SequenceTubeMap-Sapelo2: Difference between revisions
(Changed "Example Usage" section from "Sub-heading 2" to "Sub-heading 1".) |
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=== Running Program === | === Running Program === | ||
This program, like | This program, like others, should '''not''' be run on a submit node (''ss-sub2, ss-sub3, ss-sub4, etc''.). Instead, <u>run this program from within an interactive session</u>, which can be entered using the following command on a submit node:<syntaxhighlight lang="bash"> | ||
interact | interact | ||
</syntaxhighlight> | </syntaxhighlight> | ||
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==== Starting the server ==== | ==== Starting the server ==== | ||
Starting the program is as simple as | 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 <u>absolute path</u> of your data.'''<syntaxhighlight lang="bash"> | ||
export SERVER_PORT=<port>; export MOUNTED_DATA_PATH=<data_path>; sequenceTubeMap | export SERVER_PORT=<port>; export MOUNTED_DATA_PATH=<data_path>; sequenceTubeMap | ||
</syntaxhighlight> | </syntaxhighlight> | ||
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===== SSH Tunneling from Mac or Linux ===== | ===== 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 | 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:<syntaxhighlight lang="bash"> | ||
ssh -N -L PORT:HOST:PORT MyID@sapelo2.gacrc.uga.edu | ssh -N -L PORT:HOST:PORT MyID@sapelo2.gacrc.uga.edu | ||
</syntaxhighlight> | </syntaxhighlight> | ||
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===== SSH Tunneling from Windows ===== | ===== SSH Tunneling from Windows ===== | ||
Download the '''[https://the.earth.li/~sgtatham/putty/latest/x86/plink.exe 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 | Download the '''[https://the.earth.li/~sgtatham/putty/latest/x86/plink.exe 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:<syntaxhighlight lang="powershell"> | ||
plink -ssh -N -L PORT:HOST:PORT MyID@sapelo2.gacrc.uga.edu | plink -ssh -N -L PORT:HOST:PORT MyID@sapelo2.gacrc.uga.edu | ||
</syntaxhighlight> | </syntaxhighlight> | ||
==== Connecting to the Server ==== | ==== Connecting to the Server ==== | ||
To connect to the server, simply open a web browser <u>on the computer connected to the SSH tunnel</u>, and navigate to [http://localhost:3000 http://localhost:PORT] in the URL bar, | To connect to the server, simply open a web browser <u>on the computer connected to the SSH tunnel</u>, and navigate to [http://localhost:3000 http://localhost:PORT] in the URL bar, making sure to replace PORT with the actual port number used. | ||
=== Example Usage === | === Example Usage === | ||
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</syntaxhighlight>Third, he would take note of the IP address of the server on which his interactive session is currently running:<syntaxhighlight lang="bash"> | </syntaxhighlight>Third, he would take note of the IP address of the server on which his interactive session is currently running:<syntaxhighlight lang="bash"> | ||
hostname -i | hostname -i | ||
</syntaxhighlight>If he has data in a directory at the file path | </syntaxhighlight>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:<syntaxhighlight lang="bash"> | ||
export SERVER_PORT=8972; export MOUNTED_DATA_PATH="/home/itd72797/testData"; sequenceTubeMap | export SERVER_PORT=8972; export MOUNTED_DATA_PATH="/home/itd72797/testData"; sequenceTubeMap | ||
</syntaxhighlight>He would then set up an SSH tunnel by issuing the following from a separate terminal <u>'''on his personal computer'''</u> using the IP address he identified earlier:<syntaxhighlight lang="bash"> | </syntaxhighlight>He would then set up an SSH tunnel by issuing the following from a separate terminal <u>'''on his personal computer'''</u> using the IP address he identified earlier, the desired port, and his UGA MyID:<syntaxhighlight lang="bash"> | ||
ssh -N -L 8972:10.33.30.130:8972 itd72797@sapelo2.gacrc.uga.edu | ssh -N -L 8972:10.33.30.130:8972 itd72797@sapelo2.gacrc.uga.edu | ||
</syntaxhighlight>To connect, he would open a browser window on his personal computer and navigate to http://localhost:8972 . | </syntaxhighlight>To connect, he would open a browser window on his personal computer and navigate to http://localhost:8972 . | ||
Revision as of 09:43, 7 September 2023
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 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.
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