2. Installation

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# 2. 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).

## 2.1. Installing stable releases

### 2.1.1. Compiling from source via Google Code

Stable, versioned releases of bedtools are made available The following commands will install `bedtools` in a local directory on an UNIX or OS X machine. Note that the “<version>” refers to the latest posted version number on http://bedtools.googlecode.com/.

Note

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

    $ curl http://bedtools.googlecode.com/files/BEDTools.<version>.tar.gz > BEDTools.tar.gz
    $ tar -zxvf BEDTools.tar.gz
    $ cd BEDTools-<version>
    $ 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.

### 2.1.2. 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

## 2.2. 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/bedtools.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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