add initial usage and getting started sections

README.md

@@ -17,15 +17,48 @@ Less is known of "The Mule" than of any character of comparable signifigance to
 **MULE** is a centralised repository for the data acquisition and analysis software used within the University of Manchester's neutrino lab.
 
 The functionality of this repository should cover:
-- **Data acquisition** and **processing** for **PMTs** and **SiPMs** interfaced with CAEN hardware/software,
+- **Data acquisition** and **processing** using the WaveDump 1 and 2 software for **PMTs** and **SiPMs** interfaced with CAEN hardware,
 - **Analysis software** and scripts implemented directly upon the acquired data or provided for use once data is processed,
 - **Adequate documentation** to allow for simple use of the respective tools provided within this repository.
 
+## Getting Started
+
+The simplest method of installation is one done by cloning the github repository and running the setup.sh file from the terminal, as explained below.
+
+To clone the directory, one should have `git` installed for their terminal.
+
+Then, one can clone the repo to the desired directory. The environemnt then needs to be created and activated. This can be achieved by running the following commands:
+```
+git clone https://github.com/nu-ZOO/MULE.git
+cd MULE
+source setup.sh
+```
+> **_WARNING_** The above code will attempt to install miniconda
+
+> **_WARNING_** The `setup.sh` currently only works on x86_64 machines with plans to fix this in the future
+
+> **_NOTE_** The above link is taken from the repo's github page
+
+One can also create an alias to activate the environment easily on every session.
+
 ## Usage
 
-Implement description of full usage, perhaps move this section to docs.
+Usage is currently focused on binary files for readout from the above named systems.
 
-## Getting Started
+After data collection and having saved the unprocessed files, one should copy the file path into the config file using a text editor (such as vim). In addtion, the destination file path and name should be enetered in the save_path line. Finally, ensure to have the correct wavedump edition as that will affect decoding.
+
+> **_NOTE_** One can find the config file in /MULE/packs/configs
+
+Once the config file has been edited and saved, one can execute the program from the terminal, including the location of the config file if nexessary. For instance,
+
+`mule proc process_WD2_3channel.conf`
+
+While choice of packs remains limited, there is work being done to expand this. As such, the pack `proc` above is only an example and one should make an appropriate choice of pack. The general form of the above is,
+
+`mule <PACK> <CONFIG>`
+
+This will generate the output, processed file and store them in the predefined location.
 
-EXPLAIN SIMPLEST METHOD FOR INSTALLATION/SETUP
+## MULE Auxilary Tools
 
+There are several additonal processing funcitons which are not yet run automatically from the config file but that can be found in /MULE/packs/proc