SequenceTubeMap-Sapelo2
Category
Bioinformatics
Program On
Sapelo2
Version
20230906
Author / Distributor
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 other 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 setting the environment variables that define the port and data to, and running the server. Make sure to pass the absolute path to 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.
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 and MyID with your actual 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 and MyID with your actual 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:
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