$NetBSD: patch-ak,v 1.1.1.1 2004/11/19 19:27:31 daprice Exp $

--- jemboss/utils/install-jemboss-server.sh.orig	Sun Jul 11 01:53:03 2004
+++ jemboss/utils/install-jemboss-server.sh	Tue Aug 10 12:53:33 2004
@@ -157,12 +157,12 @@
   echo
   echo "--------------------------------------------------------------"
   echo
-  echo "Install EMBASSY packages (y,n) [y]?"
-  read EMBASSY
+#  echo "Install EMBASSY packages (y,n) [y]?"
+#  read EMBASSY
 
-  if [ "$EMBASSY" = "" ]; then
+#  if [ "$EMBASSY" = "" ]; then
     EMBASSY="y"
-  fi
+#  fi
 
   echo "$EMBASSY" >> $RECORD
   
@@ -171,37 +171,37 @@
     if [ ! -d $EMBOSS_DOWNLOAD/embassy ]; then
       mkdir $EMBOSS_DOWNLOAD/embassy
     fi
-    echo
-    echo "To install EMBASSY Packages:"
-    echo "(1) Download these from ftp://ftp.uk.embnet.org/pub/EMBOSS/"
-    echo "(2) And unpack (gunzip and untar) them in: "
-    echo "$EMBOSS_DOWNLOAD/embassy"
-    echo "(3) *before* pressing return to continue!"
-    read BLANK
+#    echo
+#    echo "To install EMBASSY Packages:"
+#    echo "(1) Download these from ftp://ftp.uk.embnet.org/pub/EMBOSS/"
+#    echo "(2) And unpack (gunzip and untar) them in: "
+#    echo "$EMBOSS_DOWNLOAD/embassy"
+#    echo "(3) *before* pressing return to continue!"
+#    read BLANK
 
     cd $EMBOSS_DOWNLOAD/embassy
 
-    echo
-    echo "Install all packages that are downloaded in"
-    echo "$EMBOSS_DOWNLOAD/embassy "
-    echo "(if no prompts will be given for each package to install)"
-    echo "(y,n) [y]?"
+ #   echo
+ #   echo "Install all packages that are downloaded in"
+ #   echo "$EMBOSS_DOWNLOAD/embassy "
+ #   echo "(if no prompts will be given for each package to install)"
+ #   echo "(y,n) [y]?"
     
-    read ALL
-    if [ "$ALL" = "" ]; then
+ #   read ALL
+ #   if [ "$ALL" = "" ]; then
       ALL="y"
-    fi
+ #   fi
 
     for dir in *
     do
       if [ $ALL = "y" ]; then
         INST="y"
       else
-        echo "Install $dir (y,n) [y]?"
-        read INST
-        if [ "$INST" = "" ]; then
+#        echo "Install $dir (y,n) [y]?"
+#        read INST
+#        if [ "$INST" = "" ]; then
           INST="y"
-        fi
+#        fi
       fi
       if [ $INST = "y" ]; then
 
@@ -376,7 +376,7 @@
   
   JEMBOSS_PROPERTIES=$EMBOSS_INSTALL/share/EMBOSS/jemboss/resources/jemboss.properties
 
-  mv $JEMBOSS_PROPERTIES $JEMBOSS_PROPERTIES.orig
+  mv $JEMBOSS_PROPERTIES $JEMBOSS_PROPERTIES.ORIGINAL
   touch $JEMBOSS_PROPERTIES
 
   if [ $AUTH = "y" ]; then
@@ -408,12 +408,12 @@
 #                                                    >> $JEMBOSS_PROPERTIES
   echo "acdDirToParse=$EMBOSS_INSTALL/share/EMBOSS/acd/" >> $JEMBOSS_PROPERTIES
   echo "embossURL=$EMBOSS_URL" >> $JEMBOSS_PROPERTIES
-  cp $JEMBOSS_PROPERTIES $JEMBOSS_PROPERTIES.bak
+#  cp $JEMBOSS_PROPERTIES $JEMBOSS_PROPERTIES.bak
 
