Page History

...

1. $R_HOME/bin/R
2. At the R prompts:
   1. source("http://www.bioconductor.org/biocLite.R")
   2. biocLite()
   3. biocLite("RCurl")
   4. biocLite("SJava")
   5. biocLite("RWebServices")
   6. biocLite("RUnit")
   7. biocLite("DNAcopy")
   8. q()
3. Build SJava links missed by install:
   1. cd $R_HOME/lib64/R/library/SJava/libs
   2. ln -s SJava.so libRInterpreter.so
   3. ln -s SJava.so libSJava.so
4. Build and test SJava/RWebServices installation (as described in Customizing and Deploying Web and Grid Services. , as described in Customizing and Deploying Web and Grid Services. Chris, even though I have created this link, I think it's confusing. On the one hand, you are saying to build and test the installation as described on the other page, but you are providing numbered steps here. Are they different from the other instructions. What are these steps for? The build and test sentence suggests these steps are to build and test... This comment applies to the other places on the page that link to these other instructions, (now on the new page). . This comm

1. 1. $R_HOME/bin/R
   2. At the R prompts:
      1. library(RWebServices)
      2. unpackAntScript("/tmp/rservices")
      3. q()
   3. cd /tmp/rservices
   4. ant recompile-sjava
   5. ant basic-prop
      • Look for any errors.
   6. ant rservices-test
      • This step is optional.

...

1. cd /usr/local/bioconductor
2. $R_HOME/bin/R
   At the R prompts:
   1. library(RWebServices)
   2. unpackAntScript("caDNAcopy")
   3. q()
3. Optionally, fix the timeout value for all R workers to be 2 hours instead of 60 seconds.
   1. Edit $R_HOME/lib64/R/library/RWebServices/scripts/RWebServicesTuning.properties. Change to: jms.timeout=7200000.
4. cd caDNAcopy
5. ant map-package -Dpkg=caDNAcopy
6. ant unpack-package -Dpkg=caDNAcopy
7. ant precompile
8. Optionally, test RWebService (as per Bioconductor Installation Guide, page 11) , as described in Customizing and Deploying Web and Grid Services.
   1. Start up Tomcat (If Tomcat is already running, you must shut it down before using the following command): $CATALINA_HOME/bin/startup.sh
   2. Start up ActiveMQ: $JMS_HOME/bin/activemq &
   3. Start up R worker for caDNAcopy: nohup ant start-worker &
   4. Run the test: ant local-test

...

1. cd /usr/local/bioconductor
2. $R_HOME/bin/R
3. At the R prompts:
   1. library(RWebServices)
   2. unpackAntScript("caCGHcall")
   3. q()
4. Optionally, fix timeout value for all R workers to be 2 hours instead of 60 seconds.
   1. Edit $R_HOME/lib64/R/library/RWebServices/scripts/RWebServicesTuning.properties. Change to: jms.timeout=7200000.
5. cd caCGHcall
6. Change the queue name for caCGHcall so it does not conflict with caDNAcopy, editing RWebServicesTuning.properties. Change to: jms.queue=CGHC.
7. ant map-package -Dpkg=caCGHcall
8. ant unpack-package -Dpkg=caCGHcall
9. ant precompile
10. Optionally, test RWebService (as per the Bioconductor Installation Guide page 11, as described in Customizing and Deploying Web and Grid Services.
    1. Start up Tomcat (If Tomcat is already running, you must shut it down before using the following command): $CATALINA_HOME/bin/startup.sh
    2. Start up ActiveMQ: $JMS_HOME/bin/activemq &
    3. Start up R worker for caCGHcall nohup ant start-worker &
    4. Run the test: ant local-test

...