This image facilitates the usage of auto-phylo, a pipeline maker for phylogenetic studies.
An online manual is available here.
An online manual is available here.
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 files of the pipeline.
Please note that you must have a pipeline and a config file under /your/data/dir in order for the program to work. Detailed instructions are given in the online manual, where the available modules as well as the parameters that must be declared for each module are described in detail.
The online manual provides multiple test data examples that can be used to test the program.
Please note that data must be under the same drive than the Docker Toolbox installation (usually C:) and in a folder with write permissions (e.g. C:/Users/User_name/).
You should adapt and run the following command: docker run --rm -v "/c/Users/User_name/dir/":/data -v /var/run/docker.sock:/var/run/docker.sock pegi3s/auto-phylo
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