biobuntu 1.2.2__tar.gz

biobuntu-1.2.2/LICENSE

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+MIT License
+
+Copyright (c) 2024 GenomeHouse
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

biobuntu-1.2.2/PKG-INFO

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+Metadata-Version: 2.4
+Name: biobuntu
+Version: 1.2.2
+Summary: A comprehensive platform for running genomic analysis pipelines with CLI, GUI, and web interfaces. Perfect for researchers, labs, and bioinformatics teams.
+Author-email: BioBuntu <info@biobuntu.com>
+License-Expression: MIT
+Project-URL: Homepage, https://biobuntu.github.io/
+Project-URL: Source, https://github.com/biobuntu/biobuntu
+Project-URL: Tracker, https://github.com/biobuntu/biobuntu/issues
+Project-URL: Documentation, https://biobuntu.github.io/docs
+Keywords: bioinformatics,genomics,pipelines,workflow,cli,gui,web
+Classifier: Programming Language :: Python :: 3
+Classifier: Operating System :: OS Independent
+Requires-Python: >=3.8
+Description-Content-Type: text/markdown
+License-File: LICENSE
+Requires-Dist: click
+Requires-Dist: pyyaml
+Requires-Dist: flask
+Dynamic: license-file
+
+<p align="center">
+  <img width="607" height="215" alt="biobuntu" src="https://github.com/user-attachments/assets/0d82cc8f-82ef-468a-b615-4f35a5a141c6" />
+</p>
+
+
+
+[![License: MIT](https://img.shields.io/badge/License-MIT-yellow.svg)](https://opensource.org/licenses/MIT)
+[![Python 3.8+](https://img.shields.io/badge/python-3.8+-blue.svg)](https://www.python.org/downloads/)
+
+A comprehensive bioinformatics platform for running pipelines, with CLI, GUI, and web interfaces.
+
+## Features
+
+- **Project Management**: Create and manage bioinformatics projects with organized directory structures
+- **Advanced Pipelines**: Support for complex workflows with dependencies and parallel execution
+- **Multiple Interfaces**: CLI, Desktop GUI (BioBuntu Studio), and Web Dashboard
+- **Remote Lab Support**: API endpoints for remote pipeline execution with job tracking
+- **Packaging**: Available as .deb packages, PPA, and Conda packages
+- **Workflow Support**: RNA-seq, variant calling, metagenomics, and QC pipelines
+- **Tool Integration**: Wrappers for FastQC, BWA, GATK, HISAT2, Samtools
+
+## 📦 Installation
+
+### From Source
+```bash
+git clone https://github.com/biobuntu/biobuntu.git
+cd biobuntu
+pip install -e .
+```
+
+### Debian/Ubuntu (.deb)
+```bash
+sudo dpkg -i biobuntu_0.1.0_all.deb
+sudo apt-get install -f  # Install dependencies
+```
+
+### Ubuntu PPA
+```bash
+sudo add-apt-repository ppa:biobuntu/biobuntu
+sudo apt-get update
+sudo apt-get install biobuntu
+```
+
+### Conda
+```bash
+conda install -c biobuntu biobuntu
+```
+
+## 🏁 Quick Start
+
+1. **Create a project**:
+   ```bash
+   biobuntu create-project myproject --description "RNA-seq analysis"
+   ```
+
+2. **Run a pipeline**:
+   ```bash
+   biobuntu run workflows/rnaseq.yaml --project myproject --input sample.fastq
+   ```
+
+3. **Start web interface**:
+   ```bash
+   biobuntu web
+   ```
+   Open: http://localhost:5000
+
+## 💻 Usage
+
+### CLI Commands
+
+BioBuntu provides a comprehensive CLI with 8 commands:
+
+```bash
+biobuntu --help                    # Show all commands
+biobuntu create-project <name>     # Create new project
+biobuntu list-projects             # List all projects
+biobuntu delete-project <name>     # Delete project
+biobuntu list                      # List workflows
+biobuntu validate <workflow>       # Validate workflow
+biobuntu run <workflow> [options]  # Run pipeline
