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

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

Science Score: 13.0%

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

  • ○
    CITATION.cff file
  • ○
    codemeta.json file
  • ○
    .zenodo.json file
  • ✓
    DOI references
    Found 3 DOI reference(s) in README
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    Academic publication links
  • ○
    Academic email domains
  • ○
    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (6.9%) to scientific vocabulary
Last synced: 6 months ago · JSON representation

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  • Stars: 3
  • Watchers: 1
  • Forks: 0
  • Open Issues: 0
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Created over 4 years ago · Last pushed over 4 years ago

https://github.com/ahmedmoustafa/bioinformatics-toolbox-light/blob/main/ 

![Bioinformatics Toolbox](toolbox.png)

# Bioinformatics Toolbox Light

`bioinformatics-toolbox-light` is a [Docker](https://www.docker.com/) container for common bioinformatics and genomics related tools.

The list of the installed tools and packages can be found [here](Tools.md)

## Installation

### Option 1: Pulling from GitHub Registry (Recommended)

The built image can be downloaded as follows:

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

### Option 2: Building from the `Dockerfile`

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

`cd bioinformatics-toolbox/`

`sudo docker build -t bioinformatics-toolbox .`

`sudo docker run -it bioinformatics-toolbox`

### Notes
- The size of the image is about **30 GB**.
- Building the image (option #2) from the [`Dockerfile`](https://github.com/ahmedmoustafa/bioinformatics-toolbox/blob/main/Dockerfile) takes about **six hours** on a Google Cloud machine type [**e2-medium**](https://cloud.google.com/compute/docs/machine-types) in zone [**us-west2-a**](https://cloud.google.com/compute/docs/regions-zones).

## Citation

If you use `bioinformatics-toolbox` in your work, please cite DOI [10.5281/zenodo.4936052](https://doi.org/10.5281/zenodo.4936052)

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Owner

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

Bioinformatics and Genomics Data Scientist

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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 20.04 build