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#!/bin/sh
#
# This program is free software; you can redistribute it and/or
# modify it under the terms of the GNU General Public License
# as published by the Free Software Foundation; either version 2
# of the License, or (at your option) any later version.
#
# This program is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
# GNU General Public License for more details.
#
# You should have received a copy of the GNU General Public License
# along with this program; if not, write to the Free Software
# Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA.
#
# @author: Copyright (C) Tim Carver
#
#
# Installs EMBOSS & Jemboss server
#
#
######################## Functions ########################
getJavaHomePath()
{
JAVA_HOME_TMP=${JAVA_HOME_TMP-`which java 2>/dev/null`}
if [ ! -f "$JAVA_HOME_TMP" ]; then
if [ -d /usr/java/j2sdk1.4.2 ]; then
JAVA_HOME_TMP=/usr/java/j2sdk1.4.2
elif [ -d /usr/local/java/j2sdk1.4.2 ]; then
JAVA_HOME_TMP=/usr/local/java/j2sdk1.4.2
else
JAVA_HOME_TMP=0
fi
else
JAVA_HOME_TMP=`dirname $JAVA_HOME_TMP`
JAVA_HOME_TMP=`dirname $JAVA_HOME_TMP`
fi
}
getClustalWPath()
{
CLUSTALW=${CLUSTALW-`which clustalw 2>/dev/null`}
echo
echo "-------------------------- ClustalW --------------------------"
echo
echo "To use emma (EMBOSS interface to ClustalW) Jemboss needs to"
echo "know the path to the clustalw binary."
echo
if (test "$CLUSTALW" != ""); then
CLUSTALW=`dirname $CLUSTALW`
echo "Enter the path to the clustalw or press return to use the"
echo "default [$CLUSTALW]:"
read CLUSTALW_TMP
if (test "$CLUSTALW_TMP" != ""); then
CLUSTALW="$CLUSTALW_TMP"
fi
else
echo "Enter the path to clustalw or press return to set"
echo "this later (in jemboss.properties)"
read CLUSTALW
fi
if (test "$CLUSTALW" = ""); then
CLUSTALW="/packages/clustal/"
fi
}
getPrimerPath()
{
PRIMER3=${PRIMER3-`which primer3_core 2>/dev/null`}
echo
echo "-------------------------- Primer3 --------------------------"
echo
echo "To use eprimer3 (EMBOSS interface to Primer3 from the Whitehead"
echo "Institute) Jemboss needs to know the path to the primer3_core"
echo "binary."
echo
if (test "$PRIMER3" != ""); then
PRIMER3=`dirname $PRIMER3`
echo "Enter the path to the primer3_core or press return to use the"
echo "default [$PRIMER3]:"
read PRIMER3_TMP
if (test "$PRIMER3_TMP" != ""); then
PRIMER3="$PRIMER3_TMP"
fi
else
echo "Enter the path to primer3_core or press return to set"
echo "this later in (jemboss.properties)"
read PRIMER3
fi
if (test "$PRIMER3" = ""); then
PRIMER3="/packages/primer3/bin"
fi
}
embassy_install()
{
EMBOSS_DOWNLOAD=$1
RECORD=$2
PLATFORM=$3
EMBOSS_INSTALL=$4
USER_CONFIG=$5
echo
echo "--------------------------------------------------------------"
echo
echo "EMBASSY packages can optionally be installed along with"
echo "the EMBOSS applications, see:"
echo "http://emboss.sourceforge.net/apps/release/version/embassy"
echo "where 'version' corresponds to the EMBOSS version e.g. 6.0"
echo
echo "--------------------------------------------------------------"
echo
echo "Install EMBASSY packages (y,n) [y]?"
read EMBASSY
if [ "$EMBASSY" = "" ]; then
EMBASSY="y"
fi
echo "$EMBASSY" >> $RECORD
if [ $EMBASSY = "y" ]; then
if [ ! -d $EMBOSS_DOWNLOAD/embassy ]; then
mkdir $EMBOSS_DOWNLOAD/embassy
fi
echo
echo "To install EMBASSY Packages:"
echo "(1) Download these from ftp://emboss.open-bio.org/pub/EMBOSS/"
echo "(2) And unpack (gunzip and untar) them in: "
echo "$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' then prompts will be given for each package to "
echo "install) (y,n) [y]?"
read ALL
if [ "$ALL" = "" ]; then
ALL="y"
fi
for dir in *
do
if (test -d $dir ); then
if [ $ALL = "y" ]; then
INST="y"
else
echo "Install $dir (y,n) [y]?"
read INST
if [ "$INST" = "" ]; then
INST="y"
fi
fi
if [ $INST = "y" ]; then
EMBASSY_INST="$EMBOSS_DOWNLOAD/embassy/$dir"
if [ -f "$EMBASSY_INST/configure" ]; then
echo
echo " ******** $dir will be configured and installed ******** "
echo
cd $EMBASSY_INST
./configure --with-thread=$PLATFORM \
--prefix=$EMBOSS_INSTALL $USER_CONFIG
make
make -j install
cd ..
