Bioinformatics Docker Images Project

Phenotypic Evolution Group - IBMC/i3S


About this page

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).

Docker Images Advantages

  • Easy to use since it only requires the installation of Docker.
  • Portable between computers and immutable.
  • Can be deposited in public databases such as Docker Hub.
  • Can be downloaded when needed and erased when no longer needed.
  • The installed scientific software is ready to run.
  • Software invoked through the command line can be directly run in Linux and Windows platforms.
  • Docker images can be used in pipelines.

Install Docker

In order to use the Docker images maintained by pegi3s, users need to install Docker first.


To install Docker in Linux, please follow the steps provided here (additional information can be found here).


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:

Automated submission to web servers:
Compi Pipelines:
  • auto-pss-genome [doc] - Automatic detection of positively selected sites in complete genomes
  • check-cds [doc] - Compi pipeline to produce valid CDS files
  • ipssa [doc] - Automatic detection of positively selected amino acid sites
  • pss-fs [doc] - Fast identification of genes with positively selected amino acid sites for detailed analyses
  • pss-genome-fs [doc] - Fast identification of genes with positively selected amino acid sites for detailed analyses in complete genomes
  • two-way-blast [doc] - Find orthologs using a two-way BLAST (or BLAST reciprocal best hits) approach
External images:
  • trinity [doc] - de novo transcript assembly and quantification
Additional images:

Final Remarks

  • Please note that the original software licenses still apply.
  • If there is not a Dockerfile tab on an image repository just add "dockerfile" to the end of the Docker image URL.
  • 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.
  • To purge all unused or dangling images, containers, volumes and networks, please use the following command:
  • docker system prune -a
  • To remove one or more specific images, please use instead the following command:
  • docker rmi <image_name> or <image_ID>
  • To ensure using the latest version of an image, please perform:
  • 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.

Get in Touch

If you are interested in our project or would like to contribute with suggestions, you may contact us through


Please Cite Us

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 ( and to the Project (".


We are grateful to, funded by project 22231/01/SAICT/2016.


1 - Instituto de Investigação e Inovação em Saúde da Universidade do Porto (i3S), 2 - Instituto de Biologia Molecular e Celular (IBMC), 3 - SING Research Group, Universidade de Vigo (UVigo), 4 - Centro de Investigaciones Biomédicas (CINBIO), 5 - Instituto de Investigación Sanitaria Galicia Sur (IISGS).