bedtools is intended to run in a “command line” environment on UNIX, LINUX and Apple OS X operating systems. Installing bedtools involves either downloading the source code and compiling it manually, or installing stable release from package managers such as homebrew (for OS X).

Installing stable releases

Compiling from source via Github

Stable, versioned releases of bedtools are made available on Github at the bedtools2 repository under the releases tab. The following commands will install bedtools in a local directory on an UNIX or OS X machine.


1. This example is based on version 2.25.0. For future releasese, you should replace the version number with the version you intend to install.

2. The bedtools Makefiles utilize the GCC compiler. One should edit the Makefiles accordingly if one wants to use a different compiler.

$ wget
$ tar -zxvf bedtools-2.25.0.tar.gz
$ cd bedtools2
$ make

At this point, one should copy the binaries in ./bin/ to either usr/local/bin/ or some other repository for commonly used UNIX tools in your environment. You will typically require administrator (e.g. “root” or “sudo”) privileges to copy to usr/local/bin/. If in doubt, contact you system administrator for help.

Installing with package managers

In addition, stable releases of bedtools are also available through package managers such as homebrew (for OS X), apt-get and yum.

Fedora/Centos. Adam Huffman has created a Red Hat package for bedtools so that one can easily install the latest release using “yum”, the Fedora package manager. It should work with Fedora 13, 14 and EPEL5/6 ( for Centos, Scientific Linux, etc.).

yum install BEDTools

Debian/Ubuntu. Charles Plessy also maintains a Debian package for bedtools that is likely to be found in its derivatives like Ubuntu. Many thanks to Charles for doing this.

apt-get install bedtools

Homebrew. Carlos Borroto has made BEDTools available on the bedtools package manager for OSX.

brew install bedtools

MacPorts. Alternatively, the MacPorts ports system can be used to install BEDTools on OSX.

port install bedtools

Development versions

The development version of bedtools is maintained in a Github repository. Bug fixes are addressed in this repository prior to release, so there may be situations where you will want to use a development version of bedtools prior to its being promoted to a stable release. One would either clone the repository with git, as follows and then compile the source code as describe above:

git clone

or, one can download the source code as a .zip file using the Github website. Once the zip file is downloaded and uncompressed with the unzip command, one can compile and install using the instructions above.

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