else
echo
echo "Did not install $dir cannot find"
echo "$EMBASSY_INST/configure"
echo
fi
fi
fi
done
fi
}
ssl_print_notes()
{
KEYSTOREFILE=$1
TOMCAT_ROOT=$2
PORT=$3
NUM=2
echo
if [ -f $JAVA_HOME/jre/lib/security/java.security ]; then
SECURITY=`sed -n -e 's|^security.provider.\([0-9]\)=com.sun.net.ssl.internal.ssl.Provider|security|p' $JAVA_HOME/jre/lib/security/java.security`
if [ $SECURITY = "security" ]; then
NUM=1
else
echo "1) EDIT "$JAVA_HOME/jre/lib/security/java.security
echo " adding/changing the provider line (usually provider 2 or 3):"
echo " security.provider.2=com.sun.net.ssl.internal.ssl.Provider"
fi
else
if [ "$MACOSX" != "y" ]; then
echo "1) EDIT the java.security file "
echo " adding/changing the provider line (usually provider 2 or 3):"
echo " security.provider.2=com.sun.net.ssl.internal.ssl.Provider"
fi
fi
echo "$NUM) COPY & PASTE THE FOLLOWING INTO "
echo " $TOMCAT_ROOT/conf/server.xml"
echo
echo
if [ -d "$TOMCAT_ROOT/shared/classes" ]; then
TCVERSION=`sed -n -e 's|\(.*\)Running The Tomcat 4\(.*\)|4|p' $TOMCAT_ROOT/RUNNING.txt`
if [ "$TCVERSION" != "4" ]; then
#tomcat 5.x
TCVERSION=`sed -n -e 's|\(.*\)Running The Tomcat 5.5\(.*\)|5|p' $TOMCAT_ROOT/RUNNING.txt`
if [ "$TCVERSION" != "5" ]; then
echo
echo ' <!-- Define a SSL Coyote HTTP/1.1 Connector on port '$PORT' -->'
echo ' <Connector className="org.apache.coyote.tomcat5.CoyoteConnector"'
echo ' port="'$PORT'" minProcessors="5" maxProcessors="75"'
echo ' enableLookups="false"'
echo ' acceptCount="10" debug="0" scheme="https" secure="true"'
echo ' useURIValidationHack="false">'
echo ' <Factory className="org.apache.coyote.tomcat5.CoyoteServerSocketFactory"'
echo ' keystoreFile="'$KEYSTOREFILE'" keystorePass="'$PASSWD'"'
echo ' clientAuth="false" protocol="TLS"/>'
echo ' </Connector>'
echo
else
#tomcat 5.5
echo
echo ' <!-- Define a SSL Coyote HTTP/1.1 Connector on port '$PORT' -->'
echo ' <Connector port="'$PORT'" minProcessors="5" maxProcessors="75"'
echo ' enableLookups="false"'
echo ' acceptCount="10" debug="0" scheme="https" secure="true"'
echo ' useURIValidationHack="false"'
echo ' keystoreFile="'$KEYSTOREFILE'" keystorePass="'$PASSWD'"'
echo ' clientAuth="false" sslProtocol="TLS"/>'
echo
fi
else
#tomcat 4.1.x
echo
echo ' <!-- Define a SSL Coyote HTTP/1.1 Connector on port '$PORT' -->'
echo ' <Connector className="org.apache.coyote.tomcat4.CoyoteConnector"'
echo ' port="'$PORT'" minProcessors="5" maxProcessors="75"'
echo ' enableLookups="false"'
echo ' acceptCount="10" debug="0" scheme="https" secure="true"'
echo ' useURIValidationHack="false">'
echo ' <Factory className="org.apache.coyote.tomcat4.CoyoteServerSocketFactory"'
echo ' keystoreFile="'$KEYSTOREFILE'" keystorePass="'$PASSWD'"'
echo ' clientAuth="false" protocol="TLS"/>'
echo ' </Connector>'
echo
fi
else
TCVERSION=`sed -n -e 's|\(.*\)Running The Apache Tomcat 6.0\(.*\)|6|p' $TOMCAT_ROOT/RUNNING.txt`
if [ "$TCVERSION" = "6" ]; then
#tomcat 6.x
echo
echo ' <!-- Define an SSL HTTP/1.1 Connector on port '$PORT' -->'
echo ' <Connector port="'$PORT'" protocol="HTTP/1.1" minSpareThreads="5" maxSpareThreads="75"'
echo ' enableLookups="true" disableUploadTimeout="true"'
echo ' acceptCount="100" maxThreads="200"'
echo ' scheme="https" secure="true" SSLEnabled="true"'
echo ' keystoreFile="'$KEYSTOREFILE'" keystorePass="'$PASSWD'"'
echo ' clientAuth="false" sslProtocol="TLS">'
echo ' </Connector>'
echo
else
#tomcat 4.0.x
echo ' <!-- Define an SSL HTTP/1.1 Connector on port '$PORT' -->'
echo ' <Connector className="org.apache.catalina.connector.http.HttpConnector"'
echo ' port="'$PORT'" minProcessors="5" maxProcessors="75"'
echo ' enableLookups="true"'
echo ' acceptCount="10" debug="0" scheme="https" secure="true">'
echo ' <Factory className="org.apache.catalina.net.SSLServerSocketFactory"'
echo ' keystoreFile="'$KEYSTOREFILE'" keystorePass="'$PASSWD'"'
echo ' clientAuth="false" protocol="TLS"/>'
echo ' </Connector>'
echo
fi
fi
}
ssl_create_keystore()
{
HOST=$1
JEMBOSS_RES=$2
KEYSTORE=$3
ALIAS=$4
PASSWD=$5
VALID=$6
keytool -genkey -alias $ALIAS -dname "CN=$HOST, \
OU=Jemboss, O=HGMP-RC, L=CAMBRIDGE, S=CAMBRIDGE, C=UK" -keyalg RSA \
-keypass $PASSWD -storepass $PASSWD -keystore $JEMBOSS_RES/$KEYSTORE.keystore -validity $VALID
keytool -export -alias $ALIAS -storepass $PASSWD -file $JEMBOSS_RES/$KEYSTORE.cer \
-keystore $JEMBOSS_RES/$KEYSTORE.keystore
}
ssl_import()
{
FILE=$1
KEYSTORE=$2
PASSWD=$3
keytool -import -v -trustcacerts -alias tomcat -file $FILE -keystore \
$KEYSTORE -keypass $PASSWD -storepass $PASSWD -noprompt
