What is auto-p2docking v1?

auto-p2docking is a pipeline maker software, made of a series of bash and python scripts, designed for protein-protein binding inferences. A Docker image is available at this Docker Hub repository.

It uses Docker images to run third-party software, and thus, Docker must be installed (see how to install Docker at https://pegi3s.github.io/dockerfiles/). Please note that, due to copyright issues, some Docker images must be build according to the instructions given in the pegi3S Bioinformatics Docker Images Project (https://pegi3s.github.io/dockerfiles/) for haddock24-builder, hdock-builder, and pydock3-builder. If such Docker images are not build according to the provided instructions, the corresponding modules that use them will not run (haddock, hdock, and pydock_ftdock, respectively).

This manual will be updated when new modules, protocols, or features are added to auto-p2docking, as long as the changes are backwards-compatible. Therefore, it may describe modules, protocols or features that are not present in earlier versions.

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-p2docking

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-p2docking 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 (dir=), the project name (project=), and any other parameters that are required by the modules being used (see modules description).

Note

Please, note that module names (or acronyms) are used as parameter prefixes to avoid duplicated parameter names.