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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