Docker_IGV

Docker container based on Ubuntu 18.04 to run IGV 4.2.11

See Docker file for comments and Docker and https://hub.docker.com/r/jysgro/igv/ for full description.

PURPOSE

Run IGV in a container. This came about when a Mac had Java 10 (!) but IGV requires Java 8 and could not be "downgraded."

IGV: Integrative Genomics Viewer - Broad Institute https://software.broadinstitute.org/software/igv/

IGV version installed: 2.4.11

Ubutu base used: ubuntu:18.04

Windows: see below

HOW TO RUN

Displaying the graphics from IGV requires X11, read below for Mac.
Windows users might be able to replace XQuartz with MobaXterm (not tested) or another X software.

IGV will run in the Unix graphical environment X11. Below is a method I found online to accomplish this. See How to show X11 windows with Docker on Mac by Marc Reichelt https://bit.ly/2usa0bB Archived 2019-12-04

Set-up:

• Install the latest XQuartz X11 server and run it
• Activate the option ‘Allow connections from network clients’ in XQuartz settings (menu: Xquartz > Preferences... and click on Security tab.)
• Crucial: Quit & restart XQuartz (to activate the setting)

Open a Terminal and run command: xhost + 127.0.0.1 or create and run the following script:

#!/bin/bash

# allow access from localhost
xhost + 127.0.0.1

Create Docker container and run IGV

To add shared volume add -v as shown below for a (blank) directory here called dockershare mapped onto the /root home directory on the container

docker run -it --rm -v /Users/$USER/dockershare:/root -e DISPLAY=docker.for.mac.localhost:0 jysgro/igv:2.4.11 /bin/bash

Note: the DISPLAY option host.docker.internal:0 from Marc Reichelt's article (links above) also works:

docker run -it --rm -v ${PWD}:/root -e DISPLAY=host.docker.internal:0 jysgro/igv:2.4.11 /bin/bash

This command will create the container with a shell. To start IGV simply issue the command: igv & and when done type exit to exit the container.

Thank you to Marc Reichelt (link above) for the very informative blog that makes this easy. Here is the important remark from his blog:

Notice the trick using docker.for.mac.localhost as display name. That’s a hostname that points to the host machine, so we don’t have to deal with changing IP addresses.

Indeed when I check inside the container:

# printenv DISPLAY
docker.for.mac.localhost:0
# 

WINDOWS

Tested on MobaXterm Home Edition on Windows10.

Requires to turn Xserver on by clicking on top right X11 logo.

Requires to use the IP number provided by MobaXterm at start-up, for example:

➤ Your computer drives are accessible through the /drives path     │
     │ ➤ Your DISPLAY is set to 172.16.45.139:0.0                         │
     │ ➤ When using SSH, your remote DISPLAY is automatically forwarded   │
     │ ➤ Your HOME folder is not persistent: it will be erased on restart │
     │ ➤ Each command status is specified by a special symbol (✔ or ✘)   

Hence the command would be:

docker run -it --rm -v ${PWD}:/root -e DISPLAY=172.16.45.139:0.0  jysgro/igv:2.4.11 /bin/bash

However the set-up is very slow and unstable.