+biobuntu web                       # Start web dashboard
+biobuntu gui                       # Start GUI application
+```
+
+### Web Dashboard
+
+Access the web interface at http://localhost:5000 with features:
+- Create and manage projects
+- Run pipelines locally or remotely
+- Monitor remote jobs with real-time updates
+- Download results and intermediate files
+
+### GUI Application
+
+Launch BioBuntu Studio with `biobuntu gui` featuring:
+- Project selection and creation
+- Drag-and-drop file input
+- Real-time progress tracking
+- Workflow validation
+
+## 📁 Project Structure
+
+Projects are automatically organized:
+
+```
+~/biobuntu/projects/myproject/
+├── raw_data/     # Input files
+├── qc/          # Quality control results
+├── processed/   # Intermediate processing files
+├── results/     # Final analysis results
+├── reports/     # Summary reports
+├── logs/        # Execution logs
+└── config/      # Project configuration
+```
+
+## 🔬 Advanced Pipelines
+
+### Features
+- **Dependencies**: Steps can depend on previous steps
+- **Parallel Execution**: Independent steps run concurrently
+- **Parameterization**: Configurable tool arguments
+- **Validation**: Check workflow structure before execution
+
+### Example Workflow
+
+```yaml
+name: RNA-seq Pipeline
+description: Complete RNA-seq analysis
+steps:
+  - name: qc
+    tool: fastqc
+    args:
+      input_file: raw_data/sample.fastq
+      output_dir: qc/
+  - name: align
+    tool: hisat2
+    depends_on: [qc]
+    args:
+      index: genome_index
+      input_fastq1: raw_data/sample.fastq
+      output_sam: processed/sample.sam
+```
+
+## 🌐 Remote Lab Support
+
+### API Endpoints
+- `POST /api/remote/run` - Submit remote jobs
+- `GET /api/remote/status/<job_id>` - Check job status
+- `GET /api/remote/jobs` - List all remote jobs
+- Webhook callbacks for job completion
+
+### Example Remote Execution
+```python
+import requests
+
+# Submit job
+response = requests.post('http://localhost:5000/api/remote/run', json={
+    'workflow': 'rnaseq.yaml',
+    'project': 'myproject',
+    'callback_url': 'https://myapp.com/webhook'
+})
+
+job_id = response.json()['job_id']
+```
+
+## 📚 Documentation
+
+- **[Getting Started](docs/getting_started.md)** - Quick start guide
+- **[Pipelines](docs/pipelines.md)** - Pipeline creation and management
+- **[GUI Guide](docs/gui.md)** - Desktop application usage
+- **[Web Dashboard](docs/web.md)** - Web interface documentation
+- **[API Reference](docs/api.md)** - Complete API documentation
+- **[Development](docs/development.md)** - Contributing and development guide
+
+## 🛠️ Development
+
+### Prerequisites
+- Python 3.8+
+- Bioinformatics tools (optional, for testing)
+
+### Setup
+```bash
+git clone https://github.com/biobuntu/biobuntu.git
+cd biobuntu
+pip install -e .
+pip install pytest black flake8  # Development dependencies
+```
+
+### Testing
+```bash
+pytest                    # Run tests
+black .                  # Format code
+flake8 .                 # Check style
+```
+
+### Building Packages
+```bash
+./scripts/build_deb.sh    # Debian package
+./scripts/build_ppa.sh    # PPA package
+./scripts/build_conda.sh  # Conda package
+```
+
+## 🤝 Contributing
+
+We welcome contributions! Please see our [Development Guide](docs/development.md) for details.
+
+1. Fork the repository
+2. Create a feature branch
+3. Make your changes
+4. Add tests
+5. Submit a pull request
+
+## 📄 License
+
+This project is licensed under the MIT License - see the [LICENSE](LICENSE) file for details.