}
make_jemboss_properties()
{
EMBOSS_INSTALL=$1
URL=$2
AUTH=$3
SSL=$4
PORT=$5
EMBOSS_URL=$6
CLUSTALW=$7
PRIMER3=$8
RESULTSHOME=$9
EMBOSSPATH=/usr/bin/:/bin
export EMBOSSPATH
EMBOSSPATH=${EMBOSSPATH}:$CLUSTALW
EMBOSSPATH=${EMBOSSPATH}:$PRIMER3
if [ $SSL = "y" ]; then
URL=https://$URL:$PORT
else
URL=http://$URL:$PORT
fi
JEMBOSS_PROPERTIES=$EMBOSS_INSTALL/share/EMBOSS/jemboss/resources/jemboss.properties
mv $JEMBOSS_PROPERTIES $JEMBOSS_PROPERTIES.orig
touch $JEMBOSS_PROPERTIES
if [ $AUTH = "y" ]; then
echo "user.auth=true" > $JEMBOSS_PROPERTIES
else
echo "user.auth=false" > $JEMBOSS_PROPERTIES
fi
echo "jemboss.server=true" >> $JEMBOSS_PROPERTIES
echo "server.public=$URL/axis/services" \
>> $JEMBOSS_PROPERTIES
echo "server.private=$URL/axis/services" \
>> $JEMBOSS_PROPERTIES
if [ $AUTH = "y" ]; then
echo "service.public=JembossAuthServer" >> $JEMBOSS_PROPERTIES
echo "service.private=JembossAuthServer" >> $JEMBOSS_PROPERTIES
else
echo "service.public=JembossServer" >> $JEMBOSS_PROPERTIES
echo "service.private=JembossServer" >> $JEMBOSS_PROPERTIES
fi
echo "embossData=$EMBOSS_INSTALL/share/EMBOSS/data/" >> $JEMBOSS_PROPERTIES
echo "embossBin=$EMBOSS_INSTALL/bin/" >> $JEMBOSS_PROPERTIES
echo "embossPath=$EMBOSSPATH" >> $JEMBOSS_PROPERTIES
echo "results.home=$RESULTSHOME" >> $JEMBOSS_PROPERTIES
# echo "embossPath=/usr/bin/:/bin:$CLUSTALW:$PRIMER3:/packages/clustal/:/packages/primer3/bin:" \
# >> $JEMBOSS_PROPERTIES
echo "acdDirToParse=$EMBOSS_INSTALL/share/EMBOSS/acd/" >> $JEMBOSS_PROPERTIES
echo "embossURL=$EMBOSS_URL" >> $JEMBOSS_PROPERTIES
grep embossHavePDF $JEMBOSS_PROPERTIES.orig >> $JEMBOSS_PROPERTIES
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
}
deploy_axis_services()
{
JEMBOSS_LIB=$1
AXIS=$1/axis
CLASSPATH=$AXIS/axis.jar::$AXIS/jaxrpc.jar:$AXIS/saaj.jar:$AXIS/commons-logging.jar:
CLASSPATH=${CLASSPATH}:$AXIS/commons-discovery.jar:$AXIS/wsdl4j.jar:$AXIS/servlet.jar
# CLASSPATH=${CLASSPATH}:$JEMBOSS_LIB/jnet.jar:$JEMBOSS_LIB/jsse.jar:$JEMBOSS_LIB/jcert.jar
PROXY_OFF="-DproxySet=false -DproxyHost= -DproxyPort= -Dhttp.proxyHost= -Dhttp.proxyPort= -Dhttps.proxyHost= -Dhttps.proxyPort= "
SERVICE=$2
URL=$3
URL2=$4
JAVAHOME=$5
OPT_PROP1=$6
OPT_PROP2=$7
echo
# echo "$JAVAHOME/bin/java -classpath $CLASSPATH $OPT_PROP1 $OPT_PROP2 \\ "
# echo " org.apache.axis.client.AdminClient -l$URL/axis/services JembossServer.wsdd"
echo
$JAVAHOME/bin/java -classpath $CLASSPATH $OPT_PROP1 $OPT_PROP2 $PROXY_OFF \
org.apache.axis.client.AdminClient \
-l$URL/axis/services JembossServer.wsdd
echo "#!/bin/csh " > deploy.csh
echo "$JAVAHOME/bin/java -classpath $CLASSPATH $OPT_PROP1 $OPT_PROP2 $PROXY_OFF org.apache.axis.client.AdminClient -l$URL/axis/services JembossServer.wsdd" >> deploy.csh
echo "" >> deploy.csh
echo 'if ($status != 0) then' >> deploy.csh
echo " $JAVAHOME/bin/java -classpath $CLASSPATH $OPT_PROP1 $OPT_PROP2 $PROXY_OFF org.apache.axis.client.AdminClient -l$URL2/axis/services JembossServer.wsdd" >> deploy.csh
echo "endif" >> deploy.csh
chmod u+x deploy.csh
}
deploy_auth_services()
{
JEMBOSS_LIB=$1
CLASSPATH=$JEMBOSS_LIB/soap.jar:$JEMBOSS_LIB/activation.jar:$JEMBOSS_LIB/mail.jar
# CLASSPATH=${CLASSPATH}:$JEMBOSS_LIB/jnet.jar:$JEMBOSS_LIB/jsse.jar:$JEMBOSS_LIB/jcert.jar
SERVICE=$2
URL=$3
JAVAHOME=$4
OPT_PROP1=$5
OPT_PROP2=$6
echo
echo "Deploying $SERVICE "
echo "$JAVAHOME/bin/java -classpath $CLASSPATH $OPT_PROP1 $OPT_PROP2 org.apache.soap.server.ServiceManagerClient $URL/soap/servlet/rpcrouter deploy $SERVICE"
echo
$JAVAHOME/bin/java -classpath $CLASSPATH $OPT_PROP1 $OPT_PROP2 \
org.apache.soap.server.ServiceManagerClient \
$URL/soap/servlet/rpcrouter deploy $SERVICE
}
output_auth_xml()
{
AUTH=$2
if [ $AUTH = "y" ]; then
JEM_CLASS="org.emboss.jemboss.server.JembossAuthServer"
FIL_CLASS="org.emboss.jemboss.server.JembossFileAuthServer"
ID="JembossAuthServer"
else
JEM_CLASS="org.emboss.jemboss.server.JembossServer"
FIL_CLASS="org.emboss.jemboss.server.JembossFileServer"
ID="JembossServer"
fi
XML_FILE=$1
echo '<deployment xmlns="http://xml.apache.org/axis/wsdd/"' > $XML_FILE
echo ' xmlns:java="http://xml.apache.org/axis/wsdd/providers/java">' >> $XML_FILE
echo " <service name=\"$ID\" provider=\"java:RPC\">" >> $XML_FILE
echo " <parameter name=\"className\" value=\"$JEM_CLASS\"/>" >> $XML_FILE
echo ' <parameter name="allowedMethods" value="*"/>' >> $XML_FILE
echo ' </service>' >> $XML_FILE
echo ' <service name="EmbreoFile" provider="java:RPC">' >> $XML_FILE
echo " <parameter name=\"className\" value=\"$FIL_CLASS\"/>" >> $XML_FILE
