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https://github.com/cbg-ethz/lollipop-in-cloud

On the fly variant deconvolution running in the cloud for on demand user requests.

https://github.com/cbg-ethz/lollipop-in-cloud

Science Score: 13.0%

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    CITATION.cff file
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    Scientific vocabulary similarity
    Low similarity (12.5%) to scientific vocabulary

Keywords

biohackeu24 elixir-cloud-aai
Last synced: 10 months ago · JSON representation

Repository

On the fly variant deconvolution running in the cloud for on demand user requests.

Basic Info
  • Host: GitHub
  • Owner: cbg-ethz
  • Language: Python
  • Default Branch: main
  • Homepage:
  • Size: 34.2 KB
Statistics
  • Stars: 0
  • Watchers: 3
  • Forks: 0
  • Open Issues: 0
  • Releases: 0
Topics
biohackeu24 elixir-cloud-aai
Created over 1 year ago · Last pushed over 1 year ago
Metadata Files
Readme

README.md

Lollipop on Cloud for On-Demand User Requests

WIP Python Flask Docker AWS S3

This package takes Lollipop, a tool used in V-Pipe's post-processing, and containerizes it to be run on-demand. This is part of the effort "V-Pipe on Cloud".

Overview

Lollipop is a powerful tool used in V-Pipe's post-processing pipeline. This project aims to containerize Lollipop, allowing it to be run on-demand via a Flask-based API. This enables users to perform deconvolution tasks on-demand, leveraging the power of cloud computing.

V-Pipe on Cloud

This project is part of the "V-Pipe on Cloud" initiative, which aims to bring the capabilities of V-Pipe to the cloud, making it more accessible and scalable.

For more information about V-Pipe, visit the V-Pipe website.

Tech Stack

  • Python: The core programming language used for the project.
  • Flask: A lightweight WSGI web application framework used to create the web server.
  • Docker: Used to containerize the application, ensuring consistency across different environments.
  • AWS S3: Used for storing and retrieving data files.

Work in Progress

This project is a work in progress and is being actively developed. Contributions and feedback are welcome.

Hackathon Project

This project was initiated as part of a hackathon project at the BioHackathon Europe 2024.

Related Repositories

This repository relates to the front-end at vpipe-biohack24-frontend.

Deployment

The current deployment of this project can be accessed at biohack24.g15n.net.

Getting Started

Prerequisites

  • Docker
  • AWS credentials with access to the required S3 buckets

Installation

  1. Clone the repository: sh git clone https://github.com/cbg-ethz/lollipop-in-cloud.git cd lollipop-in-cloud

  2. Build the Docker image: sh docker build -t lollipop-in-cloud .

  3. Run the Docker container: sh docker run --env-file .env -p 8000:8000 lollipop-in-cloud

  4. Access the API: The API will be running at http://localhost:8000.

Configuration

Ensure you have a .env file, see .env.example.

Owner

  • Name: Computational Biology Group (CBG)
  • Login: cbg-ethz
  • Kind: organization
  • Location: Basel, Switzerland

Beerenwinkel Lab at ETH Zurich

GitHub Events

Total
  • Issues event: 3
  • Member event: 1
  • Push event: 27
  • Pull request event: 11
  • Create event: 6
Last Year
  • Issues event: 3
  • Member event: 1
  • Push event: 27
  • Pull request event: 11
  • Create event: 6

Issues and Pull Requests

Last synced: 10 months ago

All Time
  • Total issues: 2
  • Total pull requests: 7
  • Average time to close issues: 17 days
  • Average time to close pull requests: 40 minutes
  • Total issue authors: 1
  • Total pull request authors: 1
  • Average comments per issue: 0.0
  • Average comments per pull request: 0.0
  • Merged pull requests: 7
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 2
  • Pull requests: 7
  • Average time to close issues: 17 days
  • Average time to close pull requests: 40 minutes
  • Issue authors: 1
  • Pull request authors: 1
  • Average comments per issue: 0.0
  • Average comments per pull request: 0.0
  • Merged pull requests: 7
  • Bot issues: 0
  • Bot pull requests: 0
View more stats
Top Authors
Issue Authors
  • gordonkoehn (2)
Pull Request Authors
  • gordonkoehn (12)
Top Labels
Issue Labels
documentation (1)
Pull Request Labels
documentation (2)

Dependencies

Dockerfile docker
  • quay.io/biocontainers/lollipop 0.5.0--pyhdfd78af_0 build
requirements.txt pypi
  • Flask *
  • boto3 *
  • matplotlib *
  • python-dotenv *