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Installation
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``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
--------------------------

.....................................
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.

.. code-block:: bash

  $ 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.

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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 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/bedtools>`_. 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/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.

    .. image:: images/github-zip-button.png