This website contains information about the Docker images maintained by the Phenotypic Evolution Group (pegi3s) at the Instituto de Biologia Molecular e Celular (IBMC) / Instituto de Investigação e Inovação em Saúde da Universidade do Porto (i3S). All images are available through our Docker Hub repository, and the respective Docker files at our GitHub repository.
In addition, this repository also contains tutorials to serve as guidance on the usage of existing Docker images (e.g. Trinity for RNA-Seq).
In order to use the Docker images maintained by pegi3s, users need to install Docker first.
To install Docker in Linux, please follow these instructions instructions:
To install Docker in Windows, please follow these instructions instructions:
List of available bioinformatic images:
sudo su
(administrator privileges) is required to run any image. As an alternative please follow the steps described here to manage Docker as a non-root user.docker system prune -a
docker rmi <image_name> or <image_ID>
docker pull pegi3s/<image_name>
Q. Are the Docker images compatible with Singularity?
A. Yes. In principle, all of our images can be run using Singularity. This guide provides some examples.
Q. Are the Docker images compatible with Podman?
A. Yes. In principle, all of our images can be run using Podman. This guide provides some examples.
If you are interested in our project or would like to contribute with suggestions, you may contact us through pegi3sdocker@gmail.com.
H. López-Fernández; P. Ferreira; M. Reboiro-Jato; C.P. Vieira; J. Vieira (2021) The pegi3s Bioinformatics Docker Images Project. 15th International Conference on Practical Applications of Computational Biology & Bioinformatics: PACBB 2021. Salamanca, Spain. 6 - October
P. Ferreira; H. López-Fernández; P. Duque; Cristina P. Vieira; F. Fdez-Riverola; Miguel Reboiro-Jato; J. Vieira (2019) Bioinformatics Docker Images. Bioinformatics Open Days: BOD 2019. Braga, Portugal. 21 - February
ELIXIR bio.tools: Bioinformatics Docker Images Project.
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If you use these Docker Images, please include in the acknowledgments section of your paper the sentence: "The authors wish to thank to the Bioinformatics Docker Images Project (https://pegi3s.github.io/dockerfiles/) and to the BioData.pt Project (https://biodata.pt)".
H. López-Fernández; P. Ferreira; M. Reboiro-Jato; C.P. Vieira; J. Vieira (2021) The pegi3s Bioinformatics Docker Images Project. 15th International Conference on Practical Applications of Computational Biology & Bioinformatics: PACBB 2021. Salamanca, Spain. 6 - October
We are grateful to BioData.pt, funded by project 22231/01/SAICT/2016.