This page was last updated on Saturday, 12-Nov-2016 08:58:34 CST

Installation notes for IGV version 2.3.40

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Prerequisites

Java

Installation

1. $ ver="2.3.40"
2. $ cd /programinstallers/
3. $ wget -N http://www.broadinstitute.org/igv/projects/downloads/IGV_$ver.zip
4. $ wget -N http://www.broadinstitute.org/igv/projects/downloads/igvtools_$ver.zip
5. $ cd /usr/local/bin/
6. $ unzip /programinstallers/IGV_$ver.zip

   Archive:  /programinstallers/IGV_2.3.40.zip
      creating: IGV_2.3.40/
     inflating: IGV_2.3.40/igv.bat      
     inflating: IGV_2.3.40/igv.command  
     inflating: IGV_2.3.40/igv.sh       
     inflating: IGV_2.3.40/batik-codec__V1.7.jar  
     inflating: IGV_2.3.40/goby-io-igv__V1.0.jar  
     inflating: IGV_2.3.40/igv.jar      
     inflating: IGV_2.3.40/readme.txt

7. $ unzip /programinstallers/igvtools_$ver.zip

   Archive:  /programinstallers/igvtools_2.3.40.zip
      creating: IGVTools/
     inflating: IGVTools/igvtools.jar
     inflating: IGVTools/igvtools
     inflating: IGVTools/igvtools.bat
     inflating: IGVTools/igvtools_gui
     inflating: IGVTools/igvtools_gui.bat
     inflating: IGVTools/igvtools_gui.command
     inflating: IGVTools/igvtools_readme.txt
      creating: IGVTools/genomes/
     inflating: IGVTools/genomes/1kg_ref.chrom.sizes

   …
8. Create version-independent symlink
   $ ln -s IGV_$ver igv
9. Create a launcher for IGV for all users
   $ sudo nano /usr/share/applications/Bioinformatics/IGV.desktop
   

   #!/usr/bin/env xdg-open
   [Desktop Entry]
   Version=1.0
   Type=Application
   Terminal=false
   Exec=java -Xmx4g -jar /usr/local/bin/igv/igv.jar
   Name=IGV
   Comment=Integrative Genomics Viewer
   Icon=IGV_32.png
   Categories=Bioinformatics

10. Create a launcher for IGVTools for all users
    $ sudo nano /usr/share/applications/Bioinformatics/IGVTools.desktop
    

    #!/usr/bin/env xdg-open
    [Desktop Entry]
    Version=1.0
    Type=Application
    Terminal=false
    Exec=java -Xmx4g -jar /usr/local/bin/IGVTools/igvtools.jar gui
    Name=IGVTools
    Comment=Integrative Genomics Viewer Tools
    Icon=IGV_32.png
    Categories=Bioinformatics

11. Link to the icon referenced in the launcher, copy to /usr/share/pixmaps/