+
+## 🙏 Acknowledgments
+
+- Built with Python, Flask, Click, and tkinter
+- Inspired by bioinformatics community needs
+- Thanks to all contributors and users
+
+## 📞 Support
+
+- **Issues**: [GitHub Issues](https://github.com/biobuntu/biobuntu/issues)
+- **Discussions**: [GitHub Discussions](https://github.com/biobuntu/biobuntu/discussions)
+- **Documentation**: [Full Docs](docs/)
+
+---
+
+**BioBuntu** - Making bioinformatics accessible through modern interfaces and powerful automation.

biobuntu-1.2.2/README.md

@@ -0,0 +1,231 @@
+<p align="center">
+  <img width="607" height="215" alt="biobuntu" src="https://github.com/user-attachments/assets/0d82cc8f-82ef-468a-b615-4f35a5a141c6" />
+</p>
+
+
+
+[![License: MIT](https://img.shields.io/badge/License-MIT-yellow.svg)](https://opensource.org/licenses/MIT)
+[![Python 3.8+](https://img.shields.io/badge/python-3.8+-blue.svg)](https://www.python.org/downloads/)
+
+A comprehensive bioinformatics platform for running pipelines, with CLI, GUI, and web interfaces.
+
+## Features
+
+- **Project Management**: Create and manage bioinformatics projects with organized directory structures
+- **Advanced Pipelines**: Support for complex workflows with dependencies and parallel execution
+- **Multiple Interfaces**: CLI, Desktop GUI (BioBuntu Studio), and Web Dashboard
+- **Remote Lab Support**: API endpoints for remote pipeline execution with job tracking
+- **Packaging**: Available as .deb packages, PPA, and Conda packages
+- **Workflow Support**: RNA-seq, variant calling, metagenomics, and QC pipelines
+- **Tool Integration**: Wrappers for FastQC, BWA, GATK, HISAT2, Samtools
+
+## 📦 Installation
+
+### From Source
+```bash
+git clone https://github.com/biobuntu/biobuntu.git
+cd biobuntu
+pip install -e .
+```
+
+### Debian/Ubuntu (.deb)
+```bash
+sudo dpkg -i biobuntu_0.1.0_all.deb
+sudo apt-get install -f  # Install dependencies
+```
+
+### Ubuntu PPA
+```bash
+sudo add-apt-repository ppa:biobuntu/biobuntu
+sudo apt-get update
+sudo apt-get install biobuntu
+```
+
+### Conda
+```bash
+conda install -c biobuntu biobuntu
+```
+
+## 🏁 Quick Start
+
+1. **Create a project**:
+   ```bash
+   biobuntu create-project myproject --description "RNA-seq analysis"
+   ```
+
+2. **Run a pipeline**:
+   ```bash
+   biobuntu run workflows/rnaseq.yaml --project myproject --input sample.fastq
+   ```
+
+3. **Start web interface**:
+   ```bash
+   biobuntu web
+   ```
+   Open: http://localhost:5000
+
+## 💻 Usage
+
+### CLI Commands
+
+BioBuntu provides a comprehensive CLI with 8 commands:
+
+```bash
+biobuntu --help                    # Show all commands
+biobuntu create-project <name>     # Create new project
+biobuntu list-projects             # List all projects
+biobuntu delete-project <name>     # Delete project
+biobuntu list                      # List workflows
+biobuntu validate <workflow>       # Validate workflow
+biobuntu run <workflow> [options]  # Run pipeline
+biobuntu web                       # Start web dashboard
+biobuntu gui                       # Start GUI application
+```
+
+### Web Dashboard
+
+Access the web interface at http://localhost:5000 with features:
+- Create and manage projects
+- Run pipelines locally or remotely
+- Monitor remote jobs with real-time updates
+- Download results and intermediate files
+
+### GUI Application
+
+Launch BioBuntu Studio with `biobuntu gui` featuring:
+- Project selection and creation
+- Drag-and-drop file input
+- Real-time progress tracking
