Protocols
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auto-p2docking includes several test data sets (protocols) that can be used as inspiration for developing a pipeline as well as learning how to use a given module. A graphical representation of the pipeline, run times, as well as the output generated when using such pipelines are also provided. Instructions on how to run these protocols are provided on the README.txt file. In order to see the available protocols create a config and declare the ``dir`` and ``project`` variables. The ``dir`` should be the actual full path to the working directory in your computer (for instance, dir=/path/to/working_dir). Project can be any name as long as there are no white spaces (for instance, project=project_name). Then create a file named pipeline and write "protocol_description" on the first line. A text file with the list of all protocols will be produced in the working directory declared in the ``dir`` parameter in the config file. To download a given protocol just write the name of the protocol(s) (each on adifferent line) on the pipeline file. Each protocol comes with the input data, config and pipeline files, a ``README.txt`` file, a graphical representation of the pipeline, a log, the running time, and the full outputs of the run.