Pong-Sapelo2

Program On

Sapelo2

Version

1.5

Author / Distributor

Pong

Description

"Fast analysis and visualization of latent clusters in population genetic data" Pong

Running Program

Versions

Please also refer to Running Jobs on Sapelo2.

Pong 1.5 is installed at /apps/eb/pong/1.5-foss-2020b-Python-3.8.6

To use pong 1.5, please load the module:

ml pong/1.5-foss-2020b-Python-3.8.6

To use pong on Sapelo2 with an interactive job

The port number for the pong server should be some random value between 8000 and 10000. Assign this value to the variable 'NOTEBOOKPORT' in the submission script below replacing 8888. Please do not use 8888. If more than one person uses that same value you cannot establish the ssh tunnel.

Sample steps to use pong 1.5, once you connect to Sapelo2, using pong's sample data:

interact
wget https://brown.edu/Research/Ramachandran_Lab/files/pong/pong-example-data_1kG-p3.zip
unzip pong-example-data_1kG-p3.zip
cd pong-example-data_1kG-p3
NOTEBOOKPORT=8888
IPUSED=$(hostname -i)
echo "NOTEBOOKPORT is " $NOTEBOOKPORT
echo "IPUSED is " $IPUSED
ml pong/1.5-foss-2020b-Python-3.8.6
pong -m pong_filemap -n pop_order_expandednames.txt -i ind2pop.txt -p 8888

After running the steps above, establish a another ssh tunnel from your desktop or laptop to sapelo2 login node at port NOTEBOOKPORT.

For Mac/Linux Users

If you are using a Linux or Apple machine for your desktop or laptop you can use the following command to establish the ssh tunnel

Make sure you replace NOTEBOOKPORT and IPUSED below with the port number and the IP address you are using (see the output of the echo commands above)

ssh -N -L NOTEBOOKPORT:IPUSED:NOTEBOOKPORT username@sapelo2.gacrc.uga.edu

Unless you have ssh key configured, you will be prompted for your MyID password and for Archpass Duo authentication. Once authentication is established, this session prompt will hang and you are ready to go to the next step.

For Windows Users

If you are using a Windows machine for your desktop or laptop download the plink program to use in place of the ssh client. The command for windows would be as follows: Assuming the plink.exe is in the current directory where you have a command window open.

Make sure you replace NOTEBOOKPORT and IPUSED below with the port number and the IP address you are using (see the output of the echo commands above)

plink -ssh -N -L NOTEBOOKPORT:IPUSED:NOTEBOOKPORT username@sapelo2.gacrc.uga.edu

Once you establish the ssh tunnel by running the command above you can access pong by going to http://localhost:NOTEBOOKPORT using the browser on your desktop or laptop (make sure you replace NOTEBOOKPORT with the port number you used in the interact session). The interact terminal might show something like this:

-------------------------------------------------------------------
                            p o n g
      by A. Behr, K. Liu, T. Devlin, G. Liu-Fang, and S. Ramachandran
                       Version 1.5 (2021)
-------------------------------------------------------------------
-------------------------------------------------------------------

Parsing input and generating cluster network graph
Matching clusters within each K and finding representative runs
For K=2, there is 1 mode across 8 runs.
For K=3, there is 1 mode across 8 runs.
For K=4, there are 2 modes across 8 runs.
For K=5, there is 1 mode across 8 runs.
For K=6, there are 3 modes across 8 runs.
For K=7, there are 3 modes across 8 runs.
For K=8, there are 2 modes across 8 runs.
Matching clusters across K
Finding best alignment for all runs within and across K
match time: 7.22s
align time: 0.02s
total time: 8.27s
-----------------------------------------------------------
pong server is now running locally & listening on port 8888
Open your web browser and navigate to http://localhost:8888 to see the visualization

Documentation

Details at http://brown.edu/Research/Ramachandran_Lab/projects/

System

64-bit Linux