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Environment Setup

This doc provides some basic setup instructions on an HPC system such as Bridges2.

Download & Install

Conda

Anaconda3 is usually available as a pre-installed module on Bridges2. If Anaconda3 does not come installed on your cluster, please install it.

✅ Step 1: Load Anaconda Module

module load anaconda3

✅ Step 2: Create and Activate Environment

conda create -n hal python=3.7
conda activate hal

HALPER expects the conda env name to be hal. If using another name, modify line 27 of halper_map_peak_orthologs.sh and change to the corresponding name. Detailed instructions on how to install hal and HALPER here.

Git

🧩 Step 1: Activate Env and Install Git

conda activate hal
conda install git

🧩 Step 2: Clone the Main Repository

https://github.com/BioinformaticsDataPracticum2025/open-chromatin-analysis.git

You may also need to install the ENCODE ATAC-seq data processing pipeline, bedtools, and MEME-suite. Refer to the hyperlinks for their respective installation instructions.