What is auto-phylo?

auto-phylo is a pipeline maker software for phylogenetic studies. A Docker image is available at this Docker Hub repository.

auto-phylo consists in a series of scripts designed for bash and therefore Linux is required (it has not been tested in the Windows Subsystem for Linux, for instance).

In addition, it uses Docker images to run any third-party software, thus Docker must be installed (see the official installation instructions at the Docker manual).

Note

If you use auto-phylo, please cite this publication:

H. López-Fernández; M. Pinto; C.P. Vieira; P. Duque; M. Reboiro-Jato; J. Vieira (2023) Auto-phylo: A Pipeline Maker for Phylogenetic Studies. 17th International Conference on Practical Applications of Computational Biology & Bioinformatics: PACBB 2023. Guimarães, Portugal. 12 - July

How to run auto-phylo

To run auto-phylo, you should adapt and run the following command:

docker run --rm -v /your/data/dir:/data -v /var/run/docker.sock:/var/run/docker.sock pegi3s/auto-phylo

In this command, you should replace /your/data/dir to point to the directory that contains the input directory with the files that you want to analyze, as well as the pipeline and config files:

  • In the pipeline file you must specify the auto-phylo modules to be invoked as well as the input and output directory names (one per line).

  • In the config file you must declare the path to the working directory as well as the SEDA version to be used, as well as any other parameters that are required by the modules being used.

To help in the creation of such files and to ease pipeline design, a graphical user interface called auto-phylo-pipeliner (see Pipeliner (GUI)).

Note

Please, note that in auto-phylo v2, the module parameters are declared in a different way than in auto-phylo v1. Now, module names are used as parameter prefixes to avoid duplicated parameter names.