/static/gmaj/docs/gmaj_install.html

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  3. <html>
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  4. <head>
    5. 

  5. <title>Installing Gmaj</title>
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  6. <meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1">
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  8. <link rel="stylesheet" type="text/css" href="gmaj.css">
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  10. <body>
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  11. <p class=vvlarge>
    12. 

  12. <h2>Installing Gmaj</h2>
    13. 

  13. <p class=vvlarge>
    14. 

  14. TABLE OF CONTENTS
    15. 

  15. <p class=small>
    16. 

  16. <ul class=notop>
    17. 

  17. <li><a href="#intro">Introduction</a>
    18. 

  18. <li><a href="#install">Installation</a>
    19. 

  19. <li><a href="#data">Data Files</a>
    20. 

  20. <li><a href="#page">Web Page</a>
    21. 

  21. </ul>
    22. 

  22. <p class=vlarge>
    23. 

  23. 

  24. <h3><a name="intro">Introduction</a></h3>
    25. 

  25. <p>
    26. 

  26. Gmaj can be run in two different modes: as a stand-alone
    27. 

  27. application (for viewing local data files yourself) or as an
    28. 

  28. applet over the world-wide web (to display your data on a server
    29. 

  29. for viewing by others).  Both forms of the program are
    30. 

  30. distributed together, so the initial download and unpacking
    31. 

  31. instructions are the same.  Setting it up as an applet, however,
    32. 

  32. requires some additional steps: ensuring that Gmaj and the data
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  33. files you want to display are accessible to your web server, and
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  34. building a web page to run the applet.
    35. 

  35. <p>
    36. 

  36. 

  37. <h3><a name="install">Installation</a></h3>
    38. 

  38. <p>
    39. 

  39. Gmaj is available for download as a compressed zip archive,
    40. 

  40. <code><a href="http://globin.bx.psu.edu/dist/gmaj/gmaj.zip"
    41. 

  41. >gmaj.zip</a></code>.  This was created with the Java jar tool,
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  42. but the format is compatible with PKUnzip and many other unzip
    43. 

  43. programs.  Unzipping the archive will produce
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  44. <code>gmaj.jar</code> (a jar file containing the program itself)
    45. 

  45. and a <code>docs</code> subdirectory containing some
    46. 

  46. documentation files in HTML format.  If your unzipper program
    47. 

  47. does not preserve the directory structure and complete file
    48. 

  48. names from the archive, you may need to move and/or rename the
    49. 

  49. documentation files manually in order for the "Help - Manual"
    50. 

  50. function to work.  Note that the <code>gmaj.jar</code> file does
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  51. not need a second round of unzipping -- Java will access it
    52. 

  52. "as is".  If you are setting up Gmaj as an applet, be sure to
    53. 

  53. unzip the archive in a directory/folder that will be accessible
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  54. to your web server, e.g., a new <code>gmaj</code> directory
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  55. somewhere in the server's document space.
    56. 

  56. <p>
    57. 

  57. If you are running Gmaj in stand-alone mode, you will also need
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  58. to have Java installed on your computer.  For applets, the
    59. 

  59. server does not need Java but the end user does; you may want to
    60. 

  60. mention this on your Gmaj web page.  In both cases <b>Java 1.3
    61. 

  61. or higher</b> is required, and for best compatibility
    62. 

  62. <a href="http://java.com/en/download/manual.jsp">Sun's JRE</a>
    63. 

  63. (or JDK) is recommended.
    64. 

  64. <p>
    65. 

  65. For stand-alone mode, that's all there is to the installation;
    66. 

  66. you will specify different start-up parameters for Gmaj each time
    67. 

  67. you run it (see <a href="gmaj_help.html"
    68. 

  68. >Starting and Running Gmaj</a>).  The remaining sections on this
    69. 

  69. page apply only to applet setup.
    70. 

  70. <p>
    71. 

  71. 

  72. <h3><a name="data">Data Files</a></h3>
    73. 

  73. <p>
    74. 

  74. In addition to the alignment data, Gmaj can display several
    75. 

  75. kinds of annotations, including genes/exons, repeats, linkbars,
    76. 

  76. color underlays, text highlights, and reconstruction scores for
    77. 

  77. ancestral sequences, with a meta-data parameters file to tie
    78. 

  78. them all together.  For detailed descriptions of these files and
    79. 

  79. their format requirements, please see <a href="gmaj_input.html"
    80. 

  80. >Input Files for Gmaj</a>.
    81. 

  81. <p>
    82. 

  82. When setting up Gmaj as an applet, the data files must be
    83. 

  83. accessible to your web server.  Also, due to Java security
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  84. restrictions, they must all be located on the same server as the
    85. 

  85. <code>gmaj.jar</code> file, because an applet is normally only
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  86. allowed to contact the same server it was loaded from.  We find
    87. 

  87. it convenient to group the files for each invocation (e.g., each
    88. 

  88. genomic region) in a separate subdirectory of the
    89. 

  89. <code>gmaj</code> directory.  It is also possible to bundle them
    90. 

  90. into a single zipped data file for each invocation, which eases
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  91. both storage requirements and download time (discussed further
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  92. in <a href="gmaj_input.html">Input Files for Gmaj</a>).
    93. 

  93. <p>
    94. 

  94. 

  95. <h3><a name="page">Web Page</a></h3>
    96. 

  96. <p>
    97. 

  97. The last step in setting up the applet is to create a web page on
    98. 

  98. your server that invokes it with the appropriate parameters for
    99. 

