Computational Cluster Programs

How to Run PLINK on ATS-Hosted Clusters

You can use any text editor to make the appropriate input files for PLINK, for example test.ped and test.map files.

Example of test.ped file:

1 1 0 0 1 1 A A G T
2 1 0 0 1 1 A C T G
3 1 0 0 1 1 C C G G
4 1 0 0 1 2 A C T T
5 1 0 0 1 2 C C G T
6 1 0 0 1 2 C C T T

Example of test.map file:

1 snp1 0 1
1 snp2 0 2

How to Run PLINK in Batch

To Run PLINK from the UCLA Grid Portal

PLINK is not available as a batch application from the UCLA Grid Portal.

To Run PLINK from the Cluster Head Node using the Queue Scripts

The easiest way to run PLINK in batch from the head node is to use the queue scripts. See Running a Batch Job on an ATS-Hosted Cluster for a discussion of the queue scripts and how they are used.

  1. First create a tiny script with your plink command and its arguments.

    Example:

    #!/bin/bash
    cd mydir
    plink --ped test.ped --map test.map --maf 0.05 --assoc

    where mydir is the directory where your data are located.

  2. Use the chmod command to mark your script executable.

    Example:

    chmod +x tinyscript

    where tinyscript is the name of your tiny script.

  3. Use job.q to create an SGE command file.

    Example:

    job.q

After job.q has built your SGE command file tinyscript.cmd it will ask you if you want to submit the job or not.

To Run PLINK from the Cluster Head Node Using SGE Comands

See Running a Batch Job on an ATS-Hosted Cluster for guidelines to follow to create the required SGE command file. Alternatively, you could create an SGE command file with the queue script listed above. After saving the command file, you can modify it if necessary. See Commonly-Used SGE Commands for a list of the most commonly used SGE commands.

How to Run PLINK Interactively

To Run PLINK Interactively from the UCLA Grid Portal

PLINK is not available as an interactive application from the UCLA Grid Portal.

To Run PLINK Interactively from a Cluster Interactive Node

To run PLINK interactively you must first connect to the cluster head node with X11 forwarding enabled.

  1. At the shell prompt, enter:
    qrsh

    Wait for qrsh to access a compute node.

  2. Change directory to where your data to be analyzed are located.
    cd mydir
  3. Enter the plink command with any arguments.
    plink arguments

    Example,

    plink -ped test.ped --map test.map --maf 0.05 --assoc

To Run gPLINK Interactively from a Cluster Interactive Node

  1. At the shell prompt, enter:
    qrsh

    Wait for qrsh to access a compute node.

  2. Enter:
    java -jar /u/local/bin/gPLINK2.jar

To Run PLINK Interactively with R and Rserve

If you need to use the functionalities of the statistical package R via Rserve (see PLINK v1.06 PDF documentation Chapter 19, "R plugin functions," around physical page 199) do the following:

  1. At the shell prompt, enter:
    qrsh

    Wait for qrsh to access a compute node.

  2. Enter:
    R-2.9.1 CMD Rserve

    Rserve will run daemonized as a server, please (verify with "ps aux | grep Rserve") PLEASE remember to kill the process when is not longer needed (get the process PID from the command "ps aux | grep Rserve" and then issue "kill [PID no]")

  3. Change directory to where your data to be analyzed are located.
    cd mydir
  4. Enter the plink command with any arguments.
    plink arguments
  5. After you finish, kill the Rserve daemon on the same node where you started it before you exit your qrsh session.
    kill process_id_number