wiki:SORTA

Version 23 (modified by cp229, 8 years ago) (diff)

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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


Step 2 - get 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"
    


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