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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.

4. make
5. make install prefix=/usr/local/R-2.9.0

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

Installs files into $R_HOME

1. $R_HOME/bin/R
2. At the R prompts:
   • source("http://www.bioconductor.org/biocLite.R")
   • biocLite()
   • biocLite("RCurl")
   • biocLite("SJava")
   • biocLite("RWebServices")
   • biocLite("RUnit")
   • biocLite("DNAcopy")
   • q()
3. 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
4. Build and test SJava/RWebServices installation (as per Bioconductor Installation Guide page 10)Need link#* $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

Install caDNAcopy

This section installs the caDNAcopy grid in three pieces: base code, R web service, and caGrid service. You may skip this section if you are only using caCGHcall.

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I'm unclear about whether each of these are steps. If so they should be numbered, if not, perhaps they should stay bulleted.
Installs into R_HOME

1. cd to your home directory~
2. svn checkout http://gforge.nci.nih.gov/svnroot/bioconductor
3. cd bioconductor/trunk/services/caDNAcopy/R
4. $R_HOME/bin/R CMD INSTALL caDNAcopy

caDNAcopy RWebService

steps?
Installs into /usr/local/bioconductor/caDNAcopy

• cd /usr/local/bioconductor
• $R_HOME/bin/R
• At the R prompts:
  • library(RWebServices)
  • unpackAntScript("caDNAcopy")
  • q()
• Optionally, fix timeout value for all R workers to be 2 hours instead of 60 seconds
  • Edit $R_HOME/lib64/R/library/RWebServices/scripts/RWebServicesTuning.properties
    • Change to: jms.timeout=7200000
• cd caDNAcopy
• ant map-package -Dpkg=caDNAcopy
• ant unpack-package -Dpkg=caDNAcopy
• ant precompile
• Optionally, test RWebService (as per Bioconductor Installation Guide page 11):
  • Start up Tomcat (shutdown if already running)
    • $CATALINA_HOME/bin/startup.sh
  • Start up ActiveMQ
    • $JMS_HOME/bin/activemq &
  • Start up R worker for caDNAcopy
  • nohup ant start-worker &
  • Run the test
    • ant local-test
    • Check any failures in test/output. Ignore failures that say "expected 79, got 80"

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1. Download Bioconductor-caGrid-Services.tar.gz from https://gforge.nci.nih.gov/docman/view.php/175/19977/Bioconductor-caGrid-Services.tar.gz
2. Unpack tar file in home directory
3. Build and deploy caDNAcopy grid service
   • cd caGrid/CaDNAcopy
   • ant deployTomcat
4. Prepare Tomcat for Grid applications
5. #* cd $GLOBUS_LOCATION

1. • ant -f share/globus_wsrf_common/tomcat/tomcat.xml deployTomcat -Dtomcat.dir="$CATALINA_HOME"
   • Copy cp $JMS_HOME/lib/*.jar to $CATALINA_HOME/webapps/wsrf/WEB-INF/lib
2. Optionally, fix timeout value in caDNAcopy.jar to be 2 hours instead of 60 seconds
   • mkdir ~/unjar; cd ~/unjar
   • unzip /usr/local/tomcat-5.5.27-8080/webapps/wsrf/WEB-INF/lib/caDNAcopy.jar
   • Edit org/bioconductor/rserviceJms/services/caDNAcopy/RWebServices4java.properties
     • Change to: jms.timeout=7200000
   • zip -r caDNAcopy.jar *
   • cd /usr/local/tomcat-5.5.27-8080/webapps/wsrf/WEB-INF/lib
   • cp ~/unjar/caDNAcopy.jar .

Install caCGHcall

This section installs the caCGHcall grid service in three pieces: base code, R web service, and caGrid service. You may skip this section if you are only using caDNAcopy.

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