Automated design of mutagenic PCR primers
Project description
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
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
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.
Project details
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