SORTA

Molgenis-connect is available as a service running at ​http://molgenis.org/molgenis-connect

The source code can be downloaded fromhttps://github.com/molgenis/molgenis/releases/tag/v1.15.0, which can be adapted and used locally as open source under the LGPLv3 license

How to deploy Molgenis-connect in tomcat 7

Step 1 - get tomcat 7

• Download tomcat 7 from: ​http://apache.xl-mirror.nl/tomcat/tomcat-7/v7.0.67/bin/apache-tomcat-7.0.67.tar.gz

Step 2 - get SORTA war

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

Step 3 - configure Molgenis-connect property file

• Create the directory ~/.molgenis/molgenis-connect 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/molgenis-connect
  admin.password=admin
  user.password=admin
  

• If these properties are not present, Molgenis-connect 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 tomcat 7

• Create a file called setenv.sh in apache-tomcat-7.0.67/bin/
• Add the configuration to the file, such as this example:

  CATALINA_OPTS="-Xmx2g -XX:MaxPermSize=256m -XX:+UseConcMarkSweepGC -XX:+CMSClassUnloadingEnabled -Dmolgenis.home=~/.molgenis/molgenis-connect"
  

Step 5 - deploy Molgenis-connect in tomcat 7

• Unzip apache-tomcat-7.0.67.tar.gz
• Move Molgenis-connect.war to apache-tomcat-7.0.67/webapps/
• Rename Molgenis-connect.war to ROOT.war
• start up tomcat

  sh apache-tomcat-7.[version.number]/bin/catalina.sh start