-  echo
-  echo "Changed $EMBOSS_INSTALL/share/EMBOSS/jemboss/resources/jemboss.properties"
-  echo "to reflect this installation (original in jemboss.properties.orig)"
-  echo
+#  echo
+#  echo "Changed $EMBOSS_INSTALL/share/EMBOSS/jemboss/resources/jemboss.properties"
+#  echo "to reflect this installation (original in jemboss.properties.orig)"
+#  echo
 
 }
 
@@ -665,39 +665,39 @@
 }
 
 
-clear
-echo
-echo "--------------------------------------------------------------"
-echo "         EMBOSS and Jemboss Server installation script"
-echo "--------------------------------------------------------------"
-echo " "
-echo "Note: any default values are given in square brackets []. "
-echo " "
-echo "There are two types of installation see details at: "
-echo "http://www.rfcgr.mrc.ac.uk/Software/EMBOSS/Jemboss/install/setup.html"
-echo " "
-echo "(1) CLIENT-SERVER"
-echo "(2) STANDALONE"
-echo "Enter type of installation [1] :"
-read INSTALL_TYPE
+#clear
+#echo
+#echo "--------------------------------------------------------------"
+#echo "         EMBOSS and Jemboss Server installation script"
+#echo "--------------------------------------------------------------"
+#echo " "
+#echo "Note: any default values are given in square brackets []. "
+#echo " "
+#echo "There are two types of installation see details at: "
+#echo "http://www.rfcgr.mrc.ac.uk/Software/EMBOSS/Jemboss/install/setup.html"
+#echo " "
+#echo "(1) CLIENT-SERVER"
+#echo "(2) STANDALONE"
+#echo "Enter type of installation [1] :"
+#read INSTALL_TYPE
 
-if (test "$INSTALL_TYPE" != "1") && (test "$INSTALL_TYPE" != "2"); then
-  INSTALL_TYPE="1"
-fi
-clear
+#if (test "$INSTALL_TYPE" != "1") && (test "$INSTALL_TYPE" != "2"); then
+  INSTALL_TYPE="2"
+#fi
+#clear
 
-echo
-echo "--------------------------------------------------------------"
-echo "         EMBOSS and Jemboss Server installation script"
-echo "--------------------------------------------------------------"
-echo
-echo "*** This script needs to be run with permissions to be able"
-echo "*** to install EMBOSS in the required directories. This may"
-echo "*** be best done as root or as a tomcat user."
-echo
-echo "Before running this script you should download the latest:"
-echo
-echo "(1) EMBOSS release (contains Jemboss) ftp://ftp.uk.embnet.org/pub/EMBOSS/"
+#echo
+#echo "--------------------------------------------------------------"
+#echo "         EMBOSS and Jemboss Server installation script"
+#echo "--------------------------------------------------------------"
+#echo
+#echo "*** This script needs to be run with permissions to be able"
+#echo "*** to install EMBOSS in the required directories. This may"
+#echo "*** be best done as root or as a tomcat user."
+#echo
+#echo "Before running this script you should download the latest:"
+#echo
+#echo "(1) EMBOSS release (contains Jemboss) ftp://ftp.uk.embnet.org/pub/EMBOSS/"
 
 
 if [ $INSTALL_TYPE = "1" ]; then
@@ -705,13 +705,13 @@
   echo "(3) Apache AXIS (SOAP) release   http://xml.apache.org/axis/"
 fi
   
-echo
-echo "Has the above been downloaded (y/n)? "
-read DOWNLOADED
+#echo
+#echo "Has the above been downloaded (y/n)? "
+#read DOWNLOADED
 
-if (test "$DOWNLOADED" != "y") && (test "$DOWNLOADED" != "Y"); then
-  exit 1
-fi
+#if (test "$DOWNLOADED" != "y") && (test "$DOWNLOADED" != "Y"); then
+#  exit 1
+#fi
 
