== 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==
[[BR]]

'''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
[[BR]]

'''Step 2 - get SORTA war'''[[BR]]
* Download SORTA war from https://molgenis26.target.rug.nl/downloads/sorta/SORTA.war

[[BR]]
'''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:
{{{
molgenis.version=28
db_driver=com.mysql.jdbc.Driver
db_user=molgenis
db_password=molgenis
db_uri=jdbc\:mysql\://localhost/sorta?innodb_autoinc_lock_mode\=2&rewriteBatchedStatements\=true
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.
[[BR]]

'''Step 4 - configure MySQL'''
* Open terminal and start mysql client (command differs in Windows, Linux, Mac):
{{{
/usr/local/mysql/bin/mysql -u root
}}}
* In MySQL client create database and permissions via command:
{{{
create database sorta;
grant all privileges on sorta.* to molgenis@localhost identified by 'molgenis';
flush privileges;
}}}


[[BR]]
'''Step 5 - 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"
}}}
* download mysql connector into the apache-tomcat-7.[version.number]/lib/ folder
{{{
cd ~/apache-tomcat/lib/
wget http://repo1.maven.org/maven2/mysql/mysql-connector-java/5.1.28/mysql-connector-java-5.1.28.jar
}}}



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'''Step 6 - 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
}}}

* If you run SORTA locally, you can access the application at http://localhost:8080. 
* You can log in with 
{{{
username: admin
password: admin
}}}