GitLocker: The Coding Marketplace

Description:

primerdriver 1.5.0

PrimerDriver: Automated design of mutagenic PCR primers

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

Python 3.8.1+
Poetry
Git

Setup

Clone the repo to your local device
git clone https://github.com/kvdomingo/primerdriver.git

Install dependencies:
poetry 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://kvdomingo.github.io/primerdriver/.
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
Task

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

Clone the repo.
Install backend dependencies:

poetry install

Wait a few minutes for all the containers to start, then access the
local server in your browser at 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
(e.g., feature/implementing-xxxx-feature, bugfix/crush-critical-yyyy-bug).
Authors

Numeriano Amer "Nomer" E. Gutierrez - Project Lead, Molecular
Biologist - Email | GitHub
Kenneth V. Domingo - Lead Developer, Technical
Consultant - 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.