Installing IGV on Bio-linux 8 - Installing All Dependancies At Once

Question

[venuraherath]

Hi,

I am wondering is there a way to install IGV on Biolinux without installing dependencies one by one? Thanks in advance.

Screenshot

[Ram]

Does biolinux have apt-get? That will take care of dependencies automatically.

[venuraherath]

Please see the attached image. I get the error unable to locate the package. PS: igv is available in ubuntu software center though.

[Ram]

Please read the how-to on adding images.

Answer 1

[venuraherath]

Thank you Folks!

I found the problem. It is because of the Java.

I installed Java using

sudo add-apt-repository ppa:webupd8team/java
sudo apt-get update
sudo apt-get install oracle-java8-installer

Then downloaded binary files from IGV website and executed igv.jnlp

Now it is running without any problems.

Cheers,

Venura

Answer 2

[dariober]

I don't think you need install IGV, you just download the binary distribution, unzip it and execute ./igv.sh

To make all users (a) able to execute (x) igv.sh:

chmod a+x igv.sh

Don't worry about the other files.

On Linux, you don't start IGV by double-clicking on an icon (or maybe you can...) rather you execute on terminal:

igv.sh # If igv.sh is on your PATH
OR
bash /path/to/igv.sh # If igv.sh is not executable
OR
/path/to/igv.sh # If executable but not on PATH

Then you will have the GUI starting. If you want to add igv.sh to your PATH copy or symlink igv.sh AND igv.jar to a directory on your PATH, e.g. ~/bin/ or /usr/local/bin/. To see which directories are on your PATH you can do echo $PATH

[rminhas]

Hi, I have downloaded and already unzip IGV. Now I have the following: batik-codec__V1.7.jar goby-io-igv__V1.0.jar igv.bat igv.command igv.jar igv.sh

I do not know how can I make this program executable. could you please help me?

[dariober]

Hello- See edited answer