sanjayk741/aptamer3d repository overview

⁠RNA Complete Pipeline (seq-str)

Containerized RNA sequence to structure generation and optimization pipeline for folding, with additional analysis, and visualization.

⁠Docker Image

sanjayk741/aptamer3d:latest

⁠Features

• Fully containerized workflow
• No dependency installation required
• Cross-platform support:
  • Linux
  • macOS
  • Windows
• Automatic output export to host machine
• Disposable execution with --rm
• Reproducible scientific environment

⁠Requirements

Install Docker Desktop or Docker Engine:

• https://www.docker.com/products/docker-desktop/⁠

Verify installation:

docker --version

⁠Pull Image

docker pull sanjayk741/aptamer3d:latest

⁠Quick Start

The container writes all outputs directly into your current local directory using Docker volume mounting.

⁠Linux

Run:

docker run --rm \
  -v "$(pwd):/work" \
  sanjayk741/aptamer3d:latest \
  "GCGCUUCGCC"

⁠macOS

Run:

docker run --rm \
  -v "$(pwd):/work" \
  sanjayk741/aptamer3d:latest \
  "GCGCUUCGCC"

⁠Windows PowerShell

Run:

docker run --rm `
  -v "${PWD}:/work" `
  sanjayk741/aptamer3d:latest `
  "GCGCUUCGCC"

⁠Output Files

All generated files appear automatically in:

./output/

⁠Example Workflow

⁠1. Create Working Directory

⁠Linux/macOS

mkdir rna_test
cd rna_test

⁠Windows PowerShell

mkdir rna_test
cd rna_test

⁠2. Run Pipeline

⁠Linux/macOS

docker run --rm \
  -v "$(pwd):/work" \
  sanjayk741/aptamer3d:latest \
  "GCGCUUCGCC"

⁠Windows PowerShell

docker run --rm `
  -v "${PWD}:/work" `
  sanjayk741/aptamer3d:latest `
  "GCGCUUCGCC"

⁠3. Inspect Results

⁠Linux/macOS

ls output/

⁠Windows PowerShell

dir output

⁠Input

Provide RNA sequence as argument:

"GCGCUUCGCC"

Example:

docker run --rm \
  -v "$(pwd):/work" \
  sanjayk741/aptamer3d:latest \
  "AUGCGGAUCCGAU"

⁠Container Behavior

The container:

1. Starts
2. Runs complete RNA workflow
3. Saves results into mounted host directory
4. Automatically exits
5. Deletes itself (--rm)

No manual cleanup required.

⁠Volume Mounting Explained

This command:

-v "$(pwd):/work"

maps your current local directory into the container:

The container writes results internally to:

/work/output/Job_<timestamp>/

which automatically appears on your host machine as:

./output/Job_<timestamp>/

⁠Troubleshooting

⁠Permission Issues (Linux/macOS)

If output files are owned by root:

sudo chown -R $USER:$USER output

⁠Docker Not Running

Start Docker Desktop or Docker daemon before running commands.

⁠Windows Path Issues

Use PowerShell instead of CMD for best compatibility.

⁠License

MIT License

⁠Citation

If you use this pipeline in research, please cite the relevant underlying tools and algorithms used in the workflow.

⁠Author

Sanjay K Mohanty