How do I make java default to a manually installed JRE/JDK?

You can do this with sudo update-alternatives :

# Adding a new alternative for "java".
sudo update-alternatives --install /usr/bin/java java /media/mydisk/jdk/bin/java 1

# Setting the new alternative as default for "java".
sudo update-alternatives --config java

You have to do this for other jdk components too. These components are appletviewer, extcheck, idlj, jar, jarsigner, java, javac, javadoc, javah, javap, javaws, jconsole, jdb, jexec, jhat, jinfo, jmap, jps, jrunscript, jsadebugd, jstack, jstat, jstatd, keytool, mozilla-javaplugin.so, native2ascii, orbd, pack200, policytool, rmic, rmid, rmiregistry, schemagen, serialver, servertool, tnameserv, unpack200, wsgen, wsimport, xjc.

For further information, you can see the man pages for update-alternatives : man update-alternatives.

The command update-java-alternatives sets alternatives for java components and it seems to use update-alternatives for this.

EDIT: The answer above targets Java 6.

  • For Java 7, you have to add jcmd to the Java 6 list.
  • For Java 8, you have to add jcmd, jjs and jdeps to the Java 6 list.
  • For Java 9, you have to add jcmd, jjs, jdeps and jshell to the Java 6 list.

Note: update-java-alternatives won't work with manual installations. In any case, it doesn't look like it has any special abilities which update-alternatives doesn't have, except convenience.

As a graphical alternative to @AnwarShah's command-line method, consider using Gnome Alternatives (sudo apt-get install galternatives):

  • Start GAlternatives, select each java option, change it to manual, and Add your alternative (the example here is the IBM JRE installed in my home directory):

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I actually use these commands to install jdk1.6.0_25. (Check the link below for updated complete update-alternatives script)

sudo update-alternatives --install /usr/bin/java java /media/mydisk/jdk/bin/java 100
sudo update-alternatives --install /usr/bin/javac javac /media/mydisk/jdk/javac 100
sudo update-alternatives --install /usr/bin/java_vm java_vm /media/mydisk/jdk/bin/java_vm 100
sudo update-alternatives --install /usr/bin/jcontrol jcontrol /media/mydisk/jdk/bin/jcontrol 100
sudo update-alternatives --install /usr/bin/jexec jexec /media/mydisk/jdk/jre/lib/jexec 100
sudo update-alternatives --install /usr/bin/jexec jexec /media/mydisk/jdk/jre/lib/jexec 100 --slave /usr/share/binfmts/jar jexec-binfmt media/mydisk/jdk/jre/lib/javaws

And then you can use these command to set as default. Most probably, these aren't needed.

sudo update-alternatives --config java
sudo update-alternatives --config javac
sudo update-alternatives --config java_vm
sudo update-alternatives --config jcontrol
sudo update-alternatives --config jexec

You can get more help by using the command man update-alternatives or you can see the manual in your browser here

The purpose of the update-java-alternatives as described in the manual page is

update-java-alternatives updates all alternatives belonging to one runtime or development kit for the Java language. A package does provide these information of it's alternatives in /usr/lib/jvm/.<jname>.jinfo.

All the jdk tools are

appletviewer extcheck idlj jar jarsigner javac javadoc javah javap jconsole jdb jhat jinfo jmap jps jrunscript jsadebugd jstack jstat jstatd native2ascii rmic schemagen serialver wsgen wsimport xjc

Hope this will help you.


Update

I use this script to to extract a downloaded jdk, and use update-alternatives to fully set it. Modify the jdk file name and JAVA_DIR to suit your need. JAVA_DIR is the path to your extracted jdk folder.

#!/bin/sh

JAVA_DIR=/usr/lib/jvm/jdk1.8.0_65

# extract a jdk file named `jdk-8u65-linux-x64.tar.gz` from current directory to `/usr/lib/jvm`
sudo tar xvf jdk-8u65-linux-x64.tar.gz -C /usr/lib/jvm/