 
 RECORD="install.record"
@@ -754,22 +754,22 @@
 esac
 
 
-echo 
-echo "Select the platform that your Jemboss server will be"
-echo "run on from 1-8 [$PLATTMP]:"
-echo "(1)  linux"
-echo "(2)  aix"
-echo "(3)  irix"
-echo "(4)  hp-ux"
-echo "(5)  solaris"
-echo "(6)  macosX"
-echo "(7)  OSF"
-echo "(8)  FreeBSD"
-read PLAT
+#echo 
+#echo "Select the platform that your Jemboss server will be"
+#echo "run on from 1-8 [$PLATTMP]:"
+#echo "(1)  linux"
+#echo "(2)  aix"
+#echo "(3)  irix"
+#echo "(4)  hp-ux"
+#echo "(5)  solaris"
+#echo "(6)  macosX"
+#echo "(7)  OSF"
+#echo "(8)  FreeBSD"
+#read PLAT
 
-if [ "$PLAT" = "" ]; then
+#if [ "$PLAT" = "" ]; then
   PLAT=$PLATTMP
-fi
+#fi
 
 echo "$PLAT" >> $RECORD
 
@@ -869,22 +869,22 @@
 # JAVA_HOME
 #
 getJavaHomePath
-JAVA_HOME=$JAVA_HOME_TMP
-if [ "$JAVA_HOME" != "0" ]; then
-  echo "Enter java (1.3 or above) location [$JAVA_HOME_TMP]: "
-  read JAVA_HOME
-
-  if [ "$JAVA_HOME" = "" ]; then 
-    JAVA_HOME=$JAVA_HOME_TMP
-  fi
-fi
+JAVA_HOME=@PKG_JAVA_HOME@
+#if [ "$JAVA_HOME" != "0" ]; then
+#  echo "Enter java (1.3 or above) location [$JAVA_HOME_TMP]: "
+#  read JAVA_HOME
+
+#  if [ "$JAVA_HOME" = "" ]; then 
+#    JAVA_HOME=$JAVA_HOME_TMP
+#  fi
+#fi
 
-while [ ! -f "$JAVA_HOME/bin/javac" ]
-do
-  echo "Enter java (1.3 or above) location (/usr/java/jdk1.3.1/): "
-  read JAVA_HOME
-done
-echo
+#while [ ! -f "$JAVA_HOME/bin/javac" ]
+#do
+#  echo "Enter java (1.3 or above) location (/usr/java/jdk1.3.1/): "
+#  read JAVA_HOME
+#done
+#echo
 echo "$JAVA_HOME" >> $RECORD
 
 #
@@ -901,29 +901,29 @@
 JAVA_INCLUDE=$JAVA_HOME/include/
 JAVA_INCLUDE_OS=$JAVA_INCLUDE
 if [ -d $JAVA_INCLUDE/linux ]; then
-  JAVA_INCLUDE_OS=${JAVA_INCLUDE}/linux
+  JAVA_INCLUDE_OS=${JAVA_INCLUDE}linux
 elif [ -d $JAVA_INCLUDE/solaris ]; then
-  JAVA_INCLUDE_OS=${JAVA_INCLUDE}/solaris
+  JAVA_INCLUDE_OS=${JAVA_INCLUDE}solaris
 elif [ -d $JAVA_INCLUDE/irix ]; then
-  JAVA_INCLUDE_OS=${JAVA_INCLUDE}/irix
+  JAVA_INCLUDE_OS=${JAVA_INCLUDE}irix
 elif [ -d $JAVA_INCLUDE/hp-ux ]; then
-  JAVA_INCLUDE_OS=${JAVA_INCLUDE}/hp-ux
+  JAVA_INCLUDE_OS=${JAVA_INCLUDE}hp-ux
 elif [ -d $JAVA_INCLUDE/alpha ]; then
-  JAVA_INCLUDE_OS=${JAVA_INCLUDE}/alpha
+  JAVA_INCLUDE_OS=${JAVA_INCLUDE}alpha
 elif [ -d $JAVA_INCLUDE/freebsd ]; then
-  JAVA_INCLUDE_OS=${JAVA_INCLUDE}/freebsd
+  JAVA_INCLUDE_OS=${JAVA_INCLUDE}freebsd
 elif [ -d $JAVA_INCLUDE ]; then
   JAVA_INCLUDE_OS=${JAVA_INCLUDE}
 else
-  echo "Enter java include/Header directory location (containing jni.h)? "
+#  echo "Enter java include/Header directory location (containing jni.h)? "
   read JAVA_INCLUDE
   JAVA_INCLUDE_OS=$JAVA_INCLUDE
   if [ -d $JAVA_INCLUDE/linux ]; then
-    JAVA_INCLUDE_OS=${JAVA_INCLUDE}/linux
+    JAVA_INCLUDE_OS=${JAVA_INCLUDE}linux
   elif [ -d $JAVA_INCLUDE/solaris ]; then
-    JAVA_INCLUDE_OS=${JAVA_INCLUDE}/solaris
+    JAVA_INCLUDE_OS=${JAVA_INCLUDE}solaris
   elif [ -d $JAVA_INCLUDE/irix ]; then
-    JAVA_INCLUDE_OS=${JAVA_INCLUDE}/irix
+    JAVA_INCLUDE_OS=${JAVA_INCLUDE}irix
   elif [ -d $JAVA_INCLUDE ]; then
     JAVA_INCLUDE_OS=${JAVA_INCLUDE}
   else
@@ -941,38 +941,38 @@
 EMBOSS_DOWNLOAD_TMP=`dirname $EMBOSS_DOWNLOAD_TMP`
 EMBOSS_DOWNLOAD_TMP=`dirname $EMBOSS_DOWNLOAD_TMP`
 
