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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.

bedtools

Collectively, the bedtools utilities are a swiss-army knife of tools for a wide-range of genomics analysis tasks.

Interactive usage

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.

Installation notes

bedtools was installed using gcc 5.2 with the script install_bedtools.sh

Testing

No test suite was found.

Modulefile

  • 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