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This page was last updated on Wednesday, 11-Feb-2015 08:46:33 CST

Installation notes for bedtools version 2.20.1

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Prerequisites

None

Installation

  1. $ sudo yum install BEDTools
    or
    $ sudo apt-get install bedtools
  2. Alternatively, install from GitHub
    $ cd /programinstallers
  3. $ ver="2.20.1"
  4. The -O parameter is optional if downloaded file name is a mess
    $ wget -N https://github.com/arq5x/bedtools2/releases/download/v$ver/bedtools-$ver.tar.gz -O bedtools-$ver.tar.gz
  5. $ tar -zxvf bedtools-$ver.tar.gz
  6. $ cd bedtools2
  7. $ make
  8. Manual install
    $ cp -puvr bin/* /usr/local/bin/
    ‘bin/annotateBed’ -> ‘/usr/local/bin/annotateBed’
    ‘bin/bamToBed’ -> ‘/usr/local/bin/bamToBed’
    ‘bin/bamToFastq’ -> ‘/usr/local/bin/bamToFastq’
    ‘bin/bed12ToBed6’ -> ‘/usr/local/bin/bed12ToBed6’
    ‘bin/bedpeToBam’ -> ‘/usr/local/bin/bedpeToBam’
    ‘bin/bedToBam’ -> ‘/usr/local/bin/bedToBam’
    ‘bin/bedToIgv’ -> ‘/usr/local/bin/bedToIgv’
    ‘bin/bedtools’ -> ‘/usr/local/bin/bedtools’
    ‘bin/closestBed’ -> ‘/usr/local/bin/closestBed’
    ‘bin/clusterBed’ -> ‘/usr/local/bin/clusterBed’
    ‘bin/complementBed’ -> ‘/usr/local/bin/complementBed’
    ‘bin/coverageBed’ -> ‘/usr/local/bin/coverageBed’
    ‘bin/expandCols’ -> ‘/usr/local/bin/expandCols’
    ‘bin/fastaFromBed’ -> ‘/usr/local/bin/fastaFromBed’
    ‘bin/flankBed’ -> ‘/usr/local/bin/flankBed’
    ‘bin/genomeCoverageBed’ -> ‘/usr/local/bin/genomeCoverageBed’
    ‘bin/getOverlap’ -> ‘/usr/local/bin/getOverlap’
    ‘bin/groupBy’ -> ‘/usr/local/bin/groupBy’
    ‘bin/intersectBed’ -> ‘/usr/local/bin/intersectBed’
    ‘bin/linksBed’ -> ‘/usr/local/bin/linksBed’
    ‘bin/mapBed’ -> ‘/usr/local/bin/mapBed’
    ‘bin/maskFastaFromBed’ -> ‘/usr/local/bin/maskFastaFromBed’
    ‘bin/mergeBed’ -> ‘/usr/local/bin/mergeBed’
    ‘bin/multiBamCov’ -> ‘/usr/local/bin/multiBamCov’
    ‘bin/multiIntersectBed’ -> ‘/usr/local/bin/multiIntersectBed’
    ‘bin/nucBed’ -> ‘/usr/local/bin/nucBed’
    ‘bin/pairToBed’ -> ‘/usr/local/bin/pairToBed’
    ‘bin/pairToPair’ -> ‘/usr/local/bin/pairToPair’
    ‘bin/randomBed’ -> ‘/usr/local/bin/randomBed’
    ‘bin/shuffleBed’ -> ‘/usr/local/bin/shuffleBed’
    ‘bin/slopBed’ -> ‘/usr/local/bin/slopBed’
    ‘bin/sortBed’ -> ‘/usr/local/bin/sortBed’
    ‘bin/subtractBed’ -> ‘/usr/local/bin/subtractBed’
    ‘bin/tagBam’ -> ‘/usr/local/bin/tagBam’
    ‘bin/unionBedGraphs’ -> ‘/usr/local/bin/unionBedGraphs’
    ‘bin/windowBed’ -> ‘/usr/local/bin/windowBed’
    ‘bin/windowMaker’ -> ‘/usr/local/bin/windowMaker’
    
  9. Cleanup
    $ cd ..
  10. $ rm bedtools2-$ver/ -rf