-echo "Enter EMBOSS download directory"
-echo "[$EMBOSS_DOWNLOAD_TMP]: "
-read EMBOSS_DOWNLOAD
+#echo "Enter EMBOSS download directory"
+#echo "[$EMBOSS_DOWNLOAD_TMP]: "
+#read EMBOSS_DOWNLOAD
 
-if [ "$EMBOSS_DOWNLOAD" = "" ]; then
+#if [ "$EMBOSS_DOWNLOAD" = "" ]; then
   EMBOSS_DOWNLOAD=$EMBOSS_DOWNLOAD_TMP
-fi
+#fi
 
-while [ ! -d "$EMBOSS_DOWNLOAD/ajax" ]
-do
-  echo "Enter EMBOSS download directory (e.g. /usr/emboss/EMBOSS-2.x.x): "
-  read EMBOSS_DOWNLOAD
-done
-echo
+#while [ ! -d "$EMBOSS_DOWNLOAD/ajax" ]
+#do
+#  echo "Enter EMBOSS download directory (e.g. /usr/emboss/EMBOSS-2.x.x): "
+#  read EMBOSS_DOWNLOAD
+#done
+#echo
 echo "$EMBOSS_DOWNLOAD" >> $RECORD
 
-echo "Enter where EMBOSS should be installed [/usr/local/emboss]: "
-read EMBOSS_INSTALL
+#echo "Enter where EMBOSS should be installed [/usr/local/emboss]: "
+#read EMBOSS_INSTALL
 
-if [ "$EMBOSS_INSTALL" = "" ]; then
-  EMBOSS_INSTALL=/usr/local/emboss
-fi
+#if [ "$EMBOSS_INSTALL" = "" ]; then
+  EMBOSS_INSTALL=@PREFIX@
+#fi
 
-if [ -d "$EMBOSS_INSTALL/share/EMBOSS/jemboss" ]; then
-  echo 
-  echo "Jemboss has already be installed to: "
-  echo "$EMBOSS_INSTALL/share/EMBOSS/jemboss "
-  echo "It is recommended this is removed before continuing."
-  echo "To continue press return."
-  read BLANK
-fi
-echo
+#if [ -d "$EMBOSS_INSTALL/share/EMBOSS/jemboss" ]; then
+#  echo 
+#  echo "Jemboss has already be installed to: "
+#  echo "$EMBOSS_INSTALL/share/EMBOSS/jemboss "
+#  echo "It is recommended this is removed before continuing."
+#  echo "To continue press return."
+#  read BLANK
+#fi
+#echo
 echo "$EMBOSS_INSTALL" >> $RECORD
 
