== SORTA ==

SORTA is available as a service running at http://molgenis.org/sorta
[[BR]][[BR]]

The source code can be downloaded from https://github.com/ChaoPang/molgenis/releases/tag/v1.1.2, which can be adapted and used locally as open source under the LGPLv3 license

Read all about SORTA at http://database.oxfordjournals.org/content/2015/bav089

== How to deploy SORTA in tomcat 7==
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'''Step 1 - get tomcat 7'''[[BR]]
* Download tomcat 7 from: https://archive.apache.org/dist/tomcat/tomcat-7/v7.[version.number]/bin/apache-tomcat-7.[version.number].tar.gz
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'''Step 2 - get SORTA war'''[[BR]]
* Download SORTA war from https://molgenis26.target.rug.nl/downloads/sorta/SORTA.war

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'''Step 3 - configure SORTA property file'''[[BR]]
* Create the directory ~/.molgenis/sorta and create a file called molgenis-server.properties in this folder (~ is your home folder)
* Add user and database properties to this file, such as this example:
{{{
db_user=molgenis
db_password=molgenis
db_uri=jdbc:mysql://localhost/sorta
admin.password=admin
user.password=admin
}}}
* If these properties are not present, SORTA will not start. This properties-file should be in your home folder, if the file is not there yet, just create it.
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'''Step 4 - configure tomcat 7'''[[BR]]
* Create a file called setenv.sh in apache-tomcat-7.[version.number]/bin/
* Add the configuration to the file, such as this example: 
{{{
CATALINA_OPTS="-Xmx2g -XX:MaxPermSize=256m -XX:+UseConcMarkSweepGC -XX:+CMSClassUnloadingEnabled -Dmolgenis.home=~/.molgenis/sorta"
}}}



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'''Step 5 - deploy SORTA in tomcat 7'''[[BR]]
* Unzip apache-tomcat-7.[version.number].tar.gz
* Move SORTA.war to apache-tomcat-7.[version.number]/webapps/
* Rename SORTA.war to ROOT.war
* start up tomcat
{{{ 
sh apache-tomcat-7.[version.number]/bin/catalina.sh start
}}}