+- Workflow validation
+
+## 📁 Project Structure
+
+Projects are automatically organized:
+
+```
+~/biobuntu/projects/myproject/
+├── raw_data/     # Input files
+├── qc/          # Quality control results
+├── processed/   # Intermediate processing files
+├── results/     # Final analysis results
+├── reports/     # Summary reports
+├── logs/        # Execution logs
+└── config/      # Project configuration
+```
+
+## 🔬 Advanced Pipelines
+
+### Features
+- **Dependencies**: Steps can depend on previous steps
+- **Parallel Execution**: Independent steps run concurrently
+- **Parameterization**: Configurable tool arguments
+- **Validation**: Check workflow structure before execution
+
+### Example Workflow
+
+```yaml
+name: RNA-seq Pipeline
+description: Complete RNA-seq analysis
+steps:
+  - name: qc
+    tool: fastqc
+    args:
+      input_file: raw_data/sample.fastq
+      output_dir: qc/
+  - name: align
+    tool: hisat2
+    depends_on: [qc]
+    args:
+      index: genome_index
+      input_fastq1: raw_data/sample.fastq
+      output_sam: processed/sample.sam
+```
+
+## 🌐 Remote Lab Support
+
+### API Endpoints
+- `POST /api/remote/run` - Submit remote jobs
+- `GET /api/remote/status/<job_id>` - Check job status
+- `GET /api/remote/jobs` - List all remote jobs
+- Webhook callbacks for job completion
+
+### Example Remote Execution
+```python
+import requests
+
+# Submit job
+response = requests.post('http://localhost:5000/api/remote/run', json={
+    'workflow': 'rnaseq.yaml',
+    'project': 'myproject',
+    'callback_url': 'https://myapp.com/webhook'
+})
+
+job_id = response.json()['job_id']
+```
+
+## 📚 Documentation
+
+- **[Getting Started](docs/getting_started.md)** - Quick start guide
+- **[Pipelines](docs/pipelines.md)** - Pipeline creation and management
+- **[GUI Guide](docs/gui.md)** - Desktop application usage
+- **[Web Dashboard](docs/web.md)** - Web interface documentation
+- **[API Reference](docs/api.md)** - Complete API documentation
+- **[Development](docs/development.md)** - Contributing and development guide
+
+## 🛠️ Development
+
+### Prerequisites
+- Python 3.8+
+- Bioinformatics tools (optional, for testing)
+
+### Setup
+```bash
+git clone https://github.com/biobuntu/biobuntu.git
+cd biobuntu
+pip install -e .
+pip install pytest black flake8  # Development dependencies
+```
+
+### Testing
+```bash
+pytest                    # Run tests
+black .                  # Format code
+flake8 .                 # Check style
+```
+
+### Building Packages
+```bash
+./scripts/build_deb.sh    # Debian package
+./scripts/build_ppa.sh    # PPA package
+./scripts/build_conda.sh  # Conda package
+```
+
+## 🤝 Contributing
+
+We welcome contributions! Please see our [Development Guide](docs/development.md) for details.
+
+1. Fork the repository
+2. Create a feature branch
+3. Make your changes
+4. Add tests
+5. Submit a pull request
+
+## 📄 License
+
+This project is licensed under the MIT License - see the [LICENSE](LICENSE) file for details.
+
+## 🙏 Acknowledgments
+
+- Built with Python, Flask, Click, and tkinter
+- Inspired by bioinformatics community needs
+- Thanks to all contributors and users
+
+## 📞 Support
+
+- **Issues**: [GitHub Issues](https://github.com/biobuntu/biobuntu/issues)
+- **Discussions**: [GitHub Discussions](https://github.com/biobuntu/biobuntu/discussions)
+- **Documentation**: [Full Docs](docs/)
+
+---
+
+**BioBuntu** - Making bioinformatics accessible through modern interfaces and powerful automation.