Question: Can I install and run igvtools on a server?
3
gravatar for Chenglin
4.9 years ago by
Chenglin110
United States
Chenglin110 wrote:

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. 

next-gen • 5.1k views
ADD COMMENTlink modified 21 months ago by steve2.3k • written 4.9 years ago by Chenglin110
1

igvtools is not equal with IGV

ADD REPLYlink written 11 months ago by lffu_003240
1
gravatar for Pierre Lindenbaum
4.9 years ago by
France/Nantes/Institut du Thorax - INSERM UMR1087
Pierre Lindenbaum123k wrote:

 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.

 

ADD COMMENTlink modified 4.9 years ago • written 4.9 years ago by Pierre Lindenbaum123k
1

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

 

ADD REPLYlink written 4.9 years ago by Chenglin110

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`)

ADD REPLYlink written 4.9 years ago by Pierre Lindenbaum123k

Thanks! I will try.

ADD REPLYlink written 4.9 years ago by Chenglin110

Thank you very much! I will try!

ADD REPLYlink written 4.9 years ago by Chenglin110
0
gravatar for steve
21 months ago by
steve2.3k
United States
steve2.3k wrote:

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:

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

ADD COMMENTlink modified 21 months ago • written 21 months ago by steve2.3k
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