  99. loading your data files.  The applet normally appears as a labeled
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  100. button that opens a Gmaj window when the user clicks on it; thus
    101. 

  101. you can have several buttons on the same page, each set up to
    102. 

  102. display a different set of data.  The basic format of the HTML
    103. 

  103. code looks like this:
    104. 

  104. 

  105. <blockquote>
    106. 

  106. <pre>
    107. 

  107. &lt;applet code="edu.psu.bx.gmaj.MajApplet.class"
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  108.         archive="gmaj.jar"
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  109.         width="200" height="30"&gt;
    110. 

  110. &lt;param name=paramfile   value="/java/gmaj/alpha/demo.gmaj"&gt;
    111. 

  111. &lt;param name=bundle      value="/java/gmaj/alpha/demo.zip"&gt;
    112. 

  112. &lt;param name=buttonlabel value="Alpha-globin"&gt;
    113. 

  113. &lt;param name=nobutton    value="false"&gt;
    114. 

  114. &lt;param name=initzoom    value="mouse 110000 147000"&gt;
    115. 

  115. &lt;param name=posturl     value="/cgi-bin/save-posted-file.pl"&gt;
    116. 

  116. &lt;param name=urlpause    value="100"&gt;
    117. 

  117. &lt;param name=debug       value="false"&gt;
    118. 

  118. &lt;i&gt;Your browser is not responding to the &amp;lt;applet&amp;gt; tag.&lt;/i&gt;
    119. 

  119. &lt;/applet&gt;
    120. 

  120. </pre>
    121. 

  121. </blockquote>
    122. 

  122. 

  123. This particular fragment is based on the alpha-globin example
    124. 

  124. from our server; naturally you need to replace the values with
    125. 

  125. your own file URLs, button label, etc.  A few things to note:
    126. 

  126. <ul>
    127. 

  127. <li>	If the <code>gmaj.jar</code> file is not in the same
    128. 

  128. 	directory as your web page, you'll need to supply the path
    129. 

  129. 	to it in the <code>archive</code> attribute.
    130. 

  130. <li>	The <code>width</code> and <code>height</code> attributes
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  131. 	are for the button, not the Gmaj windows.
    132. 

  132. <li>	You can specify either or both of the first two
    133. 

  133. 	<code>&lt;param name=...</code> lines
    134. 

  134. 	(<code>paramfile</code> and <code>bundle</code>); the
    135. 

  135. 	others are optional.
    136. 

  136. <li>	If the <code>nobutton</code> parameter is set to
    137. 

  137. 	<code>"true"</code>, Gmaj will proceed to open its window
    138. 

  138. 	immediately instead of displaying a start button.
    139. 

  139. <li>	The <code>initzoom</code> parameter specifies an initial
    140. 

  140. 	zoom setting to be applied when the window opens.  The user
    141. 

  141. 	can still invoke the Unzoom or Set Zoom features
    142. 

  142. 	interactively to see the entire sequence range.  The
    143. 

  143. 	sequence name must match one of the names from the alignment
    144. 

  144. 	file(s), and the endpoints must include the offset (if any)
    145. 

  145. 	for that sequence from the parameters file.  To specify the
    146. 

  146. 	reference sequence without a zoom region, use <code>-1</code>
    147. 

  147. 	for both endpoints.
    148. 

  148. <li>	The <code>posturl</code> parameter designates a URL on your
    149. 

  149. 	server where exported alignments should be sent.  By default
    150. 

  150. 	the Export feature is not available in applet mode, because
    151. 

  151. 	applets generally can't write to the user's local disk due
    152. 

  152. 	to security restrictions.  However, by specifying this
    153. 

  153. 	parameter you can enable the applet to send the exported data
    154. 

  154. 	to your server instead (typically a CGI script).  The output
    155. 

  155. 	is sent via an HTTP POST request using the MIME protocol for
    156. 

  156. 	web forms; currently for applets the export file format is
    157. 

  157. 	always MAF, and the filename is always
    158. 

  158. 	<code>Gmaj_output.maf</code>.
    159. 

  159. <pre class=smallfont>
    160. 

  160.   Content-Type: multipart/form-data; boundary=______AaB03x
    161. 

  161. 

  162.   --______AaB03x
    163. 

  163.   Content-Disposition: form-data; name=file_data; filename=Gmaj_output.maf
    164. 

  164.   Content-Type: application/octet-stream
    165. 

  165. 

  166.   [MAF file contents, in plain ASCII with platform-dependent line breaks]
    167. 

  167. 

  168.   --______AaB03x--
    169. 

  169. </pre>
    170. 

  170. <li>	The <code>urlpause</code> parameter specifies how many
    171. 

  171. 	milliseconds the program should pause before retrieving each
    172. 

  172. 	file from a URL, in order to avoid overloading your server.
    173. 

  173. <li>	If the <code>debug</code> parameter is set to
    174. 

  174. 	<code>"true"</code>, Gmaj will print a few extra warning
    175. 

  175. 	messages in the browser's Java console if certain problems
    176. 

  176. 	occur.  Normally you won't need this, as it is mainly for
    177. 

  177. 	development purposes.
    178. 

  178. <li>	To create several buttons, just repeat this entire block of
    179. 

  179. 	code (with new parameter values, of course).
    180. 

  180. </ul>
    181. 

  181. <p>
    182. 

  182. 

  183. <p class=vvlarge>
    184. 

  184. <hr>
    185. 

  185. <i>Cathy Riemer, June 2008</i>
    186. 

  186. </body>
    187. 

  187. </html>
    188.