73c5d1a5856c34c7d01f126fdc656d5f35084852
Merge parents b186692 47fe642
kate
  Mon Jan 23 12:08:13 2017 -0800
Merge branch 'staticPg-inc-rel' into staticPages

diff --cc src/hg/htdocs/template.html
index 807fd17,9f2ce31..e743481
--- src/hg/htdocs/template.html
+++ src/hg/htdocs/template.html
@@@ -1,110 -1,75 +1,116 @@@
  <!DOCTYPE html>
  
  <!-- template.html: Example HTML for a Genome Browser static page -->
  
  <!-- Style recommendations
  1. Capitalization: use only lowercase for HTML element names, attributes and values
  2. Quotes: Use double quotes for attribute values
  3. Whitespace: Use a new line for every block list or table element
  4. Indentation: Indent every child element 2 spaces
  5. Special characters: Don't use entity references (set editor to UTF-8), except < &
 +6. Limit lines to a maximum of 100 characters
  -->
  
  <!-- Page header -->
- <!--#set var="TITLE" value="GB Static Page Template" -->
- <!--#include virtual="/gbPageStart.html"-->
+ <!--#set var="title" value="GB Static Page Template" -->
+ 
+ <!-- Boilerplate to support mirror sites with non-standard GB docs install -->
+ <!--#if expr="$GB_DOCUMENT_ROOT" -->
+     <!--#include virtual="/gbDocs/inc/gbPageStart.html" -->
+ <!--#else -->
+     <!--#include virtual="/inc/gbPageStart.html" -->
+ <!--#endif -->
  
  <!-- Page content -->
 -<h1>Sample Genome Browser Static Page</h1>
 +<h1>Sample Genome Browser Static Page (h1)</h1>
  <p>
 -This is a standard paragraph ('p' element) of explanatory text.
 -<em>The remainder of this text is just filler</em>.
 -
 -Follow these citation guidelines when using applications from the Genome Browser
 -tool suite or data from the UCSC Genome Browser database in a research work that will
 -be published in a journal or on the Internet.
 -In addition to the relevant paper, please include a reference to the Genome Browser
 -website in your manuscript: <a href="index.html" target=_blank>http://genome.ucsc.edu/</a>.
 -Be sure to mention the release date of the genome assembly used in your work to faciliate
 -the examination of your data by reviewers and the readers.
 -Please do <strong>not</strong> include references to our development servers
 -(such as genome-test.cse.ucsc.edu) in published links or URLs.
 +This is a standard paragraph ('p' tag) of explanatory text.
 +The next part of the page demonstrates how to create a multi-column layout 
 +using the grid layout feature of bootstrap.css, a widely used stylesheet which is now 
 +included in the browser static pages.
  </p>
  
  <!-- Sections -->
  <!-- In this example, two of same size, so use 6 columns of 12 total in grid -->
  
  <div class="row">
  
  <!-- Left column -->
    <div class="col-md-6">
 -    <h2>Page section</h2>
 +    <h2>Page section (h2)</h2>
      <p>
 -    This is one of two subsections, formatted as equal-sized columns via the grid layout feature of
 -    bootstrap.css, a commonly used style sheet.
 -    The grid contains 12 columns; column widths are specified using classes 'col-md-1' through 
 -    'col-md-12'. This example contains two divs, each assigned class 'col-md-6', within a 'row' div.
 +    This is one of two subsections, formatted as equal-sized columns.
 +    The bootstrap grid contains 12 columns; column widths are specified using 
 +    classes 'col-md-1' through 'col-md-12'. 
 +    This example contains two divs, each assigned class 'col-md-6', within a 'row' div.
 +    </p>
 +    <p>
 +    NOTE: The two columns are displayed only on wide screens.  On small screens, the sections will be
 +    stacked vertically (a feature of bootstrap responsive layout).
      </p>
  