 if [ $INSTALL_TYPE = "1" ]; then
@@ -1039,21 +1039,21 @@
 
   CC="$CC -DTOMCAT_UID=$UUID "; export CC
 
-  echo
-  echo "Unix Authentication Method, see:"
-  echo "http://www.rfcgr.mrc.ac.uk/Software/EMBOSS/Jemboss/install/authentication.html"
-  echo
-  echo "(1) shadow      (3) PAM         (5) HP-UX shadow"
-  echo "(2) no shadow   (4) AIX shadow  (6) Re-entrant shadow"
-  echo "(7) Re-entrant no shadow"  
-  echo 
-  echo "Type of unix password method being used "
-  echo "(select 1, 2, 3, 4, 5, 6 or 7 )[$AUTH_TYPE_TMP]"
-  read AUTH_TYPE
+#  echo
+#  echo "Unix Authentication Method, see:"
+#  echo "http://www.rfcgr.mrc.ac.uk/Software/EMBOSS/Jemboss/install/authentication.html"
+#  echo
+#  echo "(1) shadow      (3) PAM         (5) HP-UX shadow"
+#  echo "(2) no shadow   (4) AIX shadow  (6) Re-entrant shadow"
+#  echo "(7) Re-entrant no shadow"  
+#  echo 
+#  echo "Type of unix password method being used "
+#  echo "(select 1, 2, 3, 4, 5, 6 or 7 )[$AUTH_TYPE_TMP]"
+#  read AUTH_TYPE
   
-  if [ "$AUTH_TYPE" = "" ]; then
+#  if [ "$AUTH_TYPE" = "" ]; then
      AUTH_TYPE="$AUTH_TYPE_TMP"
-  fi
+#  fi
 
   echo "$AUTH_TYPE" >> $RECORD
 
@@ -1133,41 +1133,41 @@
 USER_CONFIG=""
 get_libs $USER_CONFIG
 
-if [ "$USER_CONFIG" = "" ]; then
-  echo
-  echo "--------------------------------------------------------------"
-  echo
-  echo "The libraries for EMBOSS (libpng and gd) do not appear to"
-  echo "be in /usr. It may be necessary to use the configuration"
-  echo "flag --with-pngdriver to specify their location"
-  echo
-  echo "For details see the EMBOSS admin guide:"
-  echo "http://www.uk.embnet.org/Software/EMBOSS/Doc/Admin_guide/adminguide/"
-  echo
-  echo "Enter any other EMBOSS configuration options (e.g. --with-pngdriver=pathname)"
-  echo "or press return to leave blank:"
-  read USER_CONFIG
-elif [ "$USER_CONFIG" = "default" ]; then
-  echo
-  echo "--------------------------------------------------------------"
-  echo
-  echo "The libraries for EMBOSS (libpng and gd) appear to be in /usr,"
-  echo "if these are the correct libraries then there should be no need"
-  echo "to add any configuration options."
-  echo
-  echo "Enter any other EMBOSS configuration options (e.g. --with-pngdriver=pathname)"
-  echo "or press return to leave blank:"
-  read USER_CONFIG
-else
-  echo "Enter any other EMBOSS configuration options or press return to"
-  echo "use default [$USER_CONFIG]:"
-  read USER_CONFIG_TMP
-  if [ "$USER_CONFIG_TMP" != "" ]; then
+#if [ "$USER_CONFIG" = "" ]; then
+#  echo
+#  echo "--------------------------------------------------------------"
+#  echo
+#  echo "The libraries for EMBOSS (libpng and gd) do not appear to"
+#  echo "be in /usr. It may be necessary to use the configuration"
+#  echo "flag --with-pngdriver to specify their location"
+#  echo
+#  echo "For details see the EMBOSS admin guide:"
+#  echo "http://www.uk.embnet.org/Software/EMBOSS/Doc/Admin_guide/adminguide/"
+#  echo
+#  echo "Enter any other EMBOSS configuration options (e.g. --with-pngdriver=pathname)"
+#  echo "or press return to leave blank:"
+#  read USER_CONFIG
+#elif [ "$USER_CONFIG" = "default" ]; then
+#  echo
+#  echo "--------------------------------------------------------------"
+#  echo
+#  echo "The libraries for EMBOSS (libpng and gd) appear to be in /usr,"
+#  echo "if these are the correct libraries then there should be no need"
+#  echo "to add any configuration options."
+#  echo
+#  echo "Enter any other EMBOSS configuration options (e.g. --with-pngdriver=pathname)"
+#  echo "or press return to leave blank:"
+#  read USER_CONFIG
+#else
+#  echo "Enter any other EMBOSS configuration options or press return to"
+#  echo "use default [$USER_CONFIG]:"
+#  read USER_CONFIG_TMP
+#  if [ "$USER_CONFIG_TMP" != "" ]; then
     USER_CONFIG="$USER_CONFIG_TMP"
-  fi
-fi
+#  fi
+#fi
 
