visualise-BAM-files-on-IGV.txt

# Aim: visualise with IGV BAM files that are stored on the HPC


# Step 1: This requires setting up the X Window system, which provides the basic framework for a graphical user interface (GUI) environment 



### Set up apps on mac for a GUI environment of the HPC
# first, download XQuartz (open-source implementation of X system on macOS) and install it on mac (https://github.com/XQuartz/XQuartz/releases/download/XQuartz-2.8.5/XQuartz-2.8.5.pkg)

# second, download and install X2Go Client on mac (https://code.x2go.org/releases/binary-macosx/x2goclient/releases/4.1.2.3/x2goclient-4.1.2.3.20230629.OSX_10_13.dmg

# open X2Go Client to set up a new session
# for Cambridge's HPC
Host: login-cpu.hpc.cam.ac.uk
Login: CRSid
SSH port: 22
Use RSA/DSA key for ssh connection: /path/on/local/machine/.ssh/id_rsa
Session Type: XFCE

# include password, passphrase and MFA code to successfully login



# Step 2: Set up IGV on HPC
# First, download and install IGV on HPC
	ssh user@login-cpu.hpc.cam.ac.uk
	cd bin # this is my choice, it could go somewhere else
	wget https://data.broadinstitute.org/igv/projects/downloads/2.16/IGV_Linux_2.16.1_WithJava.zip
	unzip IGV_Linux_2.16.1_WithJava.zip


# Second, test IGV on HPC via X2Go by starting a session
# open the terminal and starts IGV
bin/IGV_Linux_2.16.1/igv.sh


### Learn more:
# what is X forwarding?
https://en.wikipedia.org/wiki/X_Window_System
# read notes from other universities' training pages: https://hpc.mediawiki.hull.ac.uk/Training/X2Go_macOS and https://sysnews.ma.ic.ac.uk/configuring-and-using-x2g0.html
# read about X2Go Client: 
https://wiki.x2go.org/doku.php/doc:usage:start