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.
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 Windows, please download the official installer Docker for Windows Installer.exe. If your system does not meet the requirements to run Docker for Windows (available here), please install Docker Toolbox instead.
As an alternative and for practical purposes, we provide an Ubuntu 18.04 LTS (Linux) virtual image with 11.8 GB, with Docker and Portainer already installed. Please note that this virtual image is limited to 100 GB. In order to run it, first download VirtualBox here. After installing VirtualBox, users just need to import the OVA file here provided. To import an existing virtual machine into VirtualBox, please follow the steps described here.The administrator's user and password are pegi3s. The username and password for Portainer are pegi3sdocker.
Note: For proper performance, we recommend the use of a machine with at least 8 GB of RAM memory in order to allocate half of that memory (4 GB) to VirtualBox. Using a smaller amount of RAM memory for the virtual machine may cause a very low performance of the entire system.
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>
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)".