mne_setup_sh

#!/bin/sh -ef
#
#   Setup script for MNE software
#
#
#   Copyright 2009
#
#   Nick Schmansky
#   Athinoula A. Martinos Center for Biomedical Imaging
#   Massachusetts General Hospital
#   Charlestown, MA, USA
#
#   $Id: mne_setup_mne 2902 2009-10-31 23:00:23Z nicks $
#

OS=`uname -s`
PROC=`uname -p`

#
# check for MNE_ROOT and MATLAB_ROOT and exit if not found
#
if [ ! "$MNE_ROOT" ] ; then
    echo "ERROR: The environment variable MNE_ROOT is not defined!"
    echo "       Set MNE_ROOT to the directory where MNE is installed."
    return 1
fi
if [ ! -e "$MNE_ROOT" ] ; then
    echo "ERROR: $MNE_ROOT "
    echo "       does not exist. Check that this value is correct.";
    return 1
fi
if [ "$MATLAB_ROOT" ] ; then
    if [ ! -e "$MATLAB_ROOT" ] ; then
  echo "ERROR: $MATLAB_ROOT "
	echo "       does not exist. Check that this value is correct.";
	return 1
    fi
fi

echo ""
echo "MNE software location set to:    $MNE_ROOT"
if [ "$MATLAB_ROOT" ] ; then
    echo "MATLAB software location set to: $MATLAB_ROOT"
else
    echo "MATLAB software not available"
fi
echo ""

#
# add MNE_ROOT/bin to path
#
MNE_BIN_PATH=$MNE_ROOT/bin
export MNE_BIN_PATH
echo $PATH | grep $MNE_BIN_PATH > /dev/null
if [ $? == 0 ] ; then
    echo "$MNE_BIN_PATH already in PATH"
else
    PATH="$MNE_BIN_PATH":$PATH
    export PATH
    echo "$MNE_BIN_PATH added to PATH"
fi
#
# add MNE_ROOT/lib to (DY)LD_LIBRARY_PATH
#

command_exists () {
    type "$1" &> /dev/null ;
}

MNE_LIB_PATH=$MNE_ROOT/lib
export MNE_LIB_PATH
if [ "x$OS" == "xLinux" ] ; then
    if [ ! "$LD_LIBRARY_PATH" ] ; then
        LD_LIBRARY_PATH=$MNE_LIB_PATH
    else
	LD_LIBRARY_PATH="$MNE_LIB_PATH":"$LD_LIBRARY_PATH"
    fi
    export LD_LIBRARY_PATH
    echo "${MNE_LIB_PATH} added to LD_LIBRARY_PATH"
elif [ "x$OS" == "xDarwin" ] ; then
	set_dyld_path=0
	if command_exists brew ; then
		brew_loc=$(command -v brew)
		echo Brew install detected at: ${brew_loc}
		if ! brew list | grep libquicktime &> /dev/null; then
			echo '... please consider installing libquicktime';
			set_dyld_path=1
		fi
		if ! brew list | grep gfortran &> /dev/null; then
			echo '... please consider installing gfortran';
			set_dyld_path=1
		fi
	else
	set_dyld_path=1	
	fi	
	if [[ set_dyld_path == 1 ]]; then
		echo falling back to shipped libraries
	    if [ ! "$DYLD_LIBRARY_PATH" ] ; then
	        DYLD_LIBRARY_PATH=$MNE_LIB_PATH
	    else
		DYLD_LIBRARY_PATH="$MNE_LIB_PATH":"$DYLD_LIBRARY_PATH"
	    fi
	    export DYLD_LIBRARY_PATH
	    echo "${MNE_LIB_PATH} added to DYLD_LIBRARY_PATH"
	else
		echo using librarries from brew
	fi
	
fi
#
# add XUSERFILESEARCHPATH so that mne_analyze and mne_browse_raw
# can find their defaults files (MneAnalyze and MneBrowse)
#
APPDEF="${MNE_ROOT}/share/app-defaults/%N"
if [ ! "$XUSERFILESEARCHPATH" ] ; then
    XUSERFILESEARCHPATH="${APPDEF}"
else
    XUSERFILESEARCHPATH="${XUSERFILESEARCHPATH}":"${APPDEF}"
fi
export XUSERFILESEARCHPATH
echo "${APPDEF} added to XUSERFILESEARCHPATH"

#
# note: setup of matlab lib dir to (DY)LD_LIBRARY_PATH is performed
# independently by wrapper scripts where needed to avoid polluting the
# environment with (DY)LD_LIBRARY_PATH paths (eg. libtiff problems)
#

if [ "$MATLAB_ROOT" ] ; then
#
# add matlab files to matlab search path
#
    SUF=$HOME/matlab/startup.m
    if [ ! -e $SUF ] ; then
	echo "INFO: $SUF does not exist ... creating"
	mkdir -p ~/matlab
	touch $SUF
	
	echo "%---------------------- MNE --------------------------%" >> $SUF
	echo "mnehome = getenv('MNE_ROOT');"                           >> $SUF
	echo "mnematlab = sprintf('%s/share/matlab',mnehome);"         >> $SUF
	echo "if (exist(mnematlab) == 7)"                              >> $SUF
	echo "    path(path,mnematlab);"                               >> $SUF
	echo "end"                                                     >> $SUF
	echo "clear mnehome mnematlab;"                                >> $SUF
	echo "%-----------------------------------------------------%" >> $SUF
	echo "" >> $SUF
    fi
    
    tmp1=`grep MNE_ROOT $SUF       | wc -l`;
    if [ $tmp1 == 0 ] ; then
	echo ""
	echo "WARNING: The $SUF file does not appear to be";
	echo "         configured correctly. You may not be able"
	echo "         to access the MNE Matlab toolbox.";
	echo "Try adding the following lines to $SUF"
	echo "%---------------------- MNE --------------------------%"
	echo "mnehome = getenv('MNE_ROOT');"
	echo "mnematlab = sprintf('%s/share/matlab',mnehome);"
	echo "if (exist(mnematlab) == 7)"
	echo "    path(path,mnematlab);"
	echo "end"
	echo "clear mnehome mnematlab;"
	echo "%-----------------------------------------------------%"
	echo ""
    fi
fi


#
# Just a friendly reminder
#
echo ""
echo "Note: Remember to set SUBJECTS_DIR and SUBJECT environment variables correctly."
echo "Note: FreeSurfer environment is needed to access tkmedit from mne_analyze."
echo ""

return 0