Warning

Iceberg reaches end-of-life on 30th November 2020. If you are running jobs on Iceberg then you need to take urgent action to ensure that your jobs/scripts will run on ShARC or Bessemer. If you have never used ShARC or Bessemer then now is the time to test your scripts. Not all software on Iceberg is available on ShARC/Bessemer.

Plink¶

PLINK is a free, open-source whole genome association analysis toolset, designed to perform a range of basic, large-scale analyses in a computationally efficient manner.

Interactive Usage¶

After connecting to iceberg (see Establishing a SSH connection), start an interactive sesssion with the `qsh or qrsh command.

The latest version of Plink is made available with the command

module load apps/binapps/plink

Alternatively, you can load a specific version. To access the latest version (build date 20 Sep 2016)

module load apps/binapps/plink/1.90b3.42

An older build of Plink 1.9 (15 Jul 2015) is also available

module load apps/binapps/plink/1.90b3v

After making a version of Plink available you can then run it using plink on the command line.

Installation notes¶

These are primarily for administrators of the system.

Both versions of Plink were installed like so

$ver=1.90b3.42  # or 1.90b3v

mkdir plink_build
cd plink_build
unzip plink_linux_x86_64.zip
rm plink_linux_x86_64.zip
mkdir -p /usr/local/packages6/apps/binapps/plink/$ver
mv * /usr/local/packages6/apps/binapps/plink/$ver

The modulefiles are at /usr/local/modulefiles/apps/binapps/plink/$ver

#%Module10.2####################################################################
#

## Module file logging
source /usr/local/etc/module_logging.tcl
##

proc ModulesHelp { } {
        global ver

        puts stderr " Makes Plink $ver available to the system."
}

# Plink version (not in the user's environment)
set     ver     1.90b3.42  # or 1.90b3v

module-whatis   "sets the necessary Plink $ver paths"

prepend-path PATH /usr/local/packages6/apps/binapps/plink/$ver