echo ' <parameter name="allowedMethods" value="*"/>' >> $XML_FILE
echo ' </service>' >> $XML_FILE
echo '</deployment>' >> $XML_FILE
}
#
# Find the likely location for the png & gd libs
get_libs()
{
USER_CONFIG=$1
include_lib_dirs="
/usr/local
/opt/freeware
/usr/freeware"
if (test -f /usr/include/png.h) && (test -f /usr/include/gd.h); then
USER_CONFIG="default"
else
for lib_dir in `echo "$include_lib_dirs"` ;
do
if (test -f $lib_dir/include/png.h) && (test -f $lib_dir/include/gd.h); then
USER_CONFIG="--with-pngdriver=$lib_dir"
fi
done
fi
}
check_libs()
{
USER_CONFIG=$1
PLATFORM=$2
if [ "$USER_CONFIG" = "" ]; then
DIR="/usr"
else
DIR=`echo $USER_CONFIG | sed -n -e 's|\(.*\)--with-pngdriver=\([^ ]*\)\(.*\)|\2|p'`
fi
lib_dirs="
$DIR/lib
$DIR/lib32
$DIR/lib64
$DIR/lib/x86_64-linux-gnu
$DIR/lib/i386-linux-gnu"
echo
echo "Inspecting $DIR"
# test for libpng
WARN="true"
if (test ! -f $DIR/include/png.h ); then
WARN="true"
else
for lib_dir in `echo "$lib_dirs"` ;
do
echo "checking $lib_dir"
if (test -f $lib_dir/libpng.a) || (test -f $lib_dir/libpng.so); then
WARN="false"
echo "...found libpng in $lib_dir"
break
elif (test -f $lib_dir/libpng.dylib); then
WARN="false"
echo "...found libpng in $lib_dir"
break
fi
done
fi
if (test $WARN = "true"); then
echo
echo "------------------------- WARNING ----------------------------"
echo
echo "The script has detected that $DIR/include/png.h"
echo "does not exist!"
echo
echo "Download libpng from"
echo " http://www.libpng.org/pub/png/libpng.html"
echo " http://libpng.sourceforge.net/"
echo
echo "For details see the EMBOSS admin guide:"
echo "http://emboss.sourceforge.net/admin/"
echo
echo "To exit use Control C or press return to continue."
echo
echo "--------------------------------------------------------------"
read REPLY
fi
# test for gd
WARN="true"
if (test ! -f $DIR/include/gd.h ); then
WARN="true"
else
for lib_dir in `echo "$lib_dirs"` ;
do
echo "checking $lib_dir"
if (test -f $lib_dir/libgd.a) || (test -f $lib_dir/libgd.so); then
WARN="false"
echo "...found gd in $lib_dir"
break
elif (test -f $lib_dir/libgd.dylib); then
WARN="false"
echo "...found libpng in $lib_dir"
break
fi
done
fi
if (test $WARN = "true"); then
echo
echo "------------------------- WARNING ----------------------------"
echo
echo "The script has detected that $DIR/include/gd.h"
echo "does not exist"
echo
echo "Download gd from"
echo " http://www.boutell.com/gd/"
echo
echo "For details see the EMBOSS admin guide:"
echo "http://emboss.sourceforge.net/admin/"
echo
echo "To exit use Control C or press return to continue."
echo
echo "--------------------------------------------------------------"
read REPLY
fi
# test for zlib which can be either in /usr/lib or $DIR/lib
lib_dirs="
$DIR/lib
$DIR/lib32
$DIR/lib64
/usr/lib
/usr/local/lib
/usr/lib64
$DIR/lib/x86_64-linux-gnu
$DIR/lib/i386-linux-gnu"
WARN="true"
for lib_dir in `echo "$lib_dirs"` ;
do
echo "checking $lib_dir"
if (test -f $lib_dir/libz.a) || (test -f $lib_dir/libz.so) || (test -f $lib_dir/libz.dylib); then
WARN="false"
echo "...found zlib in $lib_dir"
break
fi
done
if (test $WARN = "true"); then
echo
echo "------------------------- WARNING ----------------------------"
echo
echo "The script cannot find zlib installed under /usr"
if( (test $PLATFORM = "macos") || (test $PLATFORM = "linux") ); then
echo "or /usr/local"
fi
echo
echo "Download zlib from"
echo " http://www.info-zip.org/pub/infozip/zlib/"
echo
echo "For details see the EMBOSS admin guide:"
echo "http://emboss.sourceforge.net/admin/"
echo
echo "To exit use Control C or press return to continue."
echo
echo "--------------------------------------------------------------"
read REPLY
fi
}
clear
echo
echo "--------------------------------------------------------------"
echo " EMBOSS and Jemboss Server installation script"
echo "--------------------------------------------------------------"
echo " "
echo "Note: any default values are given in square brackets []."
echo " "
echo "This script installs EMBOSS as well as Jemboss."
echo "Jemboss is deployed as a Java web application in your tomcat server."
echo "A script is prepared to run the Jemboss client that by default uses the"
echo "above Jemboss web application."
echo
echo "For detailed information on installing Jemboss see: "
echo "http://emboss.sourceforge.net/Jemboss/install/setup.html"
echo
echo
echo "*** This script needs to be run with permissions to be able"
echo "*** to install EMBOSS in the required directories. This may"
echo "*** be best done as root or as a tomcat user."