-check_libs "$USER_CONFIG" $PLATFORM
+#check_libs "$USER_CONFIG" $PLATFORM
 
 echo "$USER_CONFIG" >> $RECORD
 #
@@ -1180,30 +1180,30 @@
   fi
 fi
 
-echo
-echo "  ******** EMBOSS will be configured with this information  ******** "
-echo 
-echo "./configure --with-java=$JAVA_INCLUDE \\"
-echo "            --with-javaos=$JAVA_INCLUDE_OS \\"
-echo "            --with-thread=$PLATFORM \\"
-echo "            --prefix=$EMBOSS_INSTALL \\"
-echo "           $JEMBOSS_SERVER_AUTH $USER_CONFIG"
-echo
-
-WORK_DIR=`pwd`
-cd $EMBOSS_DOWNLOAD
-
-./configure --with-java=$JAVA_INCLUDE \
-            --with-javaos=$JAVA_INCLUDE_OS \
-            --with-thread=$PLATFORM \
-            --prefix=$EMBOSS_INSTALL $JEMBOSS_SERVER_AUTH $USER_CONFIG
+#echo
+#echo "  ******** EMBOSS will be configured with this information  ******** "
+#echo 
+#echo "./configure --with-java=$JAVA_INCLUDE \\"
+#echo "            --with-javaos=$JAVA_INCLUDE_OS \\"
+#echo "            --with-thread=$PLATFORM \\"
+#echo "            --prefix=$EMBOSS_INSTALL \\"
+#echo "           $JEMBOSS_SERVER_AUTH $USER_CONFIG"
+#echo
+
+#WORK_DIR=`pwd`
+#cd $EMBOSS_DOWNLOAD
+
+#./configure --with-java=$JAVA_INCLUDE \
+#            --with-javaos=$JAVA_INCLUDE_OS \
+#            --with-thread=$PLATFORM \
+#            --prefix=$EMBOSS_INSTALL $JEMBOSS_SERVER_AUTH $USER_CONFIG
 
 make
 
-echo
-echo "  ******* EMBOSS with Jemboss will be installed in $EMBOSS_INSTALL ******* "
-echo
-sleep 2
+#echo
+#echo "  ******* EMBOSS with Jemboss will be installed in $EMBOSS_INSTALL ******* "
+#echo
+#sleep 2
 
 make install
 
@@ -1211,15 +1211,15 @@
 #
 # Config EMBASSY
 #
-embassy_install $EMBOSS_DOWNLOAD $RECORD $PLATFORM $EMBOSS_INSTALL $USER_CONFIG
+#embassy_install $EMBOSS_DOWNLOAD $RECORD $PLATFORM $EMBOSS_INSTALL $USER_CONFIG
 
 
 #
 #
 # Get clustalw and primer3_core path
 #
-getClustalWPath
-getPrimerPath
+#getClustalWPath
+#getPrimerPath
 
 #
 #
@@ -1280,69 +1280,69 @@
 #
 #
 
-rm -f tomstart
+#rm -f tomstart
 
-echo
-echo "#!/bin/csh " > tomstart
-echo "setenv JAVA_HOME $JAVA_HOME" >> tomstart
+#echo
+#echo "#!/bin/csh " > tomstart
+#echo "setenv JAVA_HOME $JAVA_HOME" >> tomstart
 
