INSTALLING HIFI

HIFI package is provided as a tar file on a CD.

HIFI can be installed either in the main directory:

/vnmr/

or in your local directory:

<home directory>/vnmrsys/

where <home directory> is the path to your home directory
where you want to install HIFI


To install it follow these simple steps:

0) HIFI uses nmrPipe to process the orthogonal and tilted planes
   and, thus, you need to install nmrPipe on the spectrometer Sun (or 
   Linux-Dell) first. 
   nmrPipe is free and is very simple to install. Go to 
   http://spin.niddk.nih.gov/bax/software/NMRPipe for more information 
   or to download the program.
   Once you have installed nmrpipe, do NOT add any source commands into 
   the .login or .cshrc files, as these may interfere with vnmr (vnmrJ).  
   As explained in more detail below, inside the hifi/com directory we also 
   provide a "nmrpipe.csh" file that will be automatically sourced each 
   time an orthogonal or tilted plane is processed.
   

1) EXTRACT THE HIFI FILES FROM THE TAR FILE TO THE PROPER DIRECTORY

cd /vnmr  
-or-  
cd <home directory>/vnmrsys		-if you are installing it locally 
					 (replace <home directory> with the
					 actual path to your home directory

tar xvf <path>/hifi.tar		-where <path> is the location of the hifi.tar file
			 	this will create a new directory "hifi" and distribute
			 	files to the "psglib" "maclib" "parlib" "templates"
			 	and "user_templates" directories
			
2) INSTALL THE MATLAB LIBRARIES
   the tilt prediction and peaklist generation programs are written using Matlab

cd hifi/com
unzip MCRInstaller.zip		-this will extract all the matlab libraries and 
				 copy them into a subdirectory named "v72" 

3) SET THE PATHS FOR THE HIFI SCRIPTS AND MACROS
   this is critical for HIFI to work at all, there are 5 files require to be
   modified
  
*** HIFI scripts in the "hifi/com" directory ***

	in the "hifi/com" directory, you need to set the proper path for two shell scripts:
		1- hifi.sh 
        	2- generate_peaklist.sh
	at the beginning of BOTH these files, set the "LIBDIR" variable to point to the 
	correct location of the "hifi/com" directory, e.g.:

	LIBDIR='/vnmr/hifi/com'				-if installing hifi in the main 
							 directory
	-or-
	LIBDIR='<home directory>/vnmrsys/hifi/com'	-example for local installation
						 	 in your vnmrsys directory
					 		(replace <home directory> with the
					 		actual path to your home directory)

*** nmrPipe source file also in the "hifi/com" directory ***

	in the same directory ("hifi/com"), set the correct nmrpipe path at the beginnig of 
	the file:
		3- nmrpipe.csh
	for example, if nmrPipe is installed in "/export/data/nmrPipe", set the variable 
	NMRBASE to point to this path:

	setenv NMRBASE         /export/data/nmrPipe

	as explained above this file is automatically sourced before each orthogonal or 
	tilted plane is processed


*** HIFI macros in the "maclib" directory ***
	
	in the maclib directory set the proper hifi path in two macro files:
		4- mHIFI
		5- VNMR2PIPE
	at the beginning of each macro, edit the variable $HIFI_DIR to point to the 
	correct location of the hifi scripts (hifi.sh and generate_peaklist.sh).
	For example:
		$HIFI_DIR='/vnmr/hifi/com'	-if installing HIFI in the main 
						 directory
		-or-
		$HIFI_DIR='<home directory>/vnmrsys/hifi/com'	-for local installation in 
								 your vnmrsys directory
					 			(replace <home directory> 
								with the actual path to 
								your home directory)

4) COMPILE THE PULSE SEQUENCES WITH "psggen"

    ***	if you are installing HIFI in the /vnmr directory, then as vnmr1, give the 
	following commands in a unix shell:

		> cd /vnmr/psglib
		> seqgen NEW*				-pulse sequences will be compiled 
							 in the vnmr1 seqlib directory 
							 (~/vnmrsys/seqlib) and need to be 
							 moved to the common psglib directory 
							 (/vnmr/seqlib)
		> mv ~/vnmrsys/seqlib/NEW* /vnmr/seqlib/.
		> rm -f ~/vnmrsys/psglib/NEW*		-delete the c files from the local 
							 psglib directory

	NOTE: "~" in these commands corresponds to the vnmr1 home directory (since you are 
	      logged in as vnmr1)


    ***	if you are installing HIFI into your local directory, then login as yourself and 
	give the following commands in a unix shell:

		> cd ~/vnmrsys/psglib
		> seqgen NEW*				-pulse sequences will be compiled 
							 into your local seqlib directory 

	NOTE: "~" in these commands corresponds to your  home directory (since you are logged 
	      in as yourself)

5) RUN ALL THE PREDICTION AND PEAK EXTRACTION PROGRAMS THE FIRST TIME BY EXECUTING 
   THE "first_run.csh" SCRIPT

    *** the first time (and only the first time) that the tilt prediction and extraction 
	programs are executed, new files are extracted and written to the disk
    *** in order to do this properly, we provide a script named "first_run.csh" that is
	located in:
		<path>/hifi/com/first_run/first_run.csh
    *** the "first_run.csh" script needs to be executed by the owner of the directory 
	where hifi is being installed
    *** simply, in a unix shell window give the commands:
		> cd <path>/hifi/com/first_run
		> ./first_run.csh
    *** be patient , running this script may take a little while depending on how fast
	is the computer.
    *** note: once these new files have been extracted, they can not be moved to a different
	directory. If you wish to move these programs, you will have