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 Semantic MOBY Provider Setup
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Set up Tomcat
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You will need jdk1.5 installed and in your path to run tomcat.
Check this with: 
	$ java -version 
	to see what java is on your path

$ cd <to wherever you want apache-tomcat-5.5.17 to reside>

Get a copy of Tomcat
  $ cp <location of tomcat zip file >/apache-tomcat-5.5.17.zip .
  $ unzip apache-tomcat-5.5.17.zip

$ cd apache-tomcat-5.5.17/conf

Setup server.xml to use your port, 8080 is the default; 
no changes necessary if this port id Ok for your setup
 
  Edit server.xml and change 8080 to your assigned HTTP port
    (e.g. 3080 ) and the Tomcat shutdown port from 8005 to
    your assigned shutdown port (e.g. 3005 )

Set up web.xml to allow directory listings
	Edit web.xml parameter <listings>false</listings> to 
	<listings>true</listings>

Remove all the non-VPIN web apps from Tomcat
  $ cd ..
  $ rm -rf webapps/*

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Set up the PDK
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$ cd <to wherever you want the PDK to reside>

Get a copy of the PDK ( download from vpin website at 
http://vpin.ncgr.org/provider.shtml

  $ unzip pdk.zip

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Build and Deploy the Fasta Example
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$ cd pdk

Build & deploy smoby.war (Fasta Example)
  $ cd pdk/examples/fasta/build
  $ cp build.properties.template build.properties
  Edit build.properties, set deploy-dir to Tomcat's webapps directory
    (e.g. <tomcat>apache-tomcat-5.5.17/webapps)
  $ ant deploy

Note: The external jar files automatically get included in smoby.war.  When
smoby.war gets expanded in webapps in tomcat, the jars should be in 
webapps/smoby/WEB-INF/lib.

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Start Tomcat & Verify Installation
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$ cd <tomcat>/bin
$ startup.sh

Check Tomcat's output
  $ cat <tomcat>/logs/catalina.out

Make sure the war file got expanded
  $ ls -l <tomcat>/webapps

There should be a webapps/smoby directory in tomcat that is the result of
smoby.war getting expanded.  If it is not there, smoby.war has not been 
expanded.  There is a bug in tomcat that sometimes causes this.  You can 
usually work around the bug by stopping and restarting tomcat after 
smoby.war has been placed there by the build process.  If the 
webapps/smoby directory is there, the fasta example should work ok.  You can 
access the index.jsp file by going to http://localhost/smoby/index.jsp 
(if you are running tomcat on localhost:80, of course)