-if [ "$SSL" = "y" ]; then
-  echo "setenv JSSE_HOME $JSSE_HOME" >> tomstart
-fi
+#if [ "$SSL" = "y" ]; then
+#  echo "setenv JSSE_HOME $JSSE_HOME" >> tomstart
+#fi
  
-if [ "$AIX" = "y" ]; then
- echo "setenv LIBPATH /usr/lib/threads:/usr/lib:/lib:$EMBOSS_INSTALL/lib" >> tomstart
- cp $EMBOSS_DOWNLOAD/ajax/.libs/libajax.so.0 $EMBOSS_INSTALL/lib
- ln -s $EMBOSS_INSTALL/lib/libajax.so.0 $EMBOSS_INSTALL/lib/libajax.so
-else
- echo "setenv JAVA_OPTS \"-Djava.library.path=$EMBOSS_INSTALL/lib\"" >> tomstart
- echo "setenv LD_LIBRARY_PATH $EMBOSS_INSTALL/lib" >> tomstart
-fi
+#if [ "$AIX" = "y" ]; then
+# echo "setenv LIBPATH /usr/lib/threads:/usr/lib:/lib:$EMBOSS_INSTALL/lib" >> tomstart
+# cp $EMBOSS_DOWNLOAD/ajax/.libs/libajax.so.0 $EMBOSS_INSTALL/lib
+# ln -s $EMBOSS_INSTALL/lib/libajax.so.0 $EMBOSS_INSTALL/lib/libajax.so
+#else
+# echo "setenv JAVA_OPTS \"-Djava.library.path=$EMBOSS_INSTALL/lib\"" >> tomstart
+# echo "setenv LD_LIBRARY_PATH $EMBOSS_INSTALL/lib" >> tomstart
+#fi
 
-if [ "$MACOSX" = "y" ]; then
- echo "setenv DYLD_LIBRARY_PATH $EMBOSS_INSTALL/lib" >> tomstart
-fi
+#if [ "$MACOSX" = "y" ]; then
+# echo "setenv DYLD_LIBRARY_PATH $EMBOSS_INSTALL/lib" >> tomstart
+#fi
 
-if [ "$PLATFORM" = "hpux" ]; then
- echo "setenv SHLIB_PATH $EMBOSS_INSTALL/lib" >> tomstart
-fi
+#if [ "$PLATFORM" = "hpux" ]; then
+# echo "setenv SHLIB_PATH $EMBOSS_INSTALL/lib" >> tomstart
+#fi
 
 
-if [ "$AUTH_TYPE" = "3" ]; then
-  if [ -f "/lib/libpam.so" ]; then
-    echo "setenv LD_PRELOAD /lib/libpam.so" >> tomstart
-  elif [ -f "/usr/lib/libpam.so" ]; then
-    echo "setenv LD_PRELOAD /usr/lib/libpam.so" >> tomstart
-  else
-    echo
-    echo "WARNING: don't know what to set LD_PRELOAD to"
-    echo "edit LD_PRELOAD in tomstart script!"
-    echo "setenv LD_PRELOAD /usr/lib/libpam.so" >> tomstart
-    echo
-  fi
-fi
+#if [ "$AUTH_TYPE" = "3" ]; then
+#  if [ -f "/lib/libpam.so" ]; then
+#    echo "setenv LD_PRELOAD /lib/libpam.so" >> tomstart
+#  elif [ -f "/usr/lib/libpam.so" ]; then
+#    echo "setenv LD_PRELOAD /usr/lib/libpam.so" >> tomstart
+#  else
+#    echo
+#    echo "WARNING: don't know what to set LD_PRELOAD to"
+#    echo "edit LD_PRELOAD in tomstart script!"
+#    echo "setenv LD_PRELOAD /usr/lib/libpam.so" >> tomstart
+#    echo
+#  fi
+#fi
 