echo
echo "Before running this script you should download the latest:"
echo
echo "(1) EMBOSS release (contains Jemboss) ftp://emboss.open-bio.org/pub/EMBOSS/"
echo "(2) Tomcat 5.5 series (or above) release http://tomcat.apache.org/"
echo "(3) Apache AXIS (SOAP) release 1.4 http://ws.apache.org/axis/"
echo
echo "Have the above been downloaded (y/n)? "
read DOWNLOADED
if (test "$DOWNLOADED" != "y") && (test "$DOWNLOADED" != "Y"); then
exit 1
fi
RECORD="install.record"
if [ -f "$RECORD" ]; then
mv $RECORD $RECORD.old
fi
echo "$DOWNLOADED" > $RECORD
PLATTMP=`uname`
case $PLATTMP in
Linux)
PLATTMP="1"
;;
AIX)
PLATTMP="2"
;;
IRIX)
PLATTMP="3"
;;
HP-UX)
PLATTMP="4"
;;
SunOS)
PLATTMP="5"
;;
Darwin)
PLATTMP="6"
;;
OSF1)
PLATTMP="7"
;;
FreeBSD)
PLATTMP="8"
;;
*)
PLATTMP="1"
;;
esac
echo
echo "Select the platform (1-8) that your Jemboss server will be"
echo "run on [$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 [ "$PLAT" = "" ]; then
PLAT=$PLATTMP
fi
echo "$PLAT" >> $RECORD
AUTH_TYPE_TMP=1
AIX="n"
MACOSX="n"
if [ "$PLAT" = "1" ]; then
PLATFORM="linux"
AUTH_TYPE_TMP=3
elif [ "$PLAT" = "2" ]; then
PLATFORM="aix"
AIX="y"
AUTH_TYPE_TMP=4
elif [ "$PLAT" = "3" ]; then
PLATFORM="irix"
AUTH_TYPE_TMP=1
elif [ "$PLAT" = "4" ]; then
PLATFORM="hpux"
AUTH_TYPE_TMP=5
elif [ "$PLAT" = "5" ]; then
PLATFORM="solaris"
AUTH_TYPE_TMP=6
elif [ "$PLAT" = "6" ]; then
PLATFORM="macos"
MACOSX="y"
AUTH_TYPE_TMP=3
elif [ "$PLAT" = "7" ]; then
PLATFORM="osf"
AUTH_TYPE_TMP=7
elif [ "$PLAT" = "8" ]; then
PLATFORM="freebsd"
AUTH_TYPE_TMP=7
else
echo "Platform not selected from 1-8."
exit 1
fi
SSL="y"
# keep the following variable for now so we have cvs compare for a while
INSTALL_TYPE="1";
if [ $INSTALL_TYPE = "1" ]; then
#
# localhost name
#
echo
echo "The IP address or fully qualified domain name (e.g. emboss.company.com)"
echo "is needed by Jemboss to access the Tomcat web server."
echo "Enter the IP address or the fully qualified domain name of the"
echo "server machine [`hostname`]:"
read LOCALHOST
if [ "$LOCALHOST" = "" ]; then
LOCALHOST=`hostname`
fi
echo "$LOCALHOST" >> $RECORD
#
# SSL
#
echo
echo "Enter if you want the Jemboss server to use data"
echo "encryption (https/SSL) (y,n) [y]?"
read SSL
echo "$SSL" >> $RECORD
JSSE_HOME=""
if (test "$SSL" = "y") || (test "$SSL" = ""); then
PORT=8443
SSL="y"
else
PORT=8080
fi
#
# PORT
#
USER_PORT=""
echo
echo "Enter port number [$PORT]:"
read USER_PORT
if [ "$USER_PORT" = "" ]; then
if [ $SSL = "y" ]; then
PORT=8443
else
PORT=8080
fi
else
PORT=$USER_PORT
fi
echo "$PORT" >> $RECORD
fi
echo
#
# JAVA_HOME
#
getJavaHomePath
JAVA_HOME=$JAVA_HOME_TMP
if [ "$JAVA_HOME" != "0" ]; then
echo "Enter java (1.4 or above) location [$JAVA_HOME_TMP]: "
read JAVA_HOME
if [ "$JAVA_HOME" = "" ]; then
JAVA_HOME=$JAVA_HOME_TMP
fi
fi
while [ ! -f "$JAVA_HOME/bin/javac" ]
do
echo "Enter java (1.3 or above) location (/usr/java/jdk1.3.1/): "
read JAVA_HOME
done
echo
echo "$JAVA_HOME" >> $RECORD
#
# add java bin to path
#
PATH=$JAVA_HOME/bin/:$PATH ; export PATH
#
#
# JNI location for linux/solaris/AIX/SGI/HP-UX
#
#
#
JAVA_INCLUDE=$JAVA_HOME/include/
JAVA_INCLUDE_OS=$JAVA_INCLUDE
if [ -d $JAVA_INCLUDE/linux ]; then
JAVA_INCLUDE_OS=${JAVA_INCLUDE}/linux
elif [ -d $JAVA_INCLUDE/solaris ]; then
JAVA_INCLUDE_OS=${JAVA_INCLUDE}/solaris
elif [ -d $JAVA_INCLUDE/irix ]; then
JAVA_INCLUDE_OS=${JAVA_INCLUDE}/irix
elif [ -d $JAVA_INCLUDE/hp-ux ]; then
JAVA_INCLUDE_OS=${JAVA_INCLUDE}/hp-ux
elif [ -d $JAVA_INCLUDE/alpha ]; then
JAVA_INCLUDE_OS=${JAVA_INCLUDE}/alpha
elif [ -d $JAVA_INCLUDE/freebsd ]; then
JAVA_INCLUDE_OS=${JAVA_INCLUDE}/freebsd
elif [ -d $JAVA_INCLUDE ]; then
JAVA_INCLUDE_OS=${JAVA_INCLUDE}
else
echo "Enter java include/Header directory location (containing jni.h)? "
read JAVA_INCLUDE
JAVA_INCLUDE_OS=$JAVA_INCLUDE
if [ -d $JAVA_INCLUDE/linux ]; then
JAVA_INCLUDE_OS=${JAVA_INCLUDE}/linux
elif [ -d $JAVA_INCLUDE/solaris ]; then
JAVA_INCLUDE_OS=${JAVA_INCLUDE}/solaris
elif [ -d $JAVA_INCLUDE/irix ]; then
JAVA_INCLUDE_OS=${JAVA_INCLUDE}/irix
elif [ -d $JAVA_INCLUDE ]; then
JAVA_INCLUDE_OS=${JAVA_INCLUDE}
else
echo "Problems finding java include libraries!"
