1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
|
############
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
--------------------------
.....................................
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. 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.
.. code-block:: bash
$ 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) <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/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
|
