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2        "http://www.w3.org/TR/html4/loose.dtd">
3<html>
4<head>
5<title>Installing Gmaj</title>
6<meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1">
7<meta http-equiv="Content-Style-Type" content="text/css">
8<link rel="stylesheet" type="text/css" href="gmaj.css">
9</head>
10<body>
11<p class=vvlarge>
12<h2>Installing Gmaj</h2>
13<p class=vvlarge>
14TABLE OF CONTENTS
15<p class=small>
16<ul class=notop>
17<li><a href="#intro">Introduction</a>
18<li><a href="#install">Installation</a>
19<li><a href="#data">Data Files</a>
20<li><a href="#page">Web Page</a>
21</ul>
22<p class=vlarge>
23
24<h3><a name="intro">Introduction</a></h3>
25<p>
26Gmaj can be run in two different modes: as a stand-alone
27application (for viewing local data files yourself) or as an
28applet over the world-wide web (to display your data on a server
29for viewing by others).  Both forms of the program are
30distributed together, so the initial download and unpacking
31instructions are the same.  Setting it up as an applet, however,
32requires some additional steps: ensuring that Gmaj and the data
33files you want to display are accessible to your web server, and
34building a web page to run the applet.
35<p>
36
37<h3><a name="install">Installation</a></h3>
38<p>
39Gmaj is available for download as a compressed zip archive,
40<code><a href="http://globin.bx.psu.edu/dist/gmaj/gmaj.zip"
41>gmaj.zip</a></code>.  This was created with the Java jar tool,
42but the format is compatible with PKUnzip and many other unzip
43programs.  Unzipping the archive will produce
44<code>gmaj.jar</code> (a jar file containing the program itself)
45and a <code>docs</code> subdirectory containing some
46documentation files in HTML format.  If your unzipper program
47does not preserve the directory structure and complete file
48names from the archive, you may need to move and/or rename the
49documentation files manually in order for the "Help - Manual"
50function to work.  Note that the <code>gmaj.jar</code> file does
51not need a second round of unzipping -- Java will access it
52"as is".  If you are setting up Gmaj as an applet, be sure to
53unzip the archive in a directory/folder that will be accessible
54to your web server, e.g., a new <code>gmaj</code> directory
55somewhere in the server's document space.
56<p>
57If you are running Gmaj in stand-alone mode, you will also need
58to have Java installed on your computer.  For applets, the
59server does not need Java but the end user does; you may want to
60mention this on your Gmaj web page.  In both cases <b>Java 1.3
61or higher</b> is required, and for best compatibility
62<a href="http://java.com/en/download/manual.jsp">Sun's JRE</a>
63(or JDK) is recommended.
64<p>
65For stand-alone mode, that's all there is to the installation;
66you will specify different start-up parameters for Gmaj each time
67you run it (see <a href="gmaj_help.html"
68>Starting and Running Gmaj</a>).  The remaining sections on this
69page apply only to applet setup.
70<p>
71
72<h3><a name="data">Data Files</a></h3>
73<p>
74In addition to the alignment data, Gmaj can display several
75kinds of annotations, including genes/exons, repeats, linkbars,
76color underlays, text highlights, and reconstruction scores for
77ancestral sequences, with a meta-data parameters file to tie
78them all together.  For detailed descriptions of these files and
79their format requirements, please see <a href="gmaj_input.html"
80>Input Files for Gmaj</a>.
81<p>
82When setting up Gmaj as an applet, the data files must be
83accessible to your web server.  Also, due to Java security
84restrictions, they must all be located on the same server as the
85<code>gmaj.jar</code> file, because an applet is normally only
86allowed to contact the same server it was loaded from.  We find
87it convenient to group the files for each invocation (e.g., each
88genomic region) in a separate subdirectory of the
89<code>gmaj</code> directory.  It is also possible to bundle them
90into a single zipped data file for each invocation, which eases
91both storage requirements and download time (discussed further
92in <a href="gmaj_input.html">Input Files for Gmaj</a>).
