Apps for IGB

The IGB Command Socket App opens up a socket on port 7084 for receiving scripting commands. This feature can be useful for orchestrating IGB scripting commands for bash scripts or for interfacing with languages like R.

Example Bash Script for looping through a list of genomic coordinates and exporting an image from the Integrated Genome Browser using the 'Command Socket' plugin

#!/bin/sh
# This script requires the 'Command Socket' plugin be enabled from the 'Plugins' tab
locationsOfInterest=('chr1:2,246,108-2,271,426' 'chr2:9,488,819-9,531,295' 'chr3:8,407,934-8,454,574' )

function igbCommand(){
  echo "$1" | ncat 127.0.0.1 7084
}

igbCommand 'genome A_thaliana_Jun_2009'

sleep 0.5

for i in "${locationsOfInterest[@]}"
do
        igbCommand 'goto '$i''
        igbCommand 'snapshotmainView /tmp/igbImage-'$i'.png'
        sleep 2
done

• Loraine Lab