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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.  .
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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.
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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 . 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)
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