How do I run IGV on the sever

Question

[mujiangxielu]

I use putty to connected to the sever, I already use wget and unzip to have IGV and Java11 download on my sever, and add them in the environment variables by edit bashrc file.

But when I try to run IGV, I got an error:The program 'igv' is currently not installed. To run 'igv' please ask your administrator to install the package 'igv' please tell me what to do to have it run, thanks!

Answer 1

[mujiangxielu]

I know why the igv not found issue occured. I should add the path to igv.sh included igv.sh tothe environment variables but not only the directory.

add this in the bashrc file the I can open IGV by input igv in shell

alias igv='bash /aboulute/path/to/igv.sh'

Answer 2

[GenoMax]

If you are logging into a remote server then you will need to have a X11 windows program on your local machine. Simple PuTTy is not enough. You will need to amend your $PATH to take care of the igv not found issue.

See this prior thread for more: How to Run IGV on Linux Remote Machine

[mujiangxielu]

Thank you very much!