93<p>
94
95<h3><a name="page">Web Page</a></h3>
96<p>
97The last step in setting up the applet is to create a web page on
98your server that invokes it with the appropriate parameters for
99loading your data files.  The applet normally appears as a labeled
100button that opens a Gmaj window when the user clicks on it; thus
101you can have several buttons on the same page, each set up to
102display a different set of data.  The basic format of the HTML
103code looks like this:
104
105<blockquote>
106<pre>
107&lt;applet code="edu.psu.bx.gmaj.MajApplet.class"
108        archive="gmaj.jar"
109        width="200" height="30"&gt;
110&lt;param name=paramfile   value="/java/gmaj/alpha/demo.gmaj"&gt;
111&lt;param name=bundle      value="/java/gmaj/alpha/demo.zip"&gt;
112&lt;param name=buttonlabel value="Alpha-globin"&gt;
113&lt;param name=nobutton    value="false"&gt;
114&lt;param name=initzoom    value="mouse 110000 147000"&gt;
115&lt;param name=posturl     value="/cgi-bin/save-posted-file.pl"&gt;
116&lt;param name=urlpause    value="100"&gt;
117&lt;param name=debug       value="false"&gt;
118&lt;i&gt;Your browser is not responding to the &amp;lt;applet&amp;gt; tag.&lt;/i&gt;
119&lt;/applet&gt;
120</pre>
121</blockquote>
122
123This particular fragment is based on the alpha-globin example
124from our server; naturally you need to replace the values with
125your own file URLs, button label, etc.  A few things to note:
126<ul>
127<li>    If the <code>gmaj.jar</code> file is not in the same
128        directory as your web page, you'll need to supply the path
129        to it in the <code>archive</code> attribute.
130<li>    The <code>width</code> and <code>height</code> attributes
131        are for the button, not the Gmaj windows.
132<li>    You can specify either or both of the first two
133        <code>&lt;param name=...</code> lines
134        (<code>paramfile</code> and <code>bundle</code>); the
135        others are optional.
136<li>    If the <code>nobutton</code> parameter is set to
137        <code>"true"</code>, Gmaj will proceed to open its window
138        immediately instead of displaying a start button.
139<li>    The <code>initzoom</code> parameter specifies an initial
140        zoom setting to be applied when the window opens.  The user
141        can still invoke the Unzoom or Set Zoom features
142        interactively to see the entire sequence range.  The
143        sequence name must match one of the names from the alignment
144        file(s), and the endpoints must include the offset (if any)
145        for that sequence from the parameters file.  To specify the
146        reference sequence without a zoom region, use <code>-1</code>
147        for both endpoints.
148<li>    The <code>posturl</code> parameter designates a URL on your
149        server where exported alignments should be sent.  By default
150        the Export feature is not available in applet mode, because
151        applets generally can't write to the user's local disk due
152        to security restrictions.  However, by specifying this
153        parameter you can enable the applet to send the exported data
154        to your server instead (typically a CGI script).  The output
155        is sent via an HTTP POST request using the MIME protocol for
156        web forms; currently for applets the export file format is
157        always MAF, and the filename is always
158        <code>Gmaj_output.maf</code>.
159<pre class=smallfont>
160  Content-Type: multipart/form-data; boundary=______AaB03x
161
162  --______AaB03x
163  Content-Disposition: form-data; name=file_data; filename=Gmaj_output.maf
164  Content-Type: application/octet-stream
165
166  [MAF file contents, in plain ASCII with platform-dependent line breaks]
167
168  --______AaB03x--
169</pre>
170<li>    The <code>urlpause</code> parameter specifies how many
171        milliseconds the program should pause before retrieving each
172        file from a URL, in order to avoid overloading your server.
173<li>    If the <code>debug</code> parameter is set to
174        <code>"true"</code>, Gmaj will print a few extra warning
175        messages in the browser's Java console if certain problems
176        occur.  Normally you won't need this, as it is mainly for
177        development purposes.
178<li>    To create several buttons, just repeat this entire block of
179        code (with new parameter values, of course).
180</ul>
181<p>
182
183<p class=vvlarge>
184<hr>
185<i>Cathy Riemer, June 2008</i>
186</body>
187</html>
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