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