Running MP-BioPath

There main tool for mp-biopath is located in the bin folder. You can determine the desired parameters to run the tool through the following command :

bin/mp-biopath --help

Typical inference command:

bin/mp-biopath inference --config <your-custom-config.yaml> --verbose

With this tool you will see that most of the configuration of the tool is done through configuration files. So far there is just one configuration file type for running inference. As there are more parts of this tool are written and made more formallized further commands will be listed in the main part of this tool.

If you would like the tool to output information for all steps that it is running use the "--verbose" flag.

For parts of the tool that have not been merged into this main command line tool there are several scripts for performing various types of analysis in the scripts folder. The majority of these scripts have similar command line interfaces with help sections describing how to use the tool. Keep in mind the interfaces for these scripts will likely change as they are more formalized and pulled in as core functionality.

Once such script is calle analyzeResults.jl. This script is used to compare your results to expected results from inference you could generate a simlar command to:

docker run -v$(pwd):/workdir -t oicr/mpbiopath:1.0.0-SNAPSHOT /bin/bash -c "julia scripts/analyzeResults.jl --verbose --downregulated-cutoff=0.96 --upregulated-cutoff=1.04 /workdir/results/S_Phase.results.tsv /workdir/expected_results/S_Phase_expected_results.tsv > /workdir/results/S_Phase.summary.txt"

This script will generage a summary file of how your file compares to those listed in the expected file. In particular is will determine. This script is used by Reactome for generating and evaluating the pathway pair-wise files.