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 https://github.com/arq5x/bedtools2/releases/download/v2.25.0/bedtools-2.25.0.tar.gz $ 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),
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
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
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
command, one can compile and install using the instructions above.