exit 1
fi
echo "$JAVA_INCLUDE" >> $RECORD
fi
#
# EMBOSS_DOWNLOAD
#
EMBOSS_DOWNLOAD_TMP=`pwd`
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
if [ "$EMBOSS_DOWNLOAD" = "" ]; then
EMBOSS_DOWNLOAD=$EMBOSS_DOWNLOAD_TMP
fi
while [ ! -d "$EMBOSS_DOWNLOAD/ajax" ]
do
echo "Enter EMBOSS download directory (e.g. /usr/emboss/EMBOSS-2.x.x): "
read EMBOSS_DOWNLOAD
done
echo
echo "$EMBOSS_DOWNLOAD" >> $RECORD
echo "Enter where EMBOSS should be installed [/usr/local/emboss]: "
read EMBOSS_INSTALL
if [ "$EMBOSS_INSTALL" = "" ]; then
EMBOSS_INSTALL=/usr/local/emboss
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
echo "$EMBOSS_INSTALL" >> $RECORD
if [ $INSTALL_TYPE = "1" ]; then
echo "Enter URL for emboss documentation for application "
echo "[http://emboss.sourceforge.net/]:"
read EMBOSS_URL
echo "$EMBOSS_URL" >> $RECORD
fi
if [ "$EMBOSS_URL" = "" ]; then
EMBOSS_URL="http://emboss.sourceforge.net/"
fi
echo
#
# set JSSE_HOME to the EMBOSS install dir
#
JSSE_HOME=$EMBOSS_INSTALL/share/EMBOSS/jemboss
JEMBOSS_SERVER_AUTH=""
AUTH=y
if [ $INSTALL_TYPE = "1" ]; then
echo "Do you want Jemboss to use unix authorisation (y/n) [y]? "
read AUTH
echo "$AUTH" >> $RECORD
else
AUTH="n"
fi
if [ "$AUTH" = "" ]; then
AUTH="y"
fi
echo
if [ "$AUTH" = "y" ]; then
echo "#include <stdio.h>" > dummy.c
echo 'int main(){ printf("%d",getuid()); }' >> dummy.c
if (cc dummy.c -o dummy >/dev/null 2>&1); then
UUIDTMP=`./dummy`
CC="cc";
else
gcc dummy.c -o dummy >/dev/null 2>&1
UUIDTMP=`./dummy`
CC="gcc";
fi
rm -f dummy.c dummy
if (test "$UUIDTMP" = "") || (test "$UUIDTMP" = "0"); then
UUIDTMP="506"
fi
echo "Provide the UID of the account (non-privileged) to run Tomcat,"
echo "it has to be greater than 100 [$UUIDTMP]:"
read UUID
echo "$UUID" >> $RECORD
if [ "$UUID" = "" ]; then
UUID="$UUIDTMP"
fi
CC="$CC -DTOMCAT_UID=$UUID "; export CC
echo
echo "Unix Authentication Method, see:"
echo "http://emboss.sourceforge.net/Jemboss/install/authentication.html"
echo
echo "(1) shadow (3) PAM (5) HP-UX shadow"
echo "(2) no shadow (4) AIX shadow (6) Re-entrant shadow"
echo "(7) Re-entrant no shadow"
echo
echo "Type of unix password method being used "
echo "(select 1, 2, 3, 4, 5, 6 or 7 )[$AUTH_TYPE_TMP]"
read AUTH_TYPE
if [ "$AUTH_TYPE" = "" ]; then
AUTH_TYPE="$AUTH_TYPE_TMP"
fi
echo "$AUTH_TYPE" >> $RECORD
if [ "$AUTH_TYPE" = "1" ]; then
JEMBOSS_SERVER_AUTH=" --with-auth=shadow"
elif [ "$AUTH_TYPE" = "2" ]; then
JEMBOSS_SERVER_AUTH=" --with-auth=noshadow"
elif [ "$AUTH_TYPE" = "3" ]; then
JEMBOSS_SERVER_AUTH=" --with-auth=pam"
elif [ "$AUTH_TYPE" = "4" ]; then
JEMBOSS_SERVER_AUTH=" --with-auth=aixshadow"
elif [ "$AUTH_TYPE" = "5" ]; then
JEMBOSS_SERVER_AUTH=" --with-auth=hpuxshadow"
elif [ "$AUTH_TYPE" = "6" ]; then
JEMBOSS_SERVER_AUTH=" --with-auth=rshadow"
elif [ "$AUTH_TYPE" = "7" ]; then
JEMBOSS_SERVER_AUTH=" --with-auth=rnoshadow"
else
JEMBOSS_SERVER_AUTH=" --with-auth=shadow"
fi
fi
echo
if [ $INSTALL_TYPE = "1" ]; then
#
#
# Results directory for jobs
#
echo "Define the directory you want to store the results in"
echo "[/tmp/SOAP/emboss]"
read JOBDIR
if (test "$JOBDIR" = ""); then
JOBDIR="/tmp/SOAP/emboss"
fi
echo "$JOBDIR" >> $RECORD
echo
#
#
# Tomcat
#
TOMCAT_ROOT=0
while [ ! -d "$TOMCAT_ROOT/webapps" ]
do
echo "Enter Tomcat root directory (e.g. /usr/local/tomcat)"
read TOMCAT_ROOT
done
echo "$TOMCAT_ROOT" >> $RECORD
echo
if [ -d "$TOMCAT_ROOT/webapps/axis/WEB-INF/classes/org" ]; then
echo
echo "It looks like an installation has already been carried out in: "
echo "$TOMCAT_ROOT/webapps/axis/WEB-INF/classes/ "
echo "It is recommended that tomcat is removed and a fresh copy of tomcat used."
echo "This installation is likely to fail if you continue."
read BLANK
fi
if [ -d "$TOMCAT_ROOT/webapps/axis/WEB-INF/classes/resources" ]; then
echo
echo "It looks like an installation has already been carried out in: "
echo "$TOMCAT_ROOT/webapps/axis/WEB-INF/classes/ "
echo "It is recommended that tomcat is removed and a fresh copy of tomcat used."
echo "This installation is likely to fail if you continue."
