MapQuant Version 2.1.1-20060117
===============================

CONTENTS
========

1. DESCRIPTION
2. DOWNLOAD
3. LIBRARY AND HEADER DEPENDENCIES (linux)
4. COMPILLING AND INSTALLING (linux)
5. COMPILING AND INSTALLING (win32 visual studio 6)

1.	DESCRIPTION
	-----------
	A MassSpec quantitation tool for Linux and Windows.

2. 	DOWNLOAD
	--------
	Choose mapquant-src-X.X.X-YYYYMMDD.tar.gz and unpack.
 
3. 	LIBRARY AND HEADER DEPENDENCIES (linux)
	---------------------------------------

	Headers   are usually installed in /usr/include or /usr/local/include
	Libraries are usually installed in /usr/lib or /usr/local/lib

	The following libraries and headers should be downloaded, build and installed:

	The executable directory is set by setting the --prefix=<directory used to install>
	option of the configure script. By default --prefix is equal to /usr/local. 
	If you do not have write permissions for that directory then set --prefix
	to a directory like your home directory.

	If libraries are installed in non-standard directories such as in directories in the home directory, 
	make sure that LD_LIBRARY_PATH points to the them.
	For example:

	$>export LD_LIBRARY_PATH=/home/leptos/lib

	3.1 	libfftw and librfftw
		--------------------
		For these libraries one has to download fftw-2.1.5.tar.gz from http://www.fftw.org
		Also it is CRUCIAL that the --enable-float option is set. 
		Options --enable-shared and --enable-i386-hacks are also useful. 
		Thus at the command prompt:

		$>./configure --enable-float --enable-shared=yes --enable-i386-hacks  
		Or if you are not the administrator use the home directory as your prefix
		$>./configure --enable-float --enable-shared=yes --enable-i386-hacks --prefix=/home/leptos

		$>make all
		$>make install

		Headers   will go to PREFIX/include (i.e. /home/leptos/include)
		Libraries will go to PREFIX/lib     (i.e. /home/leptos/lib)

	3.2	libpng
		------
		Ask your administrator to install it
		
	3.3 	libz
		----
		Ask your administrator to install it

	3.4 	glut (needed with configured --with-gui)
		----------------------------------------
		For building libglut.so.3 download the source freeglut-2.4.0.tar.gz from http://freeglut.sourceforge.net/

		At the command prompt:

		$>./configure  
		Or if you are not the administrator use the home directory as your prefix
		$>./configure --prefix=/home/leptos

		$>make all
		$>make install

		Headers   will go to PREFIX/include (i.e. /usr/local/include or /home/leptos/include)
		Libraries will go to PREFIX/lib     (i.e. /usr/local/lib or /home/leptos/lib)

		Also set the LIBGL_DRIVERS_PATH:

		export LIBGL_DRIVERS_PATH=PREFIX/lib/libglut.so.3

	3.5 	libexpat (needed with configured --with-hmsxml)
		-----------------------------------------------
		Ask your administrator to install it

4. 	COMPILLING AND INSTALLING (linux)
	---------------------------------
	
	4.1	CONFIGURING
		-----------
		The above libraries are required, but the configure script doesn't test for them.
		If the above libraries are installed in non-standard places (for example libfftw and librfftw from 2.1,1)
		you need to set the following environment variables.

		For compiling: 
			export CFLAGS=-I/home/leptos/include

		For linking: 
			export LDFLAGS=-L/home/leptos/lib

		Either
		./configure
		Or if one wants to install it in his/her home directory due to permissions:
		./configure --prefix=`pwd` --exec-prefix=/home/leptos

	4.2	COMPILING
		---------
		make all
	
	4.3	INSTALLING
		----------
		make install
  
	4.4 	POST-INSTALL
		------------
		Please follow the instructions below before you run any program.

		1. Set your environment variable MAPQUANTRC to point to the FULL PATH of .mapquantrc
		    e.g. if --exec-prefix was /home/leptos/mapquant, then in .bashrc add
		    export MAPQUANTRC=/home/leptos/mapquant/.mapquantrc

		2. Make sure that EPREFIX/mapquant/bin is part of PATH and PERL5LIB environment variables

5.	COMPILING AND INSTALLING (win32 visual studio 6)
	------------------------------------------------
	
	5.1	UNPACK
		------		
		Unpack the file mapquant-src-X.X.X-YYYYMMDD.tar.gz, 
		lets call the path where it was unpacked INSTALATION_SRC_DIR
		For this example we assume that:

		INSTALATION_SRC_DIR = C:\dev

		When you unpack everything will be in C:\dev\mapquant-src-X.X.X-YYYYMMDD

	
	5.2	ENVIRONMENT VARIABLES BEFORE COMPILING
		--------------------------------------
		BEFORE opening Visual Studio you have to have perl and bison installed

		NOTE: If you do not have cygwin then:

		bison can be downloaded from http://ftp.gnu.org/gnu/bison/
		perl can be downloaded from http://www.activestate.com/Products/ActivePerl/

		After you install bison and perl set the following environment variables to point 
		to their executable respectively.

		BISON and PERL

		for example for bison C:\cygwin\bin\bison.exe

	5.3	COMPILING
		---------
		Open workspace mapquant2.dsw found in INSTALATION_SRC_DIR/mapquant-src-X.X.X-YYYYMMDD
		Compile the mapquant project.  
   
	5.4	INSTALLING
		----------

		Lets call the path where you want to install mapquant INSTALATION_DIR
		It is a good habit for INSTALATION_DIR to be diferrent from the 
		INSTALATION_SRC_DIR mentioned above, which was set to C:\dev

		For this example we assume that:

		INSTALATION_DIR = C:\

		NOTE: Filenames and directories must not have spaces.  This includes the SRC 
		      and DEST directories.  If you try to use DOS type of workarounds 
		      (eg. C:\progra~1\) then you may need to manually edit .mapquantrc as 
		      these get expanded.

		Run .\install-vc.pl -i "C:"

	5.5	POST-INSTALL
		------------
		Set environment variables PATH, PERL5LIB, MAPQUANTRC

		set PATH 	to C:\mapquant\bin
		set PERL5LIB 	to C:\mapquant\bin
		set MAPQUANTRC 	to C:\mapquant\.mapquantrc

Kyriacos Leptos 2006-01-17