Installation — bedtools 2.31.0 documentation

# Installation

`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

### Downloading a pre-compiled binary

Note

1. The following approach will only work for Linux (non-OSX) systems.

Starting with release 2.28.0, we provide statically-linked binaries thast should work right away on Linux systems. Go to the releases page and look for the static binary named bedtools.static.binary. Right click on it, get the URL, then download it with wget or curl and you should be good to go.

As an example. First, download bedtools.static.binary from the latest release here

    mv bedtools.static.binary bedtools
    chmod a+x bedtools

### 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.

Note

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

    $ wget https://github.com/arq5x/bedtools2/releases/download/v2.29.1/bedtools-2.29.1.tar.gz
    $ tar -zxvf bedtools-2.29.1.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 tap homebrew/science
    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 https://github.com/arq5x/bedtools2.git

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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