read BLANK
fi
#
# Apache AXIS (SOAP)
#
SOAP_ROOT=0
while [ ! -d "$SOAP_ROOT/webapps/axis" ]
do
echo "Enter Apache AXIS (SOAP) root directory (e.g. /usr/local/axis-1.4)"
read SOAP_ROOT
done
echo "$SOAP_ROOT" >> $RECORD
echo
cp -R $SOAP_ROOT/webapps/axis $TOMCAT_ROOT/webapps
#already have commons-logging.jar in $TOMCAT_ROOT/server/lib/
rm -f $TOMCAT_ROOT/webapps/axis/WEB-INF/lib/commons-logging.jar
fi
#
# Configuration options
#
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://emboss.sourceforge.net/admin/"
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
check_libs "$USER_CONFIG" $PLATFORM
echo "$USER_CONFIG" >> $RECORD
#
#
if [ "$AIX" = "y" ]; then
if [ "$AUTH" = "y" ]; then
CC="xlc_r -DTOMCAT_UID=$UUID "; export CC
else
CC=xlc_r; export CC
fi
fi
echo
echo " ******** EMBOSS will be configured with this information ******** "
echo
printf "%s\n" "./configure --with-java=$JAVA_INCLUDE \\"
printf "%s\n" " --with-javaos=$JAVA_INCLUDE_OS \\"
printf "%s\n" " --with-thread=$PLATFORM \\"
printf "%s\n" " --prefix=$EMBOSS_INSTALL \\"
printf "%s\n" " $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 $USER_CONFIG
CONFIGURE_EXIT_STAT=$?
if [ $CONFIGURE_EXIT_STAT -eq 0 ];then
echo "EMBOSS configuration call has been completed."
else
echo
echo "EMBOSS configuration call returned with error."
echo "Please check error messages and run the install script again."
echo "Now terminating the install script."
exit $CONFIGURE_EXIT_STAT
fi
make
MAKE_EXIT_STAT=$?
if [ $MAKE_EXIT_STAT -eq 0 ];then
echo "EMBOSS build has been completed."
else
echo
echo "EMBOSS build returned with error."
echo "Please check error messages and run the install script again."
echo "Now terminating the install script."
exit $MAKE_EXIT_STAT
fi
echo
echo " ******* EMBOSS with Jemboss will be installed in $EMBOSS_INSTALL ******* "
echo
sleep 2
make -j install
#
#
# Config EMBASSY
#
embassy_install $EMBOSS_DOWNLOAD $RECORD $PLATFORM $EMBOSS_INSTALL $USER_CONFIG
#
#
# Get clustalw and primer3_core path
#
getClustalWPath
getPrimerPath
#
#
#
#cd $EMBOSS_INSTALL/share/EMBOSS/jemboss
JEMBOSS=$EMBOSS_INSTALL/share/EMBOSS/jemboss
#
# create resources.jar archive of the scoring matrix
#
cd $EMBOSS_INSTALL/share/EMBOSS/data
$JAVA_HOME/bin/jar cvf $JEMBOSS/resources/resources.jar EPAM* EBLOSUM* EDNA*
if [ "$MACOSX" = "y" ]; then
cd $EMBOSS_INSTALL/lib/
ln -s libajax.dylib libajax.jnilib
# ln -s $EMBOSS_INSTALL/lib/libajax.dylib $EMBOSS_INSTALL/lib/libajax.jnilib
# cp $EMBOSS_INSTALL/lib/libajax.[0-9].dylib /System/Library/Frameworks/JavaVM.framework/Libraries/libajax.jnilib
fi
cd $WORK_DIR
if [ "$PLATFORM" = "hpux" ]; then
ln -s $EMBOSS_INSTALL/lib/libajax.sl $EMBOSS_INSTALL/lib/libajax.so
fi
make_jemboss_properties $EMBOSS_INSTALL $LOCALHOST $AUTH $SSL $PORT $EMBOSS_URL $CLUSTALW $PRIMER3 $JOBDIR
#
#
# Tomcat scripts
#
#
rm -f tomstart
echo
echo "#!/bin/csh " > tomstart
echo "setenv JAVA_HOME $JAVA_HOME" >> tomstart
if [ "$SSL" = "y" ]; then
echo "setenv JSSE_HOME $JSSE_HOME" >> tomstart
fi
if [ "$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 $EMBOSS_INSTALL/lib" >> tomstart
fi
if [ "$PLATFORM" = "hpux" ]; then
echo "setenv SHLIB_PATH $EMBOSS_INSTALL/lib" >> tomstart
fi
if [ "$AUTH_TYPE" = "3" ]; then
if [ -f "/lib64/libpam.so" ]; then
echo "setenv LD_PRELOAD /lib64/libpam.so" >> tomstart
elif [ -f "/usr/lib64/libpam.so" ]; then
echo "setenv LD_PRELOAD /usr/lib64/libpam.so" >> tomstart
elif [ -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
elif [ -f "/usr/lib/libpam.dylib" ]; then
echo "setenv LD_PRELOAD /usr/lib/libpam.dylib" >> 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
rm -f 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 "$TOMCAT_ROOT/bin/shutdown.sh" >> tomstop
