Lessons learned: Gephi not starting up

Scenario: When using Ubuntu Trusty (14.04.3LTS) Gephi 0.82 initializes but gets stuck on “Loading Cached Objects”

Solution: The default Gephi startup bash script does not correctly initialize the JAVA path (it uses $jdkhome) The solution is simply to add the following to the beginning of the startup script (~/gephi/bin/gephi)

export JAVA_HOME=/usr/lib/jvm/default-java
jdkhome=$JAVA_HOME

The full script is here:

	#!/bin/sh

	#
	# resolve symlinks
	#

	#### DV: START BUGFIX ####
	export JAVA_HOME=/usr/lib/jvm/default-java
	jdkhome=$JAVA_HOME
	#### DV: END BUGFIX ####

	PRG=$0

	while [ -h "$PRG" ]; do
	ls=`ls -ld "$PRG"`
	link=`expr "$ls" : '^.-> $.$$' 2>/dev/null`
	if expr "$link" : '^/' 2> /dev/null >/dev/null; then
	PRG="$link"
	else
	PRG="`dirname "$PRG"`/$link"
	fi
	done

	progdir=`dirname "$PRG"`
	APPNAME=`basename "$PRG"`

	if [ -f "$progdir/../etc/$APPNAME".conf ] ; then
	. "$progdir/../etc/$APPNAME".conf
	fi

	# XXX does not correctly deal with spaces in non-userdir params
	args=""

	case "`uname`" in
	Darwin*)
	userdir="${default_mac_userdir}"
	;;
	*)
	userdir="${default_userdir}"
	;;
	esac
	while [ $# -gt 0 ] ; do
	case "$1" in
	–userdir) shift; if [ $# -gt 0 ] ; then userdir="$1"; fi
	;;
	*) args="$args \"$1\""
	;;
	esac
	shift
	done

	if [ -f "${userdir}/etc/$APPNAME".conf ] ; then
	. "${userdir}/etc/$APPNAME".conf
	fi

	if [ -n "$jdkhome" -a \! -d "$jdkhome" -a -d "$progdir/../$jdkhome" ]; then
	# #74333: permit jdkhome to be defined as relative to app dir
	jdkhome="$progdir/../$jdkhome"
	fi

	readClusters() {
	if [ -x /usr/ucb/echo ]; then
	echo=/usr/ucb/echo
	else
	echo=echo
	fi
	while read X; do
	if [ "$X" \!= "" ]; then
	$echo "$progdir/../$X"
	fi
	done
	}

	clusters=`(cat "$progdir/../etc/$APPNAME".clusters; echo) \| readClusters \| tr '\012' ':'`

	if [ ! -z "$extra_clusters" ] ; then
	clusters="$clusters:$extra_clusters"
	fi

	nbexec=`echo "$progdir"/../platform*/lib/nbexec`

	case "`uname`" in
	Darwin*)
	eval exec sh '"$nbexec"' \
	–jdkhome '"$jdkhome"' \
	-J-Dcom.apple.mrj.application.apple.menu.about.name='"$APPNAME"' \
	-J-Xdock:name='"$APPNAME"' \
	'"-J-Xdock:icon=$progdir/../../$APPNAME.icns"' \
	–clusters '"$clusters"' \
	–userdir '"${userdir}"' \
	${default_options} \
	"$args"
	;;
	*)
	sh=sh
	# #73162: Ubuntu uses the ancient Bourne shell, which does not implement trap well.
	if [ -x /bin/bash ]
	then
	sh=/bin/bash
	fi
	eval exec $sh '"$nbexec"' \
	–jdkhome '"$jdkhome"' \
	–clusters '"$clusters"' \
	–userdir '"${userdir}"' \
	${default_options} \
	"$args"
	exit 1
	;;
	esac

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gephi.sh

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