Make directory structure in the script consistent with docker image

[kaveelim]

A Docker image for the tools in the workflow is avialable here. The image includes all the prerequisites and dependencies.
To run the Docker image -

docker run -v pwd:pwd -w pwd -i -t stevetsa/proteomics:latest
This mounts the current working directory to the same directory structure inside the container. You will be able to access all files and folders downstream of the current working directory.
All the executibles are in /usr/bin, /usr/local/bin, MS-GF+ JAR file is /opt/MSGFPlusv2018.07.17.jar