added R lessons

CONTRIBUTING.md

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+# Contributing New Material
+
+Data Carpentry is an open source project, and we welcome contributions of all
+kinds: new and improved lessons, bug reports, and small fixes to existing
+material are all useful.
+
+By contributing, you are agreeing that Data Carpentry may redistribute your 
+work under [these licenses](LICENSE.md).
+
+
+**Table of Contents**
+
+*   [Working With GitHub](#working-with-github)
+*   [Locations and Formats](#locations-and-formats)
+*   [FAQ](#faq)
+
+
+## Working With GitHub
+
+1.  Fork the `datacarpentry/lesson-name` repository on GitHub.  
+
+2.  The default branch in our lessons is `gh-pages`. Create a 
+    new branch for your changes.  
+    Give your branch a meaningful name,
+    such as `fixing-typos-in-shell-lesson`
+    or `adding-tutorial-on-visualization`.
+
+3.  Clone this repository and branch to work with it on your computer.  
+    git clone the repository with -b 'branch name'
+
+4.  Make your changes, commit them, and push them to your repository on GitHub.
+
+5.  Send a pull request to the `gh-pages` branch of the main datacarpentry
+    repository at http://github.com/datacarpentry/lesson-name. This can
+    be done through the github web interface. 
+
+If it is easier for you to send them to us some other way,
+please mail us at
+[[email protected]](mailto:[email protected]).
+Given a choice between you creating content or wrestling with Git,
+we'd rather have you doing the former.
+
+
+## Locations and Formats
+
+Every lesson has a repository of its own, while individual topics are files
+in that directory.  For example, the `shell-ecology` directory holding our
+introduction to the shell for ecology contains the files `00-intro.md`, 
+`01-filedir.md` and so on.  (We use two digits followed by a one-word topic 
+key to ensure files
+appear in the right order when listed.)
+
+Lessons may be written in Markdown, as IPython Notebooks, or in other formats.
+However, as explained in [the README file](README.md), Jekyll (the tool GitHub
+uses to create websites) only knows how to handle Markdown and HTML.  if some
+other format is used, the author of the lesson must add the generated Markdown
+to the repository.  This ensures that people who *aren't* familiar with some
+format don't have to install the tools needed to work with it (e.g., R
+programmers don't have to install the IPython Notebook).
+
+> If a lesson is in a format we don't already handle, the author must also add
+> something to the Makefile to re-create the Markdown from the source.  Please
+> check with us if you plan to do this.
+
+
+## Formatting of the material
+
+To ensure a consistent formatting of the lessons, we recommend the following
+guidelines:
+* No trailing white space
+* Wrap lines at 80 characters (unless it breaks URLs)
+* Use unclosed atx style headers (see below)
+
+## FAQ
+
+*   *Where can I get help?*
+    <br/>
+    Mail us at [[email protected]](mailto:[email protected])
+

Ecoli_metadata.txt

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+Sample_Name_s	clade	generation	cit	amplification	strain_s	Run_sCZB152	Citplus	33000	yes	yes	REL606	SRR097977CZB154	Citplus	33000	yes	yes	REL606	SRR098026CZB199	C1	33000	no	no	REL606	SRR098027REL1166A		2000			REL606	SRR098028ZDB409		5000			REL606	SRR098281ZDB446	UC	15000	no	no	REL606	SRR098283

README.md

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-# R-genomics
-Lesson on data analysis and visualization in R for genomics
+# R Genomics	
 
+This is a repository for Data Carpentry R Genomics lessons
 
+Lesson is rendered here:
+
+http://tracykteal.github.io/R-genomics/

_config.yml

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+markdown: redcarpet
+redcarpet:
+  extensions: ["tables"]

_includes/anySetup.html

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+
+<div id="any">
+
+  <h3>Setting Up</h3>
+
+    <p>
+      This workshop may require some software installation, and details will be included here.
+
+    </p>
+
+
+    <div class="col-md-4">
+      <h4 id="windows">Windows</h4>
+      <ol>
+	<li>
+          Download and install 
+	</li>
+	<li>
+
+	</li>
+      </ol>
+    </div>
+
+
+    <div class="col-md-4">
+      <h4 id="macosx">Mac OS X</h4>
+      <ol>
+	<li>
+          Download and install
+	</li>
+	<li>
+
+	</li>
+      </ol>
+    </div>
+
+
+
+    <div class="col-md-4">
+      <h4 id="linux">Linux</h4>
+      <ol>
+	<li>
+	  Download and install
+	</li>
+	<li>
+
+	</li>
+      </ol>
+    </div>
+
+
+</div> 

