Warning
Iceberg was decommissioned on 30th November 2020. Users of Iceberg need to switch to using ShARC and/or Bessemer instead.
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.
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.
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