Warning
Iceberg was decommissioned on 30th November 2020. Users of Iceberg need to switch to using ShARC and/or Bessemer instead.
Collectively, the bedtools utilities are a swiss-army knife of tools for a wide-range of genomics analysis tasks.
After connecting to iceberg (see Establishing a SSH connection), start an interactive session with the qsh
command.
The latest version of bedtools (currently version 2.25.0) is made available with the command:
module load apps/gcc/5.2/bedtools
Alternatively, you can make a specific version available:
module load apps/gcc/5.2/bedtools/2.25.0
After that any of the bedtools commands can be run from the prompt.
bedtools was installed using gcc 5.2 with the script install_bedtools.sh
No test suite was found.
The module file is on the system at /usr/local/modulefiles/apps/gcc/5.2/bedtools/2.25.0
The contents of the module file is
#%Module1.0#####################################################################
##
## bedtools module file
##
## Module file logging
source /usr/local/etc/module_logging.tcl
##
proc ModulesHelp { } {
global bedtools-version
puts stderr " Adds `bedtools-$bedtools-version' to your PATH environment variable and necessary libraries"
}
set bedtools-version 2.25.0
module load compilers/gcc/5.2
prepend-path PATH /usr/local/packages6/apps/gcc/5.2/bedtools/2.25.0/bin