Getting Started
In this chapter we will be going over everything you will need in order to get to the point where you are runing MP-BioPath to analyze your files. This includes installing MP-BioPath to running a few example commands
Installation
In order to simplify the installation process a Docker container has already been generated. All that is required is to pull the latest verion of the container.
In case you are not familiar with Docker the idea is that we are providing to the user an environment that has already been provisioned with all the dependencies to run the tool.
Docker
Docker itself is a program that runs on your computer. You will need to install this on your computer. This can be done on OS X, Windows and Linux.
Instructions for getting Docker installed can be found here: https://docs.docker.com/engine/installation/
Docker Image
In order to obtain the latest Docker container run the following command:
docker pull oicr/mp-biopath:1.0.x
After running this command you can check that you have the container by typing the command:
docker images
You should be able to see the image "oicr/mp-biopath" in your list of images.
Running Container
In order to run command line from within the contianer run the following command:
make run-bash
This command will place you inside the container. Keep in mind that the filesystem inside the container is seperate from the filesystem inside the container. the "v" flag maps a directory ouside the container to a folder inside the container. In this example it is mapping the current directory to the a "data" directory inside the container. Changes to files made within this directory will not be lost when exiting the container.
In order to run commands inside the container from the main host you can run command similare to the following:
docker run mpbiopath julia test/run.jl
This command will run the tests that have been made for the tool. In order to run custom commands refer to section "Running MP-BioPath.
Custome setup
In order to run the tool on your own data you will need to create evidence files based on the specified format. You will also need to obtain the Reactome pathways in the pairwise interaction format from http://github.com/Reactome/PathwayAnalysis.git
After getting the desired files you will need to create a custom configuration file. Through the configuration file MP-BioPath will run and produce the results in the specified folder.
Please see specific sections of this document on developing the files in the right format.