IGViewer on Remote Environments¶

FARM¶

To visulaise BAM files available on the FARM first you need to install some software depending on your local machine.

Mac¶

You will need to install the software xquartz. This can either be done from the Sanger Self Serivce app on your machine or from the xquartz releases page.

Windows¶

You will need to install the software MobaXterm Home edition.

Connecting to FARM¶

To enable IGViewer to be seen on your local machine, remote application forwarding is needed. This can be done by adding the -Y parameter when using SSH to connect to the FARM to enable trusted X11 forwarding. X11 forwarding is a mechanism that allows a user to start up remote applications, and then forward the application display to their local machine. The full command will become ssh -Y user99@farm5-login.

Once connected simply run IGViewer using /software/cellgeni/IGV_2.15.2/igv.sh /path/to/file.bam and the BAM file should be loaded into an IGViewer window on your local machine.

JupyterHub¶

To use IGViewer on JupyterHub, a python package called igv-notebook is used.

You need to install it using pip install igv-notebook

Copy the following code and change the paths to the local of your BAM files.

Note

Pip installations do not save between sessions, so every time you restart your instance you need to reinstall igv-notebook
The BAM files must be present on your Jupyter home folder (/home/jovyan) and not on a mounted FARM path
When completing url: and indexURL: fields, do not include /home/jovyan and part of the BAM path file.
- For example, /home/jovyan/bams/my.bam should be inputted as bams/my.bam.

import igv_notebook

igv_notebook.init()

b = igv_notebook.Browser(
  {
      "genome": "hg19",
      "locus": "chr22:24,376,166-24,376,456"
  }
)

b.load_track(
  {
      "name": "Local BAM",
      "url": "path/to/fibam",
      "indexURL": "path/to/bam/index",
      "format": "bam",
      "type": "alignment"
  })

b.zoom_in()