_includes/banner.html

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+<div class="banner">
+  <a href="http://datacarpentry.org" title="Data Carpentry">
+    <img alt="Data Carpentry banner" src="{{page.root}}/img/DC1_logo_small.png" height="50px" />
+  </a>
+</div>

_includes/footer.html

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+<div class="footer">
+  <a class="label swc-blue-bg" href="{{site.facebook_url}}">Facebook</a>
+  <a class="label swc-blue-bg" href="{{site.google_plus_url}}">Google+</a>
+  <a class="label swc-blue-bg" href="{{site.twitter_url}}">Twitter</a>
+  <a class="label swc-blue-bg" href="{{site.github_url}}">GitHub</a>
+  <a class="label swc-blue-bg" href="{{page.root}}/LICENSE.html">License</a>
+  <a class="bugreport label swc-blue-bg" href="mailto:{{site.contact}}?subject=bug%20in%20{{page.path}}">Bug Report</a>
+</div>

_includes/header.html

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+<link rel="shortcut icon" type="image/x-icon" href="{{page.root}}/favicon.ico" />
+<link href="{{page.root}}/css/bootstrap/bootstrap.css" rel="stylesheet" />
+<meta name="viewport" content="width=device-width, initial-scale=1.0" />
+<link href="{{page.root}}/css/bootstrap/bootstrap-responsive.css" rel="stylesheet" />
+<link rel="stylesheet" type="text/css" href="{{page.root}}/css/swc.css" />
+<link rel="stylesheet" type="text/css" href="{{page.root}}/css/swc-bootstrap.css" />
+<meta charset="UTF-8" />
+<meta http-equiv="last-modified" content="{{site.timestamp}}" />
+<!-- HTML5 shim, for IE6-8 support of HTML5 elements -->
+<!--[if lt IE 9]>
+  <script src="http://html5shim.googlecode.com/svn/trunk/html5.js"></script>
+<![endif]-->

_includes/javascript.html

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+<!-- Le javascript
+================================================== -->
+<!-- Placed at the end of the document so the pages load faster -->
+<script src="{{page.root}}/js/jquery-1.9.1.min.js"></script>
+<script src="{{page.root}}/js/bootstrap/bootstrap.min.js"></script>

_includes/lesson-index.html

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+* [Lesson 00 Name](./00-lesson-00-name.html)
+* [Lesson 01 Name](./01-lesson-01-name.html)
+* [Lesson 02 Name](./02-lesson-02-name.html)
+* [Lesson 03 Name](./03-lesson-03-name.html)

