cytoscape java issues

[Mike Starr]

Hi there. I'm trying to install cytoscape on ubuntu. I'm pretty sure I have jre installed, and I've set the right environment variables. But the checker is yielding a negative for some reason. See attached text file for my bash session.

Thank you!

[Scooter Morris]

On 1/30/16 8:35 PM, Mike Starr wrote:

Hi there. I'm trying to install cytoscape on ubuntu. I'm pretty sure I have jre installed, and I've set the right environment variables. But the checker is yielding a negative for some reason. See attached text file for my bash session.

Thank you!

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Hi MIke,
    You may have installed a jre, but the "java" command is not on the path.  You need to make sure that /usr/bin/java or /usr/local/bin/java point to the java binary where you installed java.  You may need to run update-alternatives to select the appropriate location for java.

-- scooter

[Mike Starr]

But when I open a terminal and type "java", it looks like it runs properly. And echo $PATH shows the java binary location is there.

I am wondering if it is only valid when I have a terminal open, though? Like, the path pointer is activated in .bashrc. So, maybe the path isn't activated when I'm trying to install cytoscape?

[Scooter Morris]

On 01/31/2016 10:58 AM, Mike Starr wrote:

But when I open a terminal and type "java", it looks like it runs properly. And echo $PATH shows the java binary location is there.

What is your $PATH?

-- scooter

I am wondering if it is only valid when I have a terminal open, though? Like, the path pointer is activated in .bashrc. So, maybe the path isn't activated when I'm trying to install cytoscape?

On Saturday, January 30, 2016 at 8:39:12 PM UTC-8, Mike Starr wrote:

Hi there. I'm trying to install cytoscape on ubuntu. I'm pretty sure I have jre installed, and I've set the right environment variables. But the checker is yielding a negative for some reason. See attached text file for my bash session.

Thank you!

--

[Matthias König]

Hi Mike,
you should do the following on Ubuntu. This will also guarantee that you get the java updates.

Perform in terminal:

# remove openjdk
sudo apt-get -y purge openjdk*
sudo -E add-apt-repository -y ppa:webupd8team/java
sudo apt-get update
sudo apt-get install -y oracle-java8-installer
# switch java alternatives
sudo update-java-alternatives -s java-8-oracle
java -version
javac -version

Add to your /etc/bash.bashrc
export JAVA_HOME=/usr/lib/jvm/java-8-oracle

The best
Matthias

[Mike Starr]

Thanks.

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[Matthias König]

Posted instructions do not work anymore since oracle pulled all files.

If anybody has a simple solution to install oracle java 8 or 9 on a debian system like Ubuntu please let me know.

Best Matthias

Thanks.

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