# update alternative links
sudo update-alternatives --quiet --install /usr/lib/xulrunner-addons/plugins/libjavaplugin.so xulrunner-1.9-javaplugin.so $JAVA_DIR/jre/lib/amd64/libnpjp2.so 100
sudo update-alternatives --quiet --install /usr/lib/mozilla/plugins/libjavaplugin.so mozilla-javaplugin.so $JAVA_DIR/jre/lib/amd64/libnpjp2.so 100
sudo update-alternatives --quiet --install /usr/bin/appletviewer appletviewer $JAVA_DIR/bin/appletviewer 100 --slave /usr/share/man/man1/appletviewer.1 appletviewer.1 $JAVA_DIR/man/man1/appletviewer.1
sudo update-alternatives --quiet --install /usr/bin/apt apt $JAVA_DIR/bin/apt 100 --slave /usr/share/man/man1/apt.1 apt.1 $JAVA_DIR/man/man1/apt.1
sudo update-alternatives --quiet --install /usr/bin/extcheck extcheck $JAVA_DIR/bin/extcheck 100 --slave /usr/share/man/man1/extcheck.1 extcheck.1 $JAVA_DIR/man/man1/extcheck.1
sudo update-alternatives --quiet --install /usr/bin/idlj idlj $JAVA_DIR/bin/idlj 100 --slave /usr/share/man/man1/idlj.1 idlj.1 $JAVA_DIR/man/man1/idlj.1
sudo update-alternatives --quiet --install /usr/bin/jar jar $JAVA_DIR/bin/jar 100 --slave /usr/share/man/man1/jar.1 jar.1 $JAVA_DIR/man/man1/jar.1
sudo update-alternatives --quiet --install /usr/bin/jarsigner jarsigner $JAVA_DIR/bin/jarsigner 100 --slave /usr/share/man/man1/jarsigner.1 jarsigner.1 $JAVA_DIR/man/man1/jarsigner.1
sudo update-alternatives --quiet --install /usr/bin/javac javac $JAVA_DIR/bin/javac 100 --slave /usr/share/man/man1/javac.1 javac.1 $JAVA_DIR/man/man1/javac.1
sudo update-alternatives --quiet --install /usr/bin/javadoc javadoc $JAVA_DIR/bin/javadoc 100 --slave /usr/share/man/man1/javadoc.1 javadoc.1 $JAVA_DIR/man/man1/javadoc.1
sudo update-alternatives --quiet --install /usr/bin/javah javah $JAVA_DIR/bin/javah 100 --slave /usr/share/man/man1/javah.1 javah.1 $JAVA_DIR/man/man1/javah.1
sudo update-alternatives --quiet --install /usr/bin/javap javap $JAVA_DIR/bin/javap 100 --slave /usr/share/man/man1/javap.1 javap.1 $JAVA_DIR/man/man1/javap.1
sudo update-alternatives --quiet --install /usr/bin/jconsole jconsole $JAVA_DIR/bin/jconsole 100 --slave /usr/share/man/man1/jconsole.1 jconsole.1 $JAVA_DIR/man/man1/jconsole.1
sudo update-alternatives --quiet --install /usr/bin/jdb jdb $JAVA_DIR/bin/jdb 100 --slave /usr/share/man/man1/jdb.1 jdb.1 $JAVA_DIR/man/man1/jdb.1
sudo update-alternatives --quiet --install /usr/bin/jhat jhat $JAVA_DIR/bin/jhat 100 --slave /usr/share/man/man1/jhat.1 jhat.1 $JAVA_DIR/man/man1/jhat.1
sudo update-alternatives --quiet --install /usr/bin/jinfo jinfo $JAVA_DIR/bin/jinfo 100 --slave /usr/share/man/man1/jinfo.1 jinfo.1 $JAVA_DIR/man/man1/jinfo.1
sudo update-alternatives --quiet --install /usr/bin/jmap jmap $JAVA_DIR/bin/jmap 100 --slave /usr/share/man/man1/jmap.1 jmap.1 $JAVA_DIR/man/man1/jmap.1
sudo update-alternatives --quiet --install /usr/bin/jps jps $JAVA_DIR/bin/jps 100 --slave /usr/share/man/man1/jps.1 jps.1 $JAVA_DIR/man/man1/jps.1
sudo update-alternatives --quiet --install /usr/bin/jrunscript jrunscript $JAVA_DIR/bin/jrunscript 100 --slave /usr/share/man/man1/jrunscript.1 jrunscript.1 $JAVA_DIR/man/man1/jrunscript.1
sudo update-alternatives --quiet --install /usr/bin/jsadebugd jsadebugd $JAVA_DIR/bin/jsadebugd 100 --slave /usr/share/man/man1/jsadebugd.1 jsadebugd.1 $JAVA_DIR/man/man1/jsadebugd.1
