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############
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) <http://mxcl.github.com/homebrew/>`_.
--------------------------
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 <https://github.com/arq5x/bedtools2/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 <https://github.com/arq5x/bedtools2/releases>`_
.. code-block:: bash
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 <https://github.com/arq5x/bedtools2/>`_ under
the `releases <https://github.com/arq5x/bedtools2/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.
.. code-block:: bash
$ 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) <http://mxcl.github.com/homebrew/>`_,
``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.).
.. code-block:: bash
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.
.. code-block:: bash
apt-get install bedtools
**Homebrew**. Carlos Borroto has made BEDTools available on the bedtools
package manager for OSX.
.. code-block:: bash
brew tap homebrew/science
brew install bedtools
**MacPorts**. Alternatively, the MacPorts ports system can be used to install BEDTools on OSX.
.. code-block:: bash
port install bedtools
-----------------------------
Development versions
-----------------------------
The development version of bedtools is maintained in a Github
`repository <https://www.github.com/arq5x/bedtools2>`_. 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:
.. code-block:: bash
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.
.. image:: images/github-zip-button.png
|
