GSH_Automation

GSH_Automation is a bioinformatics automation pipeline designed to simplify the downloading, preprocessing, and preparation of genomic datasets from multiple sources like Ensembl, COSMIC, miRGene, Orthologs, EnhancerAtlas, UCSC, and more.
This repository provides a choice-based menu system (main.py) to enable users to selectively execute tasks, ensuring modularity and control over each dataset.

Warning: work in progress. This is not working yet!

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Features

• Automated Data Downloads: Fetch genomic and annotation datasets from trusted sources (Ensembl, COSMIC, miRGene, EnhancerAtlas, UCSC, etc.).\
• Choice-Based Menu System: Interactive CLI for step-by-step control over data downloads and processing.\
• Environment Setup: Easy setup via Conda with required dependencies listed.\
• Modular Scripts: Each dataset and preprocessing step is isolated in its own module under the scripts/ folder.

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Folder Structure

GSH_Automation/
│
├── main.py                 # Entry point for running the pipeline (choice-based menu system)
├── config/
│   ├── setting.py          #url links
├── scripts/                # Contains all modular scripts for downloading/processing data
│   ├── ensembl.py          # Downloads Ensembl dataset
│   ├── cosmic.py           # Downloads COSMIC dataset
│   ├── mirgene.py          # Downloads miRGene dataset
│   ├── orthologs.py        # Downloads Orthologs data
│   ├── enhanceratlas.py    # Downloads EnhancerAtlas data
│   ├── liftover.py         # Runs UCSC Liftover for genome coordinate mapping
│   ├── cosmic_env.py       # Handles COSMIC environment-specific downloads
│   ├── rna_files.py        # Downloads lncRNA and tRNA files
│   ├── gaps_ftp.py         # Downloads UCSC Gaps FTP data
│   └── wget.py             # Downloads additional chromosome info via WGET
│
└── README.md               # Documentation (this file)

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Choice-Based Menu System

The main.py script provides an interactive choice-based menu system.
This design ensures flexibility by letting users run specific tasks independently instead of executing the entire pipeline at once.

Example Menu

==== Choose from the Menu ====
1. Download Ensembl data
2. Download miRGene data
3. Download Orthologs data
4. Download COSMIC data
5. Download EnhancerAtlas (retain dr.bed)
6. Run Liftover on dr.bed file
7. Download lncRNA and tRNA files
8. USCS_Gaps_FTP
9. WGET
10. Exit

• Enter the corresponding number to run a specific module.
• Example: typing 1 runs the Ensembl download script (scripts/ensembl.py).
• You can perform multiple tasks in sequence, and exit the pipeline anytime by choosing option 10.

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Setup Instructions

1. Clone the Repository

git clone https://github.com/TheOfficialBug/GSH_Automation.git
cd GSH_Automation

2. Create a Conda Environment

We recommend using Conda to manage dependencies.

conda create -n gsh_env python=3.9 -y
conda activate gsh_env

3. Install Dependencies

Install required Python packages:

pip install -r requirements.txt

If requirements.txt is not available, install packages as needed (e.g., requests, biopython, etc.).

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Running the Pipeline

Run the main script to start the choice-based menu system:

python main.py

Follow the on-screen prompts to download and process datasets as required.

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