1. Purpose

This document is meant for the administrators of the BioMS application. This document describes the process of deploying the BioMS application and regular administration activities to be performed on the BioMS application.

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1. One Oracle 10g/11g Schema with permissions for creating table and sequences
2. 4 Server machine with the following minimum configuration
   
   1. Dual core, 4GB RAM, 50 GB HDD x 2 – for BioMS cluster nodes
      
      1. Software required on these machines : RHEL 5.0+, Oracle Client (sqlldr, tnsping, sqlplus), ftp , p7zip, jboss 5.1
      2. Open the following ports for UDP traffic on both nodes. This is required for the bioms jboss cluster to work.
         
         1. 45688

         2. 45710

         3. 44401

         4. 44402

         5. 7900

   2. Dual core, 4GB RAM, 50 GB HDDx1 -for caTissue 2.0A on BioMS, this machine should have oracle client installed on it. This is required for installing caTissue.
      
      1. Software required on this machine : RHEL 5.0+, Oracle Client (tnsping, sqlplus)
   3. Dual Core, 1GB RAM, 50 GB HDD x 1 – for the apache load balancer
      
      1. Software required on this machine : RHEL 5.0+,apache

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JAVA_OPTS="-Xms128m -Xmx2048m -XX:MaxPermSize=1024m -Dorg.jboss.resolver.warning=true -Dsun.rmi.dgc.client.gcInterval=3600000 -Dsun.rmi.dgc.server.gcInterval=3600000 -Dsun.rmi.dgc.server.gcInterval=3600000 -Dgov.nih.nci.security.configFile=$HOME/.bioms/conf/ApplicationSecurityConfig.xml"7-Dgov.nih.nci.security.configFile=$HOME/.bioms/conf/ApplicationSecurityConfig.xml"

7. Edit <jbosshome>/server/bioms-node1/deploy/cluster/jgroups-channelfactory.sar/META-INF/jgroups-channelfactory-stacks.xml and add line

bind_port="44401"

after the lines

<UDP
singleton_name="shared-udp"
mcast_port="${jboss.jgroups.udp.mcast_port:45688}"
mcast_addr="${jboss.partition.udpGroup:228.11.11.11}"

8. Edit JBOSS_HOME/server/bioms-node1/conf/login-config.xml and update the database connection details under the application-policy element with name 'bms' to point to the BioMS database schema.

89. Edit JBOSS_HOME/server/bioms-node1/deploy/bioms-ds.xml and update the database connection details

910. Copy BIOMS_INSTALL_HOME/.bioms to users home folder ($HOME)

1011. Edit $HOME/.bioms/ApplicationSecurityConfig.xml and replace ${user.home} with the home directory path of the user.

1112. Edit $HOME/.bioms/bioms-config.groovy and update the following properties

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In node2 perform the following additional configuration.

1. Edit Edit $HOME/.bioms/bioms-config.groovy and update the following configuration

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 # Define list of workers that will be used
 # for mapping requests
 worker.list=loadbalancer,status
 
 # Define Bioms-node1
 # modify the host as your host IP or DNS name.
 worker.bioms-node1.port=8009
 worker.bioms-node1.host=<bioms-node1-host> 
 worker.bioms-node1.type=ajp13
 worker.bioms-node1.lbfactor=1
 worker.bioms-node1.cachesize=10
 
 # Define Bioms-node2
 # modify the host as your host IP or DNS name.
 worker.bioms-node2.port=8009
 worker.bioms-node2.host=<bioms-node2-host> 
 worker.bioms-node2.type=ajp13
 worker.bioms-node2.lbfactor=1
 worker.bioms-node2.cachesize=10
 
 # Load-balancing behaviour
 worker.loadbalancer.type=lb
 worker.loadbalancer.balance_workers=bioms-node1,bioms-node2
 worker.loadbalancer.sticky_session=1
 
 # Status worker for managing load balancer
 worker.status.type=status

Configure the worker uri map in Apache load balancer.Add the following uriworkermap.properties file in apache config

/bioms=loadbalancer

/bioms/*=loadbalancer

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1. Set the following environment variable in $HOEM/.bash_profilebashrc

      export CTSU_HOME=$HOME/.bioms/conf/CTEP

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