

    conda env remove -n inpheC
conda env create -f inpheC_0820.yml

  • Open a GitHub Issue: If your issue persists, please open a ticket on our Github. Include detailed error logs and environment information to help us diagnose and address your issue effectively