diff --git a/docs/content/installation.rst b/docs/content/installation.rst
index 511008008a2a5630cfcabab73966a80647dfd187..39341ac6b00fe986b78ffdfe20a2e90e57864034 100755
--- a/docs/content/installation.rst
+++ b/docs/content/installation.rst
@@ -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.
diff --git a/docs/templates/page.html b/docs/templates/page.html
index 4e1e3cb09af86eaa5cd81ee5a0b1e25f2bfdfdd3..023b320193a86711cc19e1598026a65c2af3d0bd 100644
--- a/docs/templates/page.html
+++ b/docs/templates/page.html
@@ -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 %}
-
diff --git a/docs/templates/sidebar-intro.html b/docs/templates/sidebar-intro.html
index ed9f59cf6ac7111d0e35295b6bba9ac2a9643ece..262da46e7bd131b06fe996d73725d45a954ccdf0 100644
--- a/docs/templates/sidebar-intro.html
+++ b/docs/templates/sidebar-intro.html
@@ -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>
-