sudo update-alternatives --quiet --install /usr/bin/jstack jstack $JAVA_DIR/bin/jstack 100 --slave /usr/share/man/man1/jstack.1 jstack.1 $JAVA_DIR/man/man1/jstack.1
sudo update-alternatives --quiet --install /usr/bin/jstat jstat $JAVA_DIR/bin/jstat 100 --slave /usr/share/man/man1/jstat.1 jstat.1 $JAVA_DIR/man/man1/jstat.1
sudo update-alternatives --quiet --install /usr/bin/jstatd jstatd $JAVA_DIR/bin/jstatd 100 --slave /usr/share/man/man1/jstatd.1 jstatd.1 $JAVA_DIR/man/man1/jstatd.1
sudo update-alternatives --quiet --install /usr/bin/native2ascii native2ascii $JAVA_DIR/bin/native2ascii 100 --slave /usr/share/man/man1/native2ascii.1 native2ascii.1 $JAVA_DIR/man/man1/native2ascii.1
sudo update-alternatives --quiet --install /usr/bin/rmic rmic $JAVA_DIR/bin/rmic 100 --slave /usr/share/man/man1/rmic.1 rmic.1 $JAVA_DIR/man/man1/rmic.1
sudo update-alternatives --quiet --install /usr/bin/schemagen schemagen $JAVA_DIR/bin/schemagen 100 --slave /usr/share/man/man1/schemagen.1 schemagen.1 $JAVA_DIR/man/man1/schemagen.1
sudo update-alternatives --quiet --install /usr/bin/serialver serialver $JAVA_DIR/bin/serialver 100 --slave /usr/share/man/man1/serialver.1 serialver.1 $JAVA_DIR/man/man1/serialver.1
sudo update-alternatives --quiet --install /usr/bin/wsgen wsgen $JAVA_DIR/bin/wsgen 100 --slave /usr/share/man/man1/wsgen.1 wsgen.1 $JAVA_DIR/man/man1/wsgen.1
sudo update-alternatives --quiet --install /usr/bin/wsimport wsimport $JAVA_DIR/bin/wsimport 100 --slave /usr/share/man/man1/wsimport.1 wsimport.1 $JAVA_DIR/man/man1/wsimport.1
sudo update-alternatives --quiet --install /usr/bin/xjc xjc $JAVA_DIR/bin/xjc 100 --slave /usr/share/man/man1/xjc.1 xjc.1 $JAVA_DIR/man/man1/xjc.1
sudo update-alternatives --quiet --install /usr/bin/java-rmi.cgi java-rmi.cgi $JAVA_DIR/bin/java-rmi.cgi 100
sudo update-alternatives --quiet --install /usr/bin/ControlPanel ControlPanel $JAVA_DIR/jre/bin/ControlPanel 100
sudo update-alternatives --quiet --install /usr/bin/java java $JAVA_DIR/jre/bin/java 100
sudo update-alternatives --quiet --install /usr/bin/java_vm java_vm $JAVA_DIR/jre/bin/java_vm 100
sudo update-alternatives --quiet --install /usr/bin/javaws javaws $JAVA_DIR/jre/bin/javaws 100
sudo update-alternatives --quiet --install /usr/bin/jcontrol jcontrol $JAVA_DIR/jre/bin/jcontrol 100
sudo update-alternatives --quiet --install /usr/bin/keytool keytool $JAVA_DIR/jre/bin/keytool 100
sudo update-alternatives --quiet --install /usr/bin/pack200 pack200 $JAVA_DIR/jre/bin/pack200 100
sudo update-alternatives --quiet --install /usr/bin/policytool policytool $JAVA_DIR/jre/bin/policytool 100
sudo update-alternatives --quiet --install /usr/bin/rmid rmid $JAVA_DIR/jre/bin/rmid 100
sudo update-alternatives --quiet --install /usr/bin/rmiregistry rmiregistry $JAVA_DIR/jre/bin/rmiregistry 100
sudo update-alternatives --quiet --install /usr/bin/unpack200 unpack200 $JAVA_DIR/jre/bin/unpack200 100
sudo update-alternatives --quiet --install /usr/bin/orbd orbd $JAVA_DIR/jre/bin/orbd 100
sudo update-alternatives --quiet --install /usr/bin/servertool servertool $JAVA_DIR/jre/bin/servertool 100
sudo update-alternatives --quiet --install /usr/bin/tnameserv tnameserv $JAVA_DIR/jre/bin/tnameserv 100
sudo update-alternatives --quiet --install /usr/bin/jexec jexec $JAVA_DIR/jre/lib/jexec 100