BioInfoExpert

Bioinformatics day-by-day

How to install Java and JavaWS in Linux

Posted on May 22, 2019 by lpryszcz

Last night I’ve learnt Oracle changed the Java licensing which broke all channels of installation typically used in Linux.

Still, you can obtain & install Java and JavaWS free-of-charge manually for personal and developmental use. This is how to proceed:

Download Java tar.gz from Oracle website. For most users Linux x64 would be the right choice.
Unpack the tar archive (you may need to change 8u211 into right version)

cd ~/Download
tar xpfz jre-8u211-linux-x64.tar.gz

Move folder to `/opt/java`

sudo mkdir -p /opt/java
sudo mv jre1.8.0_211 /opt/java

Remove or rename symbolic links if they exists

which java
which javaws
ls -la /usr/bin/java*
sudo rm /usr/bin/java*

Link new java version

sudo ln -s /opt/java/jre1.8.0_211/bin/java /usr/bin
sudo ln -s /opt/java/jre1.8.0_211/bin/javaws /usr/bin

Now everything should work just fine 🙂

GATK error: CommandLineGATK : Unsupported major.minor version 51.0

Posted on July 7, 2015 by lpryszcz

If you see an error: CommandLineGATK : Unsupported major.minor version 51.0), while running new GATK, this means you most likely need newer java. Either:

Install the latest java with apt-get (if you have root access and Ubuntu/Debian)

sudo apt-get install oracle-java9-installer

Or download JRE from Oracle website and and set up system $PATH
ie. if you have your JRE unpacked in ~/src/jre add these lines to your ~/.bashrc:

#java RE
export PATH=~/src/jre/bin:$PATH

And open new terminal window.

You can check installed JRE version with

java -version

The location of `java` binaries can be checked with

which java