https://github.com/astrazeneca/fragler
https://github.com/astrazeneca/fragler
Last synced: 5 months ago
JSON representation
- Host: GitHub
- URL: https://github.com/astrazeneca/fragler
- Owner: AstraZeneca
- License: apache-2.0
- Created: 2022-07-05T05:36:03.000Z (almost 4 years ago)
- Default Branch: main
- Last Pushed: 2022-07-06T12:11:23.000Z (almost 4 years ago)
- Last Synced: 2025-09-09T11:50:58.340Z (9 months ago)
- Language: Python
- Size: 19.5 KB
- Stars: 4
- Watchers: 2
- Forks: 0
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
- Contributing: CONTRIBUTING.md
- License: LICENSE.md
Awesome Lists containing this project
README
# Fragler
## Overview
This tool implements an alogrithm to recycle fragments for modular DNA assembley. For details, see Öling et al ("FRAGLER: A Fragment Recycler Application Enabling Rapid and Scalable Modular DNA Assembly").
## Dependencies
The tool uses [conda](https://docs.conda.io/en/latest/) to manage its dependencies. Follow installation instructions in either the official conda repository or any other conda flavour. We recommend [mamba](https://github.com/mamba-org/mamba) as a drop-in replacement for conda.
The tool is also dependent on acces to the GeneArt API (https://www.thermofisher.com/se/en/home/life-science/cloning/gene-synthesis/geneart-gene-synthesis.html) and requires an access key. To obtain an access key, see instructions http://assets.thermofisher.com/TFS-Assets/BID/Reference-Materials/geneart-gene-synthesis-api-presentation.pdf and contact geneartapi@thermofisher.com
## Installation instructions
1. Clone the repo:
```bash
git@github.com:DS-QuBi/golden-gate-cloning.git
```
2. Install dependencies
```bash
cd golden-gate-cloning
conda env create -f environment.yaml -n golden-gate-cloning
```
## Usage
1. Activate conda environment
```bash
conda activate golden-gate-cloning
```
2. Start the server
```bash
bash start_server.sh
```
3. Access the app through a browser using the url reported in the previous step