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bioinformatics-toolbox

Docker container for bioinformatics tools and pipelines

https://github.com/ahmedmoustafa/bioinformatics-toolbox

Science Score: 57.0%

This score indicates how likely this project is to be science-related based on various indicators:

  • ✓
    CITATION.cff file
    Found CITATION.cff file
  • ✓
    codemeta.json file
    Found codemeta.json file
  • ✓
    .zenodo.json file
    Found .zenodo.json file
  • ✓
    DOI references
    Found 3 DOI reference(s) in README
  • ○
    Academic publication links
  • ○
    Academic email domains
  • ○
    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (6.8%) to scientific vocabulary

Keywords

alignment assembly bioinformatics bioinformatics-containers bioinformatics-pipeline docker genomics metagenomics phylogenetics transciptomics virtualization
Last synced: 6 months ago · JSON representation ·

Repository

Docker container for bioinformatics tools and pipelines

Basic Info
Statistics
  • Stars: 12
  • Watchers: 4
  • Forks: 6
  • Open Issues: 0
  • Releases: 5
Topics
alignment assembly bioinformatics bioinformatics-containers bioinformatics-pipeline docker genomics metagenomics phylogenetics transciptomics virtualization
Created over 4 years ago · Last pushed over 1 year ago
Metadata Files
Readme License Citation

README.md

Bioinformatics Toolbox

Bioinformatics Toolbox

bioinformatics-toolbox is a Docker container for common bioinformatics and genomics related tools.

The list of the installed tools and packages can be found here

Installation

Option 1: Pulling from GitHub Registry (Recommended)

The built image can be downloaded as follows:

bash sudo docker run -it ghcr.io/ahmedmoustafa/bioinformatics-toolbox /bin/bash

Option 2: Building from the Dockerfile

bash git clone https://github.com/ahmedmoustafa/bioinformatics-toolbox.git

bash cd bioinformatics-toolbox/

bash sudo docker build -t bioinformatics-toolbox .

bash sudo docker run -it bioinformatics-toolbox

Notes

  • The size of the image is about 64 GB.
  • Pulling the image (option #1) takes about 30 minutes on a Google Cloud machine type e2-standard-2 in zone us-central1-a.
  • Building the image (option #2) takes about 5 hours on a Google Cloud machine type e2-standard-2 in zone us-central1-a.

Citation

If you use bioinformatics-toolbox in your work, please cite 10.5281/zenodo.8103969

Owner

  • Name: Ahmed Moustafa
  • Login: ahmedmoustafa
  • Kind: user
  • Location: Egypt
  • Company: American University in Cairo

Bioinformatics and Genomics Data Scientist

Citation (CITATION.cff) 

cff-version: 1.1.0
message: "If you use this software, please cite it as below."
authors:
  - family-names: Moustafa
    given-names: Ahmed
    orcid: https://orcid.org/0000-0002-0111-3555
title: ahmedmoustafa/bioinformatics-toolbox: bioinformatics-toolbox v1.3
version: v1.3
date-released: 2023-07-01

GitHub Events

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Dependencies

.github/workflows/docker-publish.yml actions
  • actions/checkout v2 composite
  • docker/build-push-action ad44023a93711e3deb337508980b4b5e9bcdc5dc composite
  • docker/login-action 28218f9b04b4f3f62068d7b6ce6ca5b26e35336c composite
  • docker/metadata-action 98669ae865ea3cffbcbaa878cf57c20bbf1c6c38 composite
Dockerfile docker
  • ubuntu 22.04 build