SequenceTubeMap-Sapelo2

Category

Bioinformatics

Program On

Sapelo2

Version

20230906

Author / Distributor

vgteam

Description

"A JavaScript module for the visualization of genomic sequence graphs. It automatically generates a "tube map"-like visualization of sequence graphs which have been created with vg."

Running Program

This program, like others, should not be run on a submit node (ss-sub2, ss-sub3, ss-sub4, etc.). Instead, run this program from within an interactive session, which can be entered using the following command on a submit node:

interact

Load Module

module load sequenceTubeMap/20230906-GCCcore-11.3.0

Obtain IP Address

Obtain the IP address of the server that will host sequenceTubeMap for use in a later step:

hostname -i

Starting the server

Starting the program is as simple as defining the port and data path in environment variables and running the server. Make sure to provide the absolute path of your data.

export SERVER_PORT=<port>; export MOUNTED_DATA_PATH=<data_path>; sequenceTubeMap

Configure SSH Tunnel

It will be necessary to use SSH tunneling to connect to the web frontend from within a web browser. Please note that this step is to be performed on your local computer. It is recommended to setup the SSH tunnel from a new, separate terminal.

Note: Successfully creating an SSH tunnel at the command line may cause the terminal to seem as though it froze or hung with no response, which is the expected behavior.

SSH Tunneling from Mac or Linux

From your local terminal, issue the following command while making sure to replace HOST with the actual IP address obtained in the previous step, PORT with the port number used, and MyID with your UGA MyID:

ssh -N -L PORT:HOST:PORT MyID@sapelo2.gacrc.uga.edu

SSH Tunneling from Windows

Download the plink program, open a command window--the current directory of this command window should contain the plink.exe file--and execute the following command, replacing HOST with the actual IP address obtained in the previous step, PORT with the port number used, and MyID with your UGA MyID:

plink -ssh -N -L PORT:HOST:PORT MyID@sapelo2.gacrc.uga.edu

Connecting to the Server

To connect to the server, simply open a web browser on the computer connected to the SSH tunnel, and navigate to http://localhost:PORT in the URL bar, making sure to replace PORT with the actual port number used.

Example Usage

If the user, itd72797, would like to host this program to visualize his data, he would first enter into an interactive session:

interact

Second, he would load the corresponding module:

module load sequenceTubeMap/20230906-GCCcore-11.3.0

Third, he would take note of the IP address of the server on which his interactive session is currently running:

hostname -i

If he has data in a directory at the file path /home/itd72797/testData and would like to host it on port 8972, he would execute the following from within the same interactive session:

export SERVER_PORT=8972; export MOUNTED_DATA_PATH="/home/itd72797/testData"; sequenceTubeMap

He would then set up an SSH tunnel by issuing the following from a separate terminal on his personal computer using the IP address he identified earlier, the desired port, and his UGA MyID:

ssh -N -L 8972:10.33.30.130:8972 itd72797@sapelo2.gacrc.uga.edu

To connect, he would open a browser window on his personal computer and navigate to http://localhost:8972 .

Documentation

Please reference the program's GitHub page at https://github.com/vgteam/sequenceTubeMap for further reading.

System

64-bit Linux