[MOBY-guts] biomoby commit

Eddie Kawas kawas at dev.open-bio.org
Tue May 27 17:23:53 UTC 2008 

kawas
Tue May 27 13:23:53 EDT 2008
Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/service/dashboard/help
In directory dev.open-bio.org:/tmp/cvs-serv11100/src/main/org/biomoby/service/dashboard/help

Modified Files:
	PerlMoSeSPanel.html 
Log Message:
* new documentation for the 'Local User Config' sub panel
* modifed the the 'generator' section to reflect some ui changes
moby-live/Java/src/main/org/biomoby/service/dashboard/help PerlMoSeSPanel.html,1.1,1.2
===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/service/dashboard/help/PerlMoSeSPanel.html,v
retrieving revision 1.1
retrieving revision 1.2
diff -u -r1.1 -r1.2
--- /home/repository/moby/moby-live/Java/src/main/org/biomoby/service/dashboard/help/PerlMoSeSPanel.html	2008/05/15 18:58:47	1.1
+++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/service/dashboard/help/PerlMoSeSPanel.html	2008/05/27 17:23:53	1.2
@@ -18,11 +18,14 @@
 <p> All activities are done using the command line utilities installed by the Perl-MoSeS module. </p>
 <h2>MoSeS Toolkit</h2>
 <p>The MoSeS Toolkit sub panel allows you to:</p>
-<ul>
-  <li>	<strong><a href="#gen">Generate</a></strong> -  generate perl modules for services that you select,</li>
+<ul><li><strong><a href="#gen">Generate</a></strong> -  generate perl modules for services that you select,</li>
   <li><strong><a href="#utilities">Utilities</a></strong> - for synchronizing Perl-MoSeS with the Dashboard, and an</li>
   <li><strong><a href="#editor">Editor</a></strong> - .for easily editing the business logic of services that you create.</li>
+  <li><a href="#local_user_config"><strong>Local User Config</strong></a> - for those users without root access when they installed Perl-MoSeS<em><strong>*</strong></em></li>
 </ul>
+<blockquote>
+  <p><em><strong>* when the panel is created, it makes a best attempt to determine whether or not the cpan module MOSES-MOBY was installed as root. If it was not, this sub panel is visible.</strong></em></p>
+</blockquote>
 <p><em><strong>Possible caveats:</strong></em></p>
 <ul>
   <li> The actions in this panel depend on the availability of certain command line tools (installed by MOSES-MOBY) being available on the system PATH.</li>
@@ -31,7 +34,8 @@
 <p> There is one <em><strong>generator</strong></em> in this panel for creating services, with a couple of options.</p>
 <ul>
   <li><strong>Overwrite Existing Code</strong> - use this to overwrite any service code that has already been generated with MoSeS</li>
-  <li><strong>Generate CGI Service</strong> - use this to generate a category 'cgi' BioMOBY web service.</li>
+  <li><strong>Generate CGI Service</strong> - use this to generate a category '<em><strong>cgi</strong></em>' BioMOBY web service.</li>
+  <li><strong>Generate SOAP Service</strong> - use this to generate a category '<em><strong>moby</strong></em>' BioMOBY web service.</li>
 </ul>
 <p>Once you have chosen your desired options, you can click on the <strong>Generate Skeletons</strong> button. This will go through and generate perl modules that represent the services that you selected in the '<em><strong>Service Browser</strong></em>'.</p>
 <p>All files are generated into your local <strong><em>Perl-MoSeS/</em></strong> installation. For instance, <em><strong>assuming</strong></em> that your <strong>username</strong> is <em><strong>moby_user</strong></em> and that your <strong>home directory</strong> is <em><strong>/home/moby_user/</strong></em>, then you could <strong>find</strong> your <strong>service skeletons</strong> in <em><strong>/home/moby_user/Perl-MoSeS/services/Service/</strong></em> directory.</p>
@@ -50,6 +54,27 @@
   <li><strong>Close</strong> - used to remove the script from view.</li>
 </ul>
 <p>There are also a two buttons for enlarging or shrinking the text in the editor.</p>
+<h3><a name="local_user_config" id="local_user_config"></a>Local User Config</h3>
+<p>The configuration sub panel allows you to specify:</p>
+<ul>
+  <li><strong>Perl Install Path</strong> - this is the path to the PERL executable, for instance, /usr/bin/perl <strong><em>[required]</em></strong></li>
+  <li><strong>PERL5LIB directory</strong> - a directory to add to Perls' <strong>@INC <em>[optional]</em></strong></li>
+  <li><strong>PERL5LIB directory (2)</strong> - another directory to add to Perls' <strong>@INC</strong> <strong><em>[optional]</em></strong></li>
+  <li><strong>MoSeS Scripts Directory</strong> - the directory that contains the moses-*.pl scripts <em><strong>[required]</strong></em></li>
+</ul>
+<p>Once this information is entered, and the <em><strong>'Test user config'</strong></em> is clicked, we check whether the required MOSES scripts are accessible. If everything is deemed to be fine, the other sub panels are enabled. Otherwise, you will be prompted to check your values.</p>
+<h4>Help on setting your local user configuration</h4>
+<p>Some users find this information hard to obtain. One trick that I use is to enter 'perl -V' at the command prompt. Among other things, one of the last things that you will see displayed is something like:</p>
+<pre>Built under linux<br />  Compiled at Nov 27 2007 10:44:36<br />  @INC:<br />    /etc/perl<br />    /usr/local/lib/perl/5.8.8<br />    /usr/local/share/perl/5.8.8<br />    /usr/lib/perl5<br />    /usr/share/perl5<br />    /usr/lib/perl/5.8<br />    /usr/share/perl/5.8<br />    /usr/local/lib/site_perl<br />    .</pre>
+<p>Keeping the above in mind and remembering that when you installed (locally for just you and not system wide!) MOSES-MOBY from the command prompt, you specified a <strong>PREFIX</strong>=/some/path/, similar to the following:</p>
+<pre>   perl Makefile.PL <strong>PREFIX</strong>=/home/ekawas/usr/local</pre>
+<p>The values that you would then enter for <strong>PERL5LIB</strong> are:</p>
+<ul>
+  <li>/home/ekawas/usr/local/lib/perl/5.8.8</li>
+  <li>/home/ekawas/usr/local/lib/site_perl</li>
+</ul>
+<p>In other words, you are interested in using the <strong>PREFIX</strong><em><strong>/lib/</strong></em> directories. </p>
+<p>The value that you should set for the <strong>MoSeS Scripts Directory</strong> are usually located in the <strong>PREFIX<em>/bin/</em></strong> directory.</p>
 <h2>Service deployment</h2>
 <p>Once you have created your service, you will want to deploy it. Depending on whether you have generated a SOAP service or a CGI based service, the steps to involved to deploy your service.</p>
 <h3>Deploying a SOAP Service</h3>

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