_includes/pythonSetup.html

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+
+<div id="python"> <!-- Start of 'Python' section. Remove the third paragraph if
+           the workshop will teach Python using something other than
+           the IPython notebook.
+           Details at http://ipython.org/ipython-doc/2/install/install.html#browser-compatibility -->
+  <h3>Setting Up Python</h3>
+
+  <p>
+    <a href="http://python.org">Python</a> is a popular language for
+    scientific computing, and great for general-purpose programming as
+    well.  Installing all of its scientific packages individually can be
+    a bit difficult, so we recommend an all-in-one installer.
+  </p>
+
+    <p>
+      Regardless of how you choose to install it,
+      <strong>please make sure you install Python version 2.x and not version 3.x</strong>
+      (e.g., 2.7 is fine but not 3.4).
+      Python 3 introduced changes that will break some of the code we teach during the workshop.
+    </p>
+
+    <p>
+      We will teach Python using the IPython notebook, a programming environment
+      that runs in a web browser. For this to work you will need a reasonably
+      up-to-date browser. The current versions of the Chrome, Safari and
+      Firefox browsers are all <a
+      href='http://ipython.org/ipython-doc/2/install/install.html#browser-compatibility'>supported</a>
+      (some older browsers, including Internet Explorer version 9
+      and below, are not).
+    </p>
+
+
+    <div class="col-md-4">
+      <h4 id="python-windows">Windows</h4>
+      <ul>
+	<li>
+          Download and
+          install <a href="https://store.continuum.io/cshop/anaconda/">Anaconda</a>.
+	</li>
+	<li>
+          Download the default Python 2 installer (do not follow the link to version 3).
+	  Use all of the defaults for installation
+          <em>except</em> make sure to check
+	  <b>Make Anaconda the default Python</b>.
+	</li>
+      </ul>
+    </div>
+
+
+
+    <div class="col-md-4">
+      <h4 id="python-macosx">Mac OS X</h4>
+      <ul>
+	<li>
+          Download and
+          install <a href="https://store.continuum.io/cshop/anaconda/">Anaconda</a>.
+	</li>
+	<li>
+          Download the default Python 2 installer (do not follow the link to version 3).
+	  Use all of the defaults for installation.
+	</li>
+      </ul>
+    </div>
+
+
+
+    <div class="col-md-4">
+      <h4 id="python-linux">Linux</h4>
+      <p>
+	We recommend the all-in-one scientific Python installer
+	<a href="http://continuum.io/downloads.html">Anaconda</a>.
+	(Installation requires using the shell and if you aren't
+	comfortable doing the installation yourself just
+	download the installer and we'll help you at the boot
+	camp.)
+      </p>
+      <ol>
+	<li>
+          Download the installer that matches your operating
+          system and save it in your home folder.
+	  Download the default Python 2 installer (do not follow the link to version 3).
+	</li>
+	<li>
+          Open a terminal window.
+	</li>
+	<li>
+          Type <pre>bash Anaconda-</pre> and then press
+          tab. The name of the file you just downloaded should
+          appear.
+	</li>
+	<li>
+          Press enter. You will follow the text-only prompts.  When
+          there is a colon at the bottom of the screen press the down
+          arrow to move down through the text. Type <code>yes</code> and
+          press enter to approve the license. Press enter to approve the
+          default location for the files. Type <code>yes</code> and
+          press enter to prepend Anaconda to your <code>PATH</code>
+          (this makes the Anaconda distribution the default Python).
+	</li>
+      </ol>
+    </div>
+
+
+</div> 

_includes/rSetup.html

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+<div id="r"> <!-- Start of 'R' section. -->
+  <h3>R</h3>
+
+  <p>
+    <a href="http://www.r-project.org">R</a> is a programming language
+    that is especially powerful for data exploration, visualization, and
+    statistical analysis. To interact with R, we use
+    <a href="http://www.rstudio.com/">RStudio</a>.
+  </p>
+
+  <div class="row">
+    <div class="col-md-4">
+      <h4 id="r-windows">Windows</h4>
+      <p>
+	Install R by downloading and running
+	<a href="http://cran.r-project.org/bin/windows/base/release.htm">this .exe file</a>
+	from <a href="http://cran.r-project.org/index.html">CRAN</a>.
+	Also, please install the
+	<a href="http://www.rstudio.com/ide/download/desktop">RStudio IDE</a>.
+      </p>
+    </div>
+    <div class="col-md-4">
+      <h4 id="r-macosx">Mac OS X</h4>
+      <p>
+	Install R by downloading and running
+	<a href="http://cran.r-project.org/bin/macosx/R-latest.pkg">this .pkg file</a>
+	from <a href="http://cran.r-project.org/index.html">CRAN</a>.
+	Also, please install the
+	<a href="http://www.rstudio.com/ide/download/desktop">RStudio IDE</a>.
+      </p>
+    </div>
+    <div class="col-md-4">
+      <h4 id="r-linux">Linux</h4>
+      <p>
+	You can download the binary files for your distribution
+	from <a href="http://cran.r-project.org/index.html">CRAN</a>. Or
+	you can use your package manager (e.g. for Debian/Ubuntu
+	run <code>sudo apt-get install r-base</code> and for Fedora run
+        <code>sudo yum install R</code>).  Also, please install the
+	<a href="http://www.rstudio.com/ide/download/desktop">RStudio IDE</a>.
+      </p>
+    </div>
+  </div>
+</div> <!-- End of 'R' section. -->