Installation Instructions for MapQuant version 1.4.81

The installation process involves three steps:
1. Unpacking files
2. Set four environment variables
3. Edit MAPQUANT_PATHFILE

Step 1: Unpack 
--------------

Unpack mapquant-bin-linux-1.4.81.tar.gz 

tar xzvf mapquant-bin-linux-1.4.81.tar.gz

All files are found in a directory called mapquant
The directory where the mapquant folder is located we refer 
to as $(MAPQUANT_DATADIR) 

Step 2: Environment variables PATH, PERL5LIB, MAPQUANT_PATHFILE (example here for bash shell)
-----------------------------------------------------------------------------------------------------

In file .bashrc

a. For environment variables PATH, PERL5LIB
-------------------------------------------

WARNING FOR NEWLY DEFINED PATH:
If variable PATH is not set in .bashrc in order not to 
lose predefined paths issue command:
>>echo PATH
and copy the paths to the newly defined variable PATH

Append path INSTALLATION_DIR/mapquant/bin in
environment variable PATH and PERL5LIB and export 
them as well. Other paths separated by colon

e.g. if INSTALLATION_DIR is /home/leptos in .bashrc include the following

export PATH=/home/leptos/mapquant/bin
export PERL5LIB=/home/leptos/mapquant/bin

b. For environment variable MAPQUANT_PATHFILE
---------------------------------------------

The file provided by me is called .mapquantrc and is found in 
the mapquant directory.
The user can change its name and location as long as
it is the same as the values of this environment variable

e.g. if INSTALLATION_DIR is /home/leptos in .bashrc include the following

export MAPQUANT_PATHFILE=/home/leptos/mapquant/.mapquantrc


In order for editing to take place issue command:
>>source .bashrc


Step 3: Edit MAPQUANT_PATHFILE
------------------------------

Replace string INSTALLATION_DIR in .mapquantrc to reflect 
the INSTALLATION_DIR

e.g. in vi press ':' and type

% s/INSTALLATION_DIR/\/home\/leptos/g