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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

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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.

Chris: Yes, these are all steps.  Anything that I make red is a Unix or R command that the user needs to type at the command line.  You were going to make them all monoface bold italic I think.

Installs into R_HOME

1. cd ~ (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? Chris: Yes, every single section is steps and should be numbered.
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"

caDNAcopy Grid Service

These are worded like steps, so it's clearer to me that they can be numbered.Are the indented bullets steps as well? If so, I'll "letter" them. Chris: Yes, all steps.
Installs into $CATALINA_HOME

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"
   • cp $JMS_HOME/lib/*.jar $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 .

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caCGHcall Base Code

Installs into R_HOME

• cd to ~ (your home directory)
• svn checkout http://gforge.nci.nih.gov/svnroot/bioconductor
• cd bioconductor/branches/caIntegrator/services/caCGHcall/R
• $R_HOME/bin/R CMD INSTALL caCGHcall

caCGHcall RWebService

If these are steps, just number the first one and I'll finish them.
Installs into /usr/local/bioconductor/caCGHcall

1. cd /usr/local/bioconductor

• $R_HOME/bin/R
• At the R prompts:
  • library(RWebServices)
  • unpackAntScript("caCGHcall")
  • 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 caCGHcall
• Change the queue name for caCGHcall to not conflict with caDNAcopy:
  • Edit RWebServicesTuning.properties
    • Change to: jms.queue=CGHC
• ant map-package -Dpkg=caCGHcall
• ant unpack-package -Dpkg=caCGHcall
• 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 caCGHcall
    • nohup ant start-worker &
  • Run the test
    • ant local-test

Check any failures in test/output. Ignore failures that say "expected 79, got 80"

caCGHcall Grid Service

Installs into $CATALINA_HOME

1. Build and deploy caCGHcall grid service
   • cd /usr/local/bioconductor/caCGHcall
   • ant deployTomcat
2. Prepare Tomcat for Grid applications
3. cd $GLOBUS_LOCATION
4. ant -f share/globus_wsrf_common/tomcat/tomcat.xml deployTomcat -Dtomcat.dir="$CATALINA_HOME"
5. Copy cp $JMS_HOME/lib/*.jar to $CATALINA_HOME/webapps/wsrf/WEB-INF/lib

Launch Bioconductor Services

...

1. Start up Tomcat (shutdown if already running)
   • $CATALINA_HOME/bin/startup.sh
2. Start up ActiveMQ
   • $JMS_HOME/bin/activemq &
3. Start up R worker for caDNAcopy (skip if only using caDNAcopy)
   • cd /usr/local/bioconductor/caDNAcopy
   • nohup ant start-worker &
4. Start up R worker for caCGHcall (skip if only using caCGHcall)
   • cd /usr/local/bioconductor/caCGHcall
   • nohup ant start-worker &

Optional Improvements

Scripts to startup/shutdown Bioconductor

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One disadvantage to having multiple separate processes for Bioconductor is that each process creates a separate log file by default. By using the following steps, the log files for Tomcat, ActiveMQ, and caDNAcopy/caCGHcall are placed into a single directory (/usr/local/bioconductor/logs). If the scripts in the above section are used, it further improves logging by placing all messages into a single log file (/usr/local/bioconductor/logs/bioconductor-combined.log).

• mkdir /usr/local/bioconductor/logs
• Edit /usr/local/activemq/conf/log4j.properties
  • Change "log4j.rootLogger=INFO, stdout" to "log4j.rootLogger=INFO, out"
  • Change "log4j.appender.out.file=${activemq.home}/data/activemq.log" to "log4j.appender.out.file=/usr/local/bioconductor/logs/activemq.log"
• cd /usr/local/bioconductor/logs
• ln -s /usr/local/bioconductor/caDNAcopy/nohup.out ./rworker.log
• ln -s $CATALINA_HOME/logs/catalina.out ./tomcat.log