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 ShARC (see Establishing a SSH connection), start an interactive session with the qrshx command.

The latest version of bedtools (currently version 2.30.0) is made available with the command:

module load apps/bedtools/2.30.0/gcc-8.2-cmake-3.17.1

After this any of the bedtools commands can be run from the prompt.

Installation notes

Bedtools was installed using GCC 8.2 with the script /usr/local/packages/apps/bedtools/2.30.0/gcc-8.2-cmake-3.17.1/install_bedtools.sh

Modulefile

The module file is on the system at /usr/local/modulefiles/apps/bedtools/2.30.0/gcc-8.2-cmake-3.17.1

The contents of the module file is:

#%Module
proc ModulesHelp { } {
    puts stderr {

Description
===========
BEDTools: a powerful toolset for genome arithmetic.
The BEDTools utilities allow one to address common genomics tasks such as finding feature overlaps and
computing coverage.
The utilities are largely based on four widely-used file formats: BED, GFF/GTF, VCF, and SAM/BAM.


More information
================
 - Homepage: https://bedtools.readthedocs.io/
    }
}

module-whatis {Description: BEDTools: a powerful toolset for genome arithmetic.
The BEDTools utilities allow one to address common genomics tasks such as finding feature overlaps and
computing coverage.
The utilities are largely based on four widely-used file formats: BED, GFF/GTF, VCF, and SAM/BAM.}
module-whatis {Homepage: https://bedtools.readthedocs.io/}
module-whatis {URL: https://bedtools.readthedocs.io/}

set root /usr/local/packages/apps/bedtools/2.30.0/gcc-8.2-cmake-3.17.1


module load dev/gcc/8.2
module load dev/cmake/3.17.1/gcc-8.2

prepend-path    CMAKE_PREFIX_PATH               $root
prepend-path    PATH            $root/bin