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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 Should this be here?
   When I printed this document off, there was a "made install prefix+/usr/local/R-2.90" here, but I see it's gone. Did you delete it? Just wanted to make sure I didn't do anything I shouldn't.

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)
   • $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.

caDNAcopy Base Code

are only using caCGHcall.

caDNAcopy Base Code

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"

...

• • • . 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.
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 $GLOBUS_LOCATION
   • ant -f share/globus_wsrf_common/tomcat/tomcat.xml deployTomcat -Dtomcat.dir="$CATALINA_HOME"
   • Copy $JMS_HOME/lib/*.jar to $CATALINA_HOME/webapps/wsrf/WEB-INF/lib
6. 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.

...

• 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
* 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"

h3. caCGHcall Grid Service

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

h2. 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?

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

...