CIPRES Framework Software
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1. for instructions on how to build CIPRES library, please see instructions at:
   http://www.phylo.org/software/maintainer/index.php  

CIPRES Web Application 
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1. checkout the src from svn:
    http://nladr-cvs.sdsc.edu/svn/CIPRES/cipresdev/trunk/cipres-web/

 2. Make sure you have the following installed:
     tomcat (I use 5.5.26)
     maven 2.0.9
     jdk 1.5
     CIPRES Framework Software (see instruction above)

 3. make sure the following environment variables are set:
    $CATALINA_HOME:  (directory to where tomcat is installed, 
	e.g / home/users/.../apache-tomcat-5.5.17)
    $JAVA_HOME
    $CIPRES_HOME (e.g. your_dir/../CIPRES-and/deps/cipres)
    $CIPRES_WEB_HOME (directory where the result files and any temp files 
	from the web, can be anywhere on your FS)

    * there's a file called "cipresweb.properties" in your checked out src 
	directory (it's under src/main/resources) that have 4 variables that 
	are machine dependent and need to be configured when running on different 
	machines, please set them acoordingly:
    CIPRES_HOME
    CIPRES_WEB_HOME
    EMAIL_HOST (your email server)
    EMAIL_SENDER (tell user the sender of our email. I'm using mine till we 
	have one set up);

4.  Now start tomcat:
    *${CATALINA_HOME}/bin/catalina.sh start* (use *stop* if you want to 
	bring down the server) make sure *.sh files in $CATALINA_HOME/bin/*.sh 
	"+x" bit is turned on (by default, it isn't);

 5. build the source, and package it by going to the top level source 
    directory (where you find "pom.xml" file) and run: 
	mvn clean install;
	upon successful completion, this generates a cipres-web.war file in 
    targets/cipres-web.war,

 	copy this file to $CATALINA_HOME/webapps/.
    (make sure tomcat is already running at this point.  Otherwise, restart 
	tomcat)

 6. if everything works, you should be able to go to 
    http:// your_machine_name:8080/cipres-web
    (by default, tomcat is installed on port 8080, but can be changed in 
	$CATALINA_HOME/conf/server.xml)

 * The hardest part is the initialization of the first 3 step, but
   once that's once, it's a matter of checking out the source code, 
   building it, and copying the *.war file to tomcat (no need to restart 
   tomcat at that point assuming you keep it up and running).

 Maven actually comes with one plugin that allows you to deploy (and
 undeploy) the *.war file directly to tomcat (i.e. no need to copy
 it manually), but that involves a few more setup. That only helps
 if you are doing a lot of deploying or undeploying.  Otherwise, I
 think the above steps are good enough.

CIPRES REST Services
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+ all services provided from the web are also available via REST services.
  for REST service documentation, please visit:

  http://www.phylo.org/rest/rest_api.php