SORTA

SORTA is available as a service running at ​http://molgenis.org/sorta

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

Step 1 - get tomcat 7

• Download tomcat 7 from: ​https://archive.apache.org/dist/tomcat/tomcat-7/v7.[version.number]/bin/apache-tomcat-7.[version.number].tar.gz

Step 2 - get SORTA war

• Download SORTA war from ​https://molgenis26.target.rug.nl/downloads/sorta/SORTA.war

Step 3 - configure SORTA property file

• 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.

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;
  

Step 5 - configure tomcat 7

• 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
  

Step 6 - deploy SORTA in tomcat 7

• 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