Can I install and run igvtools on a server?

Question

[Chenglin]

I want to check a sequence in my NGS data using IGV. I am wondering if I can install and run this software on a server since all .bam files (which are huge) were stored on a server and it will take forever to download to my computer.

[lffu_0032]

igvtools is not equal with IGV

Answer 1

[steve]

You can run IGV from a remote server, provided that you have X11 installed on the remote server (https://en.wikipedia.org/wiki/X_Window_System) and an X11 window program on the local machine.

On a Mac, you would:

• make sure you have XQuartz installed

• ssh into your server with the -Y flag, e.g. ssh [e-mail] -Y

• start IGV on the remote server with the supplied igv.sh file as described here: https://software.broadinstitute.org/software/igv/download

If everything works, a window will pop up on your local computer, which will display the GUI for IGV running on the remote server. Note that since the entire interface & user interaction is being transmitted across your network, this can be a bit laggy and buggy, but it is tolerable for some basic poking around in large .bam files stored on your remote server. However I would not recommend using this extensively as the latency and XQuartz bugs will drive you crazy. You are better off either converting the large .bam files to some other format like bigwig which is smaller & useable locally, or look into the IGV Snapshot Automator script which I posted about here:

Automatic IGV snapshot script

source code here:

https://github.com/stevekm/IGV-snapshot-automator

Answer 2

[Pierre Lindenbaum]

remote bam files can be loaded from IGV: http://www.broadinstitute.org/software/igv/LoadData

load data from an HTTP URL: Select File>Load from URL. Enter the HTTP or FTP URL for a data file or sample information file, then click OK. Notes: For .bam, .tdf, and indexed file formats the server must support byte-range requests.

[Chenglin]

Hello Pierre,

Actually I have done all the bioinformatic work on a server in our University HPC server (http://www.hpc.lsu.edu/resources/hpc/system.php?system=SuperMike-II) and also generated data (including the .bam files, which I want to load onto IGV for checking the sequence) there. I am wondering if I can install and use IGV tool on the server. If yes so it will be easier to load the huge .bam file onto IGV. I hope you can understand what I mean. Thanks!

Chenglin

[Pierre Lindenbaum]

if I can install and use IGV tool on the server: yes you can if your shell+server support X-Window system (.eg: log to the server using ssh -X login@ip)

[Chenglin]

Thanks! I will try.

[Chenglin]

Thank you very much! I will try!