MapQuant
A MassSpec quantitation tool for Linux and Windows.

1. DOWNLOAD
-----------
The sources are available by CVS
cvs -d :ext:club.med.harvard.edu:/home/cvs co mapquant
For questions e-mail mapquant-support@genetics.med.harvard.edu

2. COMPILING
------------
The automatic compiling is the beta stage as we switch
to a GNU automake style build.  There are a couple of points
we are having problems with.

2.1. Dependencies of headers and libraries
------------------------------------------
Headers are usually found in /usr/include or /usr/local/include
Libraries are usually found in /usr/lib or /usr/local/lib

The following libraries and headers should be downloade and installed:

2.1.1 libfftw and librfftw
--------------------------

For these libraries one has to download fftw-2.1.5.tar.gz from http://www.fftw.org
It is preferable to build this library in one's home directory (--prefix=/home/leptos option, see below)
Also it is CRUCIAL that the --enable-float option is set. Options --enable-shared and --enable-i386-hacks 
are also useful. Thus:

./configure --enable-float --enable-shared=yes --enable-i386-hacks --prefix=/home/leptos
make all
make install

libraries will go to PREFIX/lib (i.e. /home/leptos/lib)
headers will go to PREFIX/include (i.e. /home/leptos/include)

2.1.2 libz
----------

Ask your administrator to install it

2.1.3 glut
----------

Ask your administrator to install it
export LIBGL_DRIVERS_PATH=<directory where libglut.so.3 is installed>

2.1.4 libexpat
--------------

Ask your administrator to install it

2.2. Other options
------------------

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 headers: 
	export CFLAGS=-I/home/leptos/include
For libraries: 
	export LDFLAGS=-L/home/leptos/lib
For shared libraries: 
	export LD_LIBRARY_PATH=-L/home/leptos/lib

2.2 Creating Makefiles
----------------------
You need to run some build commands vis-a-vis GNU automake
aclocal && autoheader && autoconf && automake -a

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

make all
make install
  
3. INSTALL
----------

Please follow the instructions below before you run any program.

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

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

   
4. RUN
------

Before you run any of these programs run with the -h or -help flag
to view the commandline syntax.

An example of running vmap would be:

vmap_1.0 -e BSATEST-200fmole-06 -S "1000 2000" -m "500 700"

This means we want to view a map from the experiment in BSATEST-200fmole-06
directory that is from scan 1000 to scan 2000 and from m/z 500 to 700

5. TROUBLESHOOTING
------------------

5.1 Compilation Troubleshooting
-------------------------------
The make script should get hung up, but in prior versions it did at a 
couple of places and needed manual intervention.

if you see the following:
  /home/nwalsh/dev/mapquant/src/mapquant/mapquant.c:101: error: `USAGE' undeclared (first use in this function)
try
  dos2unix src/mqparser/procscriptparser.y || \
  sed -i 's/\r//g' src/mqparser/procscriptparser.y
  make all
  
if you see the following:
  /home/nwalsh/dev/mapquant/src/mapquant/mapquant.c:101: error: 
    `USAGE' undeclared (first use in this function)
  /home/nwalsh/dev/mapquant/src/mapquant/mapquant.c:102: error: 
    `HELP' undeclared (first use in this function)
try
  ./bin/createrc.pl src/mapquant/mapquant.hh
  make all
  


DOCUMENTATION
-------------

CREATING HTML DOCUMENTATION
---------------------------

Run:

doxygen mapquant-dox.config
cp -R doc/html /var/www/html/MapQuant/documentation

Press the h key to view the control keys of vmap

Pressing 'z' triggers zoom mode where one can select a rectangle to zoom in.
Pressing 'm' pops up an ms spectrum of the corresponding scan that the mouse 
  pointer.
was placed at, at the time. Key 'n' does the same for a mass chromatogram.