PrimerDriver: Automated design of mutagenic PCR primers

Important

PrimerDriver is no longer under active development. It may occasionally receive minor updates, but these will not add new functionality. The web app will be kept running on a best-effort basis, but note that we do not guarantee any SLAs. This project remains open-source, so anyone may fork and deploy their own instance.

Introduction

PrimerDriver is a user-friendly bioinformatics platform specifically designed to generate primers for site-directed mutagenesis experiments into workflows with an easy-to-use command-line interface. “Traversing” PrimerDriver lanes, users can generate possible mutagenic primers upon input of a DNA sequence (DNA), design primers for an array of species codon expression systems through direct mutation of the amino acid (PRO), characterize and report user-designed primers (CHAR).

Usage

A. Running standalone

You can access and download the CLI from the releases page. Currently, we only have prebuilt binaries for 64-bit Windows and Linux. For other OS/architectures, see the section on Building from Source, under Developing Locally.

Run the program in a terminal using

primerdriver -h

This will run the help program. For first-time users, the program can be run in interactive mode by passing the -i flag:

primerdriver -i

This will walk you through each option step-by-step. Batch design can be performed by including primerdriver as part of a shell script.

B. Running as Python module

Prerequisites

• Git
• Mise

Setup

1. Clone the repo to your local device and cd into it

   git clone https://github.com/kvdomingo/primerdriver.git
   cd primerdriver

2. Install dependencies:

   mise install

Run the program as follows:

poetry run python -m primerdriver -h

C. Running from Docker

Run as follows:

docker run -it --entrypoint python kvdomingo/primerdriver -m primerdriver -h

Web application

For a more interactive experience, visit the web application.

Documentation

The documentation is available at https://primerdriver-docs.kvd.studio.

Contributing

Open a PR or raise an issue. You may also email Nomer or Kenneth, depending on the nature of the issue.

Developing locally

Prerequisites

• Docker
• Mise

Installing

A step by step series of examples that tell you how to get a development environment running

1. Clone the repo.
2. Install prerequisites:

   mise install
   pip install -U pre-commit
   pre-commit install

3. Install backend dependencies:

   poetry install --no-root --with dev

4. Run the development servers:

   task

Wait a few minutes for all the containers to start, then access the local servers in your browser at:

• Web app: http://localhost:3000
• Docs: http://localhost:8000

Building from source

Run the script:

# On a Linux machine, will build for Linux x64 only
# On a Windows machine, will build for Windows and Linux x64
task build

Deployment

git add .
git commit -m "DESCRIPTIVE_COMMIT_MESSAGE"
git push origin your_feature_branch

where your_feature_branch should summarize the changes you are implementing following the Conventional Commits format (e.g., feat/xxxx, fix/yyyy).

Authors

• Numeriano Amer "Nomer" E. Gutierrez - Project Lead, Molecular Biologist - Email | GitHub
• Kenneth V. Domingo - Technical Lead - Email | Website | GitHub
• Shebna Rose D. Fabilloren - Technical Consultant - Email
• Carlo M. Lapid - Project Adviser - Email

Versioning

This project complies with SemVer for versioning. For all available versions, see tags.

License

This project is licensed under the GPLv3 License.