Metadata-Version: 2.4
Name: PlantOmicsGwas
Version: 0.1.3
Summary: Integrated GWAS and genomic prediction pipeline with a GUI for plant genomics.
Author-email: "Ahmed Yassin, Computational Biologist" <ahmedyassin300@outlook.com>, "Falak Sher Khan, Post-doctoral scientist" <falak.khan@pku.edu.cn>
Maintainer-email: Ahmed Yassin <ahmedyassin300@outlook.com>
License: MIT
Project-URL: Homepage, https://github.com/AHMEDY3DGENOME/PlantOmicsGWAS
Project-URL: Documentation, https://github.com/AHMEDY3DGENOME/PlantOmicsGWAS/wiki
Project-URL: Repository, https://github.com/AHMEDY3DGENOME/PlantOmicsGWAS
Project-URL: Issue Tracker, https://github.com/AHMEDY3DGENOME/PlantOmicsGWAS/issues
Keywords: GWAS,genomics,plants,bioinformatics,variant-calling,machine-learning,genomic-prediction,pangenome,plant-breeding
Classifier: Development Status :: 3 - Alpha
Classifier: Intended Audience :: Science/Research
Classifier: Intended Audience :: Developers
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Classifier: Topic :: Scientific/Engineering :: Artificial Intelligence
Classifier: Programming Language :: Python :: 3
Classifier: Programming Language :: Python :: 3.10
Classifier: Programming Language :: Python :: 3.11
Classifier: Programming Language :: Python :: 3.12
Classifier: Operating System :: POSIX :: Linux
Classifier: License :: OSI Approved :: MIT License
Classifier: Natural Language :: English
Requires-Python: >=3.10
Description-Content-Type: text/markdown
Requires-Dist: numpy>=1.26
Requires-Dist: pandas>=2.0
Requires-Dist: scipy>=1.11
Requires-Dist: matplotlib>=3.7
Requires-Dist: scikit-learn>=1.3
Requires-Dist: dearpygui>=1.11
Provides-Extra: ml
Requires-Dist: xgboost>=2.0; extra == "ml"
Provides-Extra: gwas
Requires-Dist: fastlmm; python_version < "3.12" and extra == "gwas"
Requires-Dist: pysnptools; extra == "gwas"
Requires-Dist: geneview; extra == "gwas"
Provides-Extra: all
Requires-Dist: xgboost>=2.0; extra == "all"
Requires-Dist: fastlmm; python_version < "3.12" and extra == "all"
Requires-Dist: pysnptools; extra == "all"
Requires-Dist: geneview; extra == "all"

# PlantOmicsGwas: An Integrated GWAS and Genomic Prediction Pipeline for Plant Genomes

## Developers & Contributors

| Developer                                 | Expertise                     |
|-------------------------------------------|-------------------------------|
| **Ahmed Yassin**                          | Computational Biologist       |
| **Falak Sher Khan**                       | Computational Biologist       |
| **PlantOmicsGwas Software (Affiliation)** | Ye-Lab (PKU-IAAS)        |
 | **PlantOmicsGwas Status** | Early Demonstration Release (Under Active Development) |

------------------------------------------------------------------------------------------------------------------------
## Developed By: 

- Ahmed Yassin, Computational Biologist || PhD Candidate
- Falak Sher Khan, PhD, computational biologist 
The Peking university of Advanced Agricultural Science (PKU-IAAS), China


> **⚠️ Early Demonstration Release (v0.1.3)**
>
> **PlantOmicsGwas v0.1.0** is the **first public demonstration release** of the software and is intended exclusively for evaluation, testing, and feedback from researchers, collaborators, and the plant genomics community.
>
> The platform is currently under active development. Although the core analytical workflow is functional, we are continuously improving computational performance, large-scale genomic data processing, workflow efficiency, the graphical user interface, and the overall user experience.
>
> Following the publication of our accompanying research manuscript, we will release the **complete production version** of PlantOmicsGwas, including comprehensive documentation, finalized software licensing, detailed installation guides, tutorials, and the full implementation of all planned analytical modules.
>
> We sincerely appreciate feedback from researchers and early adopters, as it will play an important role in the continued refinement and development of the platform.


## Quick Installation (Linux)

PlantOmicsGwas depends on several external bioinformatics tools in addition to the Python package. Please follow the steps below to install all required components.

### Step 1 — Install Miniforge (Conda)

Download and install Miniforge:

```bash
wget https://github.com/conda-forge/miniforge/releases/latest/download/Miniforge3-Linux-x86_64.sh

bash Miniforge3-Linux-x86_64.sh

source ~/.bashrc
```

---

### Step 2 — Create the PlantOmicsGwas Environment

Create a dedicated Conda environment and install all required bioinformatics dependencies.

```bash
mamba create -n plantomicsgwas \
-c conda-forge \
-c bioconda \
python=3.11 \
samtools \
bcftools \
bowtie2 \
minimap2 \
plink \
-y
```

---

### Step 3 — Activate the Environment

```bash
conda activate plantomicsgwas
```

---

### Step 4 — Install PlantOmicsGwas

Install the latest release from **PyPI** together with all optional modules.

```bash
pip install --upgrade pip

pip install plantomicsgwas
```

---

### Step 5 — Launch PlantOmicsGwas

Start the graphical user interface.

```bash
plantomicsgwas-gui
```

Alternatively, launch the command-line interface.

```bash
plantomicsgwas --help
```

---

##  Verify Installation

Verify that all required bioinformatics tools are correctly installed.

```bash
samtools --version
bcftools --version
bowtie2 --version
minimap2 --version
plink --version
```

If all commands return their version numbers without errors, PlantOmicsGwas has been installed successfully and is ready for use.
````
