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Commit 699172fa authored by Matt Shirley's avatar Matt Shirley
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Update links in docs to point to the bedtools2 github pages.

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docs/content/installation.rst
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......@@ -3,10 +3,10 @@ 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
``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/>`_.
......@@ -20,14 +20,14 @@ 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
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
The bedtools Makefiles utilize the GCC compiler. One should edit the
Makefiles accordingly if one wants to use a different compiler.
.. code-block:: bash
......@@ -36,10 +36,10 @@ on http://bedtools.googlecode.com/.
$ 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
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.
......@@ -48,11 +48,11 @@ 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/>`_,
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
**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.).
......@@ -60,8 +60,8 @@ 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
**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
......@@ -69,11 +69,11 @@ Charles for doing this.
apt-get install bedtools
**Homebrew**. Carlos Borroto has made BEDTools available on the 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.
......@@ -86,11 +86,11 @@ package manager for OSX.
Development versions
-----------------------------
The development version of bedtools is maintained in a Github
`repository <https://www.github.com/arq5x/bedtools>`_. Bug fixes are addressed
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
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
......@@ -98,7 +98,7 @@ 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
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.
......
docs/templates/page.html
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......@@ -5,7 +5,7 @@
{# note, currently these must be set... #}
{% set github_base_account = 'arq5x' %}
{% set github_project = 'bedtools' %}
{% set github_project = 'bedtools2' %}
{##################################################}
{# for plone-derived "edit me" & Google analytics #}
......@@ -137,4 +137,3 @@
{% endif %}
{%- endblock %}
docs/templates/sidebar-intro.html
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......@@ -3,9 +3,9 @@
</p>
<h3>Bedtools links</h3>
<ul>
<li><a target="_blank" href="https://github.com/arq5x/bedtools/issues">Issue Tracker</a></li>
<li><a target="_blank" href="https://github.com/arq5x/bedtools">Source @ GitHub</a></li>
<li><a target="_blank" href="https://bedtools.googlecode.com">Releases @ Google Code</a></li>
<li><a target="_blank" href="https://github.com/arq5x/bedtools2/issues">Issue Tracker</a></li>
<li><a target="_blank" href="https://github.com/arq5x/bedtools2">Source @ GitHub</a></li>
<li><a target="_blank" href="https://bedtools.googlecode.com">Old Releases @ Google Code</a></li>
<li><a target="_blank" href="http://groups.google.com/group/bedtools-discuss">Mailing list @ Google Groups</a></li>
<li><a target="_blank" href="http://www.biostars.org/show/tag/bedtools/">Queries @ Biostar</a></li>
<li><a target="_blank" href="http://quinlanlab.org">Quinlan lab @ UVa</a></li>
......@@ -13,10 +13,9 @@
</ul>
<h3>Sources</h3>
<p><a href="https://github.com/arq5x/bedtools">Browse source @ GitHub</a>.</p>
<p><a href="https://github.com/arq5x/bedtools2">Browse source @ GitHub</a>.</p>
<h3>Releases</h3>
<ul>
<li><a href="https://github.com/arq5x/bedtools2/releases">Stable releasees now @ Github</a></li>
<li><a href="https://github.com/arq5x/bedtools2/releases">Stable releases now @ Github</a></li>
</ul>
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