 -<!-- Preformatted code example -->
 +
 +      <h3>Subsection (h3)</h3>
      <p>
 -    Here is some code:
 +    This is the next level, a subsection.  Use an 'h3' tag for this. To structure content
 +    below this level use a list, table, or titled paragraph:
      </p>
 -<pre><code>sudo -i
 -bash browserSetup.sh install</code></pre>
 +
 +    <h6>Titled paragraph</h6>
 +    <p>
 +    Use the 'h6' tag at any level in the section hierarchy to precede a paragraph with a bolded title.
 +    </p>
 +
 +      <h3>Lists</h3>
 +<p>
 +The description of lists below is formatted as an HTML definition list. Use this format when defining terms or phrases.  (You will not see this much in our current pages -- instead, this type of text was usually styled ad-hoc using 'strong' and 'br' tags).
 +</p>
 +<dl>
 +<dt>Definition list</dt>
 +<dd>
 +Use the 'dl' tag to enclose the full list, then 'dt' for each item term, and 'dd' for each item definition.
 +</dd>
 +<dt>Bulleted list</dt>
 +Use the 'ul' (unordered list tag) to enclose the full list, then 'li' for each list item.
 +<dd>
 +<dd>
 +<dt>Numbered list</dt>
 +<dd>
 +Use the 'ol' (ordered list) tag to enclose the full list, then 'li' for each list item.
 +</dd>
 +
 +</dl>
 +  </div>
 +
 +<!-- Right column -->
 +  <div class="col-md-6">
 +    <h2>Another section</h2>
 +
 +<!-- Subsections -->
 +      <h3>List Examples</h3>
 +        <p>
 +        Here is a bulleted list ('ul' and 'li' elements). To suppress the 'bullet' add the
 +        class 'gbsNoBullet' to the 'ul' tag.
 +        </p>
 +<!-- Bulleted list example -->
 +      <ul>
 +        <li>red</li>
 +        <li>white</li>
 +        <li>blue</li>
 +      </ul>
 +<p>
  
  <!-- Numbered list example -->
      <p>
      Here is a numbered list ('ol' and 'li' elements):
      </p>
      <ol>
        <li>
        <strong>chrom</strong> - The name of the chromosome (e.g. chr3, chrY, chr2_random) or 
        scaffold (e.g. scaffold10671).</li>
        <li>
        <strong>chromStart</strong> - The starting position of the feature in the chromosome or 
        scaffold.  The first base in a chromosome is numbered 0.</li>
        <li>
        <strong>chromEnd</strong> - The ending position of the feature in the chromosome or scaffold. 
        The <em>chromEnd</em> base is not included in the display of the feature. 
@@@ -124,49 -103,40 +130,54 @@@
          <th>Total</th>
        </tr>
        <tr>
          <td>Chromosomes</td>
          <td>261</td>
        </tr>
        <tr>
          <td>Haplotypes</td>
          <td>261</td>
        </tr>
        <tr>
          <td>Unlocalized contigs</td>
          <td>1270</td>
        </tr>
      </table>
 -  </div>
 -</div>
 +
 +<!-- Preformatted code example -->
 +      <h3>Code</h3>
 +    <p>
 +    Here is some code in a preformatted section ('pre' and 'code' tags):
 +    </p>
 +
 +<pre><code>sudo -i
 +bash browserSetup.sh install</code></pre>
 +
 +<p>
 +And here is some text with a <code>bit of code</code> embedded (just the 'code' tag)..
 +</p>
 +
 +  </div> <!-- end column -->
 +</div>   <!-- end row -->
  
  <h2>Section with a picture and caption</h2>
  <p>
  Use the 'img' tag to include the picture file, which is typically in .jpg or .png format.
 -Images should normally have their 'width' and 'height' attributes set in the 'img' tag.
 +Images should normally have their 'width' and 'height' attributes set in the 'img' lement.
  To right-align the image add the 'gbsAlignRight' class.
  The caption is a 'p' element, which is assigned the 'gbsCaption' class.
  </p>
  <div class="row">
    <div class="col-md-12">
        <img src= "images/gbstaff16.jpg" width=499 height=299 alt="Genome Browser staff">
      <p class="gbsCaption">
      Browser staff in native habitat.
      </p>
    </div>
  </div>
  
- <!--#include virtual="/gbPageEnd.html"-->
+ <!--#if expr="$GB_DOCUMENT_ROOT" -->
+     <!--#include virtual="/gbDocs/inc/gbPageEnd.html" -->
+ <!--#else -->
+     <!--#include virtual="/inc/gbPageStart.html" -->
+ <!--#endif -->
+