chmod u+x tomstart
chmod u+x tomstop
#
#
# Run Jemboss script
#
# The runJemboss.sh script is now generated from an Autoconf template
# runJemboss.sh.in with the location of the Java Application Launcher
# substituted.
# RUNFILE=$JEMBOSS/runJemboss.sh
# sed "s|^java |$JAVA_HOME/bin/java |" $RUNFILE > $RUNFILE.new
# rm -f $RUNFILE
# mv $RUNFILE.new $RUNFILE
#
# Add classes to Tomcat path
#
cp $JEMBOSS/lib/mail.jar $TOMCAT_ROOT/webapps/axis/WEB-INF/lib
cp $JEMBOSS/lib/activation.jar $TOMCAT_ROOT/webapps/axis/WEB-INF/lib
cp -R $JEMBOSS/resources $TOMCAT_ROOT/webapps/axis/WEB-INF/classes/
cp -R $EMBOSS_DOWNLOAD/jemboss/lib/axis $JEMBOSS/lib
# Ensure that the native library is not loaded more than once.
# To avoid place classes that load native libraries outside of the
# web app, and ensure that the loadLibrary() call is executed only once
# during the lifetime of a particular JVM.
cd $JEMBOSS;
echo "moving Ajax class from jemboss.jar into ajax.jar"
mkdir tmp;
cd tmp;
jar -xf ../lib/jemboss.jar org/emboss/jemboss/server/Ajax.class
jar -cf ../lib/ajax.jar org
jar -xf ../lib/jemboss.jar
rm org/emboss/jemboss/server/Ajax.class
echo "copying Java class files to axis web-application classes folder"
cp -R org $TOMCAT_ROOT/webapps/axis/WEB-INF/classes/
cd ..;
rm -rf tmp;
echo "copying ajax.jar to Tomcat shared libraries folder"
if [ -d "$TOMCAT_ROOT/shared/lib" ]; then
#tomcat 4.1.x and 5.5.x
cp lib/ajax.jar $TOMCAT_ROOT/shared/lib/
elif [ -d "$TOMCAT_ROOT/lib" ]; then
#tomcat 4.1.x and 5.5.x
cp lib/ajax.jar $TOMCAT_ROOT/lib/
else
echo "WARNING: no $TOMCAT_ROOT/lib or $TOMCAT_ROOT/shared/lib found"
echo "ajax.jar not added to Tomcat shared libraries folder"
fi
cd $WORK_DIR
#
#
# Create XML deployment descriptor files
#
output_auth_xml JembossServer.wsdd $AUTH
if [ "$SSL" != "y" ]; then
echo
echo "Tomcat XML deployment descriptors have been created for"
echo "the Jemboss Server. Would you like an automatic deployment"
echo "of the Jemboss web services to be tried (y/n) [y]?"
echo "(Please make sure your Tomcat server not running currently,"
echo " install script will start it.)"
read DEPLOYSERVICE
if (test "$DEPLOYSERVICE" = "y") || (test "$DEPLOYSERVICE" = ""); then
echo
echo "Please wait, starting tomcat......."
./tomstart
sleep 2
deploy_axis_services $JEMBOSS/lib JembossServer.wsdd http://localhost:$PORT/ http://$LOCALHOST:$PORT/ $JAVA_HOME "" ""
fi
else
echo
echo "--------------------------------------------------------------"
echo
echo "Client and server certificates need to be generated for the"
echo "secure (https) connection. These are then imported into"
echo "keystores. The keystores act as databases for the security"
echo "certificates."
echo
echo "For details see:"
echo "http://emboss.sourceforge.net/Jemboss/install/ssl.html"
echo
echo "--------------------------------------------------------------"
echo
PASSWD=""
while [ "$PASSWD" = "" ]
do
echo "Provide a password (must be at least 6 characters): "
read PASSWD
done
echo
echo "Provide the validity period for these certificates, i.e. the"
echo "number of days before they expire and new ones need to be made [90]:"
read VALID
echo
if [ "$VALID" = "" ]; then
VALID=90
fi
echo "Please wait, creating certificates......."
ssl_create_keystore $LOCALHOST $JEMBOSS/resources "server" "tomcat-sv" $PASSWD $VALID
ssl_create_keystore "Client" $JEMBOSS/resources "client" "tomcat-cl" $PASSWD $VALID
ssl_import $JEMBOSS/resources/server.cer $JEMBOSS/resources/client.keystore $PASSWD
ssl_import $JEMBOSS/resources/client.cer $JEMBOSS/resources/server.keystore $PASSWD
cd $JEMBOSS/resources
$JAVA_HOME/bin/jar cvf client.jar client.keystore
cd $WORK_DIR
echo
echo "Tomcat XML deployment descriptors have been created for the Jemboss Server."
echo "Would you like an automatic deployment of these to be tried (y/n) [y]?"
echo "(Please make sure your Tomcat server is not currently running as"
echo "the install script will start it.)"
read DEPLOYSERVICE
if (test "$DEPLOYSERVICE" = "y") || (test "$DEPLOYSERVICE" = ""); then
ssl_print_notes $JEMBOSS/resources/server.keystore $TOMCAT_ROOT $PORT
echo
VAL=0
while [ $VAL != "y" ]
do
echo "To continue you must have changed the above file(s)!"
echo "Have the above files been edited (y/n)?"
read VAL
done
echo
echo "Please wait, starting tomcat......."
./tomstart
sleep 2
OPT_PROP1="-Djava.protocol.handler.pkgs=com.sun.net.ssl.internal.www.protocol"
OPT_PROP2="-Djavax.net.ssl.trustStore=$JEMBOSS/resources/client.keystore"
deploy_axis_services $JEMBOSS/lib JembossServer.wsdd https://localhost:$PORT/ https://$LOCALHOST:$PORT $JAVA_HOME $OPT_PROP1 $OPT_PROP2
fi
fi
#
# Change jemboss.properties to reflect server location
# $EMBOSS_INSTALL/share/EMBOSS/jemboss/resources/jemboss.properties
#
#
echo
echo "--------------------------------------------------------------"
echo "--------------------------------------------------------------"
if [ "$AUTH" = "y" ]; then
if [ $SSL = "y" ]; then
URL=https://$LOCALHOST:$PORT
else
URL=http://$LOCALHOST:$PORT
fi
echo
echo "Tomcat should be running and the Jemboss web services deployed!"
echo "(see $URL/axis/)"
echo
echo "It is *very* important to now:"
echo "1. As root:"
echo " chown root $EMBOSS_INSTALL/bin/jembossctl"
echo " chmod u+s $EMBOSS_INSTALL/bin/jembossctl"
echo "2. Ensure that tomcat is running as the non-privileged user,"
echo " with the same UID (i.e. $UUID) that was given to this script"
echo " (and NOT as root!)."
echo "3. Use the tomstop & tomstart scripts in this directory"
echo " to stop & start tomcat."
echo
else
echo
echo "Note: Tomcat may still be running!"
echo "Use the tomstop & tomstart scripts to stop & start tomcat."
echo
fi
if [ ! -d "$JOBDIR" ]; then
echo "Create the user results directory (and ensure this is world read/write-able): "
echo " mkdir $JOBDIR"
echo
fi
echo "Try running Jemboss with the script:"
# The runJemboss.sh script is now automatically installed by Automake as
# bin_SCRIPT in the bin directory.
# echo " $JEMBOSS/runJemboss.sh"
echo " runJemboss.sh"
echo
echo "To create a web launch page see:"
echo "http://emboss.sourceforge.net/Jemboss/install/deploy.html"
echo
# The runJemboss.sh script is now automatically installed by Automake as
# bin_SCRIPT in the bin directory.
# chmod a+x $JEMBOSS/runJemboss.sh
chmod u+x $JEMBOSS/utils/*sh
exit 0;
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