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If these are steps, just number the first one and I'll finish them.
Installs into /usr/local/bioconductor/caCGHcall *
- cd /usr/local/bioconductor
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- $R_HOME/bin/R
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- At the R prompts:
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- library(RWebServices)
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- unpackAntScript("caCGHcall")
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- q()
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- Optionally, fix timeout value for all R workers to be 2 hours instead of 60 seconds
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- Edit $R_HOME/lib64/R/library/RWebServices/scripts/RWebServicesTuning.properties
- Edit $R_HOME/lib64/R/library/RWebServices/scripts/RWebServicesTuning.properties
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- Change to: jms.timeout=7200000
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- cd caCGHcall
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- Change the queue name for caCGHcall to not conflict with caDNAcopy:
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- Edit RWebServicesTuning.properties
- Edit RWebServicesTuning.properties
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- Change to: jms.queue=CGHC
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- ant map-package -Dpkg=caCGHcall
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- ant unpack-package -Dpkg=caCGHcall
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- ant precompile
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- Optionally, test RWebService (as per Bioconductor Installation Guide page 11):
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- Start up Tomcat (shutdown if already running)
- Start up Tomcat (shutdown if already running)
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- $CATALINA_HOME/bin/startup.sh
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- Start up ActiveMQ
- Start up ActiveMQ
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- $JMS_HOME/bin/activemq &
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- Start up R worker for caCGHcall
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- nohup ant start-worker &
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- Run the test
- Run the test
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- ant local-test
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- Check any failures in test/output. Ignore failures that say "expected 79, got 80"
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caCGHcall Grid Service
Installs into $CATALINA_HOME #
- Build and deploy caCGHcall grid service
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- cd /usr/local/bioconductor/caCGHcall
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- ant deployTomcat
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- Prepare Tomcat for Grid applications
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- cd $GLOBUS_LOCATION
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- ant -f share/globus_wsrf_common/tomcat/tomcat.xml deployTomcat -Dtomcat.dir="$CATALINA_HOME"
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- Copy $JMS_HOME/lib/*.jar to $CATALINA_HOME/webapps/wsrf/WEB-INF/lib
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Launch Bioconductor Services
This section describes how to start up all the pieces of the Bioconductor installation once they have been successfully installed. In the section following this one, you can find optional scripts that can automate the startup and shutdown of all processes. h3.
Starting Bioconductor Services
As per Bioconductor Installation Guide page 11: Do you have a link for this?
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