Overview
caIntegrator provides the capability to perform level 3 copy number analysis using either caDNAcopy or caCGHcall. Both of these tools are part of the Bioconductor suite and are implemented as caGrid services wrapping the R Bioconductor code. One or both of these tools can be installed either on a separate server from caIntegrator or on the same server. Be aware that the R processing associated with caDNAcopy and/or caCGHcall can be very CPU and memory intensive. Also, the current installation instructions only support installation on Linux platforms. Recommended configurations are given at the bottom.
Prerequisites
The following software packages must be installed prior to beginning the instructions:
- Java Development Kit (JDK) 1.6.x
- Ensure that JAVA_HOME is defined, preferably in the user or system profile
- Ensure that $JAVA_HOME/bin is in PATH
- Ant 1.7.x
- Ensure that ANT_HOME is defined, preferably in the user or system .profile
- Ensure that $ANT_HOME/bin is in PATH
- Tomcat 5.5.x
- Instructions assume Tomcat is configured to run on port 8080, if you are using another port, please substitute it into later instructions
- Ensure that CATALINA_HOME is set
- Tomcat may be autostarted or started as part of the Bioconductor launch script (provided later in these instructions)
Install Dependent Packages
The caIntegrator Bioconductor installation also depends on several other packages that may not be installed on your system. Summaries of these packages and how to install them follow.
Globus 4.0.3
Installed at /usr/local/ws-core-4.0.3
- Download from http://www-unix.globus.org/ftppub/gt4/4.0/4.0.3/ws-core/bin/ws-core-4.0.3-bin.tar.gz
- Unpack tar file into /usr/local/ws-core.4.0.3
- Ensure that GLOBUS_LOCATION is set to /usr/local/ws-core-4.0.3
Apache Axis 1.4
Installs files into $CATALINA_HOME
- Download from http://apache.cs.utah.edu/ws/axis/1_4/axis-bin-1_4.tar.gz
- Unpack tar file in home directory
- Move axis-1_4/webapps/axis directory to $CATALINA_HOME/webapps
- Stop and restart Tomcat ($CATALINA_HOME/bin/shutdown.sh; $CATALINA_HOME/bin/startup.sh)
- You can test Axis installation at http://YOUR-HOSTNAME:8080/axis/happyaxis.jsp
ActiveMQ 4.0.2
Installed at /usr/local/incubator-activemq-4.0.2
- Download from http://people.apache.org/repository/incubator-activemq/distributions/incubator-activemq-4.0.2.tar.gz
- Unpack tar file into /usr/local/incubator-activemq-4.0.2
- Ensure that JMS_HOME is set to /usr/local/incubator-activemq-4.0.2
- Edit file $JMS_HOME/conf/activemq.xml
- Change line that reads "<broker useJmx="true">" to "<broker useJmx="true" persistent="false">"
- Replace line that reads "<transportConnector name="default" uri="tcp://localhost:61616" discoveryUri="multicast://default"/>" with " <transportConnector name="default" uri="tcp://localhost:61616"/>"
- Comment out or remove line that reads "<networkConnector name="default" uri="multicast://default"/>"
- Make main binary executable
- chmod 755 $JMS_HOME/bin/activemq
- ActiveMQ may be autostarted or started as part of the Bioconductor launch script (provided later in these instructions)
