Styjun

I have succesfully installed the IGV program using the terminal, but for some time have not been able to start it no matter what i try. What are the necessary commands to achieve this?
sudo apt install IGV has worked and command output has run smoothly.

So far i have installed it multiple times, trying to figure out what is the problem, however i haven't gotten anywhere.

Can anybody help me?

Note: I recommend that you remove the previously installed IGV package before performing the following steps to avoid conflicts. Simply execute:

$ sudo apt remove --purge igv

First you need at least Java 11 installed (because of incompatibility with previous versions).

Installing the Default JRE/JDK

The easiest option for installing Java is to use the version packaged with Ubuntu. By default, Ubuntu 18.04 includes Open JDK, which is an open-source variant of the JRE and JDK.

To install this version, first update the package index and upgrade your system:

$ sudo apt update && apt upgrade

Next, check if Java is already installed:

$ java -version

If Java is not currently installed, you'll see an output similar to this:

bash: java: Command not found.

Execute the following command to install OpenJDK:

$ sudo apt install default-jre

This command will install the Java Runtime Environment (JRE). You'll then be able to run almost all Java software.

Now verify the installation with:

$ java -version

You'll see the following output (the versions may differ):

openjdk version "11.0.3" 2019-04-16
OpenJDK Runtime Environment (build 11.0.3+1-Ubuntu-3ubuntu1)
OpenJDK 64-Bit Server VM (build 11.0.3+1-Ubuntu-3ubuntu1, mixed mode)

The next step is to download IGV and unzip the file to a location of your choice (for example to /opt).

Then open that directory in a terminal (via "Open in Terminal") or launch a terminal and switch to the directory via cd command (the name of the directory may differ):

$ cd /opt/IGV_Linux_2.5.0

To start IGV (from the command line), execute the following:

$ java --module-path=lib -Xmx4g @igv.args --module=org.igv/org.broad.igv.ui.Main

Alternatively, you can start IGV with the script igv.sh inside the IGV_Linux_2.5.0 directory. You might have to make the script executable first by typing:

$ sudo chmod a+x igv.sh

Note: The command line has become a bit more complex with Java 11 compared to previous versions.