-echo 'set path=($path '"$JAVA_HOME/bin)"  >> tomstart
-echo "rehash"  >> tomstart
-echo "$TOMCAT_ROOT/bin/startup.sh"  >> tomstart
+#echo 'set path=($path '"$JAVA_HOME/bin)"  >> tomstart
+#echo "rehash"  >> tomstart
+#echo "$TOMCAT_ROOT/bin/startup.sh"  >> tomstart
 
 
-rm -f tomstop
+#rm -f tomstop
 
-echo
-echo "#!/bin/csh " > tomstop
-echo "setenv JAVA_HOME $JAVA_HOME" >> tomstop
-echo "setenv LD_LIBRARY_PATH $EMBOSS_INSTALL/lib" >> tomstop
+#echo
+#echo "#!/bin/csh " > tomstop
+#echo "setenv JAVA_HOME $JAVA_HOME" >> tomstop
+#echo "setenv LD_LIBRARY_PATH $EMBOSS_INSTALL/lib" >> tomstop
 #if [ "$AUTH_TYPE" = "3" ]; then
 #  echo "setenv LD_PRELOAD /lib/libpam.so" >> tomstop
 #fi
-echo 'set path=($path '"$JAVA_HOME/bin)"  >> tomstop
-echo "rehash"  >> tomstop
-echo "$TOMCAT_ROOT/bin/shutdown.sh"  >> tomstop
+#echo 'set path=($path '"$JAVA_HOME/bin)"  >> tomstop
+#echo "rehash"  >> tomstop
+#echo "$TOMCAT_ROOT/bin/shutdown.sh"  >> tomstop
 
 
-chmod u+x tomstart
-chmod u+x tomstop
+#chmod u+x tomstart
+#chmod u+x tomstop
 
 
 #
@@ -1360,13 +1360,13 @@
   if [ -f "$RUNFILE.bak" ]; then
     rm -f $RUNFILE.bak
   fi
-  sed "s|^#java org|$JAVA_HOME/bin/java org|" $RUNFILE > $RUNFILE.new
-  sed "s|^java org.emboss.jemboss.Jemboss &|#java org.emboss.jemboss.Jemboss &|" $RUNFILE.new  > $RUNFILE.new1
-  sed "s|^#EMBOSS_INSTALL=\(.*\)|EMBOSS_INSTALL=$EMBOSS_INSTALL/lib; export EMBOSS_INSTALL|" $RUNFILE.new1 > $RUNFILE.new2
+#  sed "s|^#java org|$JAVA_HOME/bin/java org|" $RUNFILE > $RUNFILE.new
+#  sed "s|^java org.emboss.jemboss.Jemboss &|#java org.emboss.jemboss.Jemboss &|" $RUNFILE.new  > $RUNFILE.new1
+#  sed "s|^#EMBOSS_INSTALL=\(.*\)|EMBOSS_INSTALL=$EMBOSS_INSTALL/lib; export EMBOSS_INSTALL|" $RUNFILE.new1 > $RUNFILE.new2
   sed "s|^#LD_LIBRARY_PATH|LD_LIBRARY_PATH|" $RUNFILE.new2 > $RUNFILE.new3
-  rm -f $RUNFILE.new $RUNFILE.new1 $RUNFILE.new2
-  mv $RUNFILE $RUNFILE.bak1
-  mv $RUNFILE.new3 $RUNFILE
+#  rm -f $RUNFILE.new $RUNFILE.new1 $RUNFILE.new2
+#  mv $RUNFILE $RUNFILE.bak1
+#  mv $RUNFILE.new3 $RUNFILE
 
 
   if [ "$AIX" = "y" ]; then
@@ -1377,11 +1377,11 @@
 
   chmod a+x $RUNFILE
 
-  echo
-  echo "To run Jemboss:"
-  echo "cd $JEMBOSS"
-  echo "./runJemboss.sh"
-  echo
+#  echo
+#  echo "To run Jemboss:"
+#  echo "cd $JEMBOSS"
+#  echo "./runJemboss.sh"
+#  echo
 
   exit 0
 else