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caIntegrator provides the capability to perform level 3 Should "level 3" be defined? 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.&nbsp.

  Also, the The current installation instructions only support installation on Linux platforms.What is this? It keeps appearing in the markup.  ; Recommended configurations are given at the bottom.

Prerequisites please check links

The following software packages must be installed prior to beginning the instructions:

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• 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 need link
  • Instructions assume Tomcat is configured to run on port 8080. If you are using another port, 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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Installed at /usr/local/ws-core-4.0.3

1. Download

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2. Unpack tar file into /usr/local/ws-core.

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1. 4.0.3

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2. Ensure that GLOBUS_LOCATION is set to /usr/local/ws-core-4.0.3

Apache Axis 1.4

Installs files into $CATALINA_HOME

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HOME

1. Download
2. Unpack tar file in home directory
3. Move axis-1_4/webapps/axis directory to $CATALINA_HOME/webapps
4. Stop and restart Tomcat ($CATALINA_HOME/bin/shutdown.sh; $CATALINA_HOME/bin/startup.sh)

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1. Test Axis installation at http://YOUR-HOSTNAME:8080/axis/happyaxis.jsp

ActiveMQ 4.0.2

Installed at /usr/local/incubator-activemq-4.0.2

1. Download

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2. Unpack tar file into /usr/local/incubator-activemq-4.0.2
3. Ensure that JMS_HOME is set to /usr/local/incubator-activemq-4.0.2
4. Edit file $JMS_HOME/conf/activemq.xml
   1. 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"/>"
5. Make main binary executable
   • chmod 755 $JMS_HOME/bin/activemq
     ActiveMQ

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1. • can be autostarted or started as part of the Bioconductor launch script (provided later in these instructions)

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R

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2.9.0

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Installed at /usr/local/R-2.9.0

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1. Download
2. Unpack tar file in home directory
3. Configure, build, and install
   • cd R-2.9.0
   • ./configure --enable-R-shlib --with-readline=no --with-x=no
   • Fix src/modules/Makefile as follows (fix is from http://tolstoy.newcastle.edu.au/R/e6/devel/09/04/1434.html)
     • Change lines that read:

       Code Block
       for d in "$(R_MODULES)"; do \ (cd $${d} && $(MAKE) $@) || exit 1; \ done

     • To read:

       Code Block
       @if test "$(R_MODULES)" != ""; then \ for d in "$(R_MODULES)"; do \ (cd $${d} && $(MAKE) $@) || exit 1; \ done; \ fi

       Warning
       title Warning
       Be very careful of tabs in the lines, one tab to start each line, indent beyond that with spaces. Be careful to have no spaces at the end of the lines too. Use rest of Makefile as an example.

   • make

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1. • Should this be here?

Dependent R packages (RCurl, SJava, RWebServices, RUnit, DNAcopy)

Installs files into $R_HOME

1. $R_HOME/bin/R

• At the R prompts:
  • source("http://www.bioconductor.org/biocLite.R")
  • biocLite()
  • biocLite("RCurl")
  • biocLite("SJava")
  • biocLite("RWebServices")
  • biocLite("RUnit")
  • biocLite("DNAcopy")
  • q()
• Build SJava links missed by install:
  • cd $R_HOME/lib64/R/library/SJava/libs
  • ln -s SJava.so libRInterpreter.so
  • ln -s SJava.so libSJava.so
• Build and test SJava/RWebServices installation (as per Bioconductor Installation Guide page 10)
  • $R_HOME/bin/R
  • At the R prompts:
    • library(RWebServices)
    • unpackAntScript("/tmp/rservices")
    • q()
  • cd /tmp/rservices
  • ant recompile-sjava
  • ant basic-prop
    • Look for any errors)
  • ant rservices-test
    • This step is optional

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