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This document provides instructions for installing caIntegrator Bioconductor.
Topics in this document include:
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Text in this document formatted as monoface bold type indicates Unix or R commands you should type, as indicated, at the command line. |
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- Download
- Unpack tar file in home directory
- 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.
make
make install prefix=/usr/local/R-2.9.0
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Installs into $CATALINA_HOME
- Download Bioconductor-caGrid-Services.tar.gz.
- Unpack tar file in home directory.
- Build and deploy caDNAcopy grid service.
cd caGrid/CaDNAcopy
ant -Dno.deployment.validation=true deployTomcat
- Prepare Tomcat for Grid applications.
cd $GLOBUS_LOCATION
ant -f share/globus_wsrf_common/tomcat/tomcat.xml deployTomcat -Dtomcat.dir="$CATALINA_HOME"
cp $JMS_HOME/lib/*.jar $CATALINA_HOME/webapps/wsrf/WEB-INF/lib
- Optionally, fix the timeout value in
caDNAcopy.jar
to be 2 hours instead of 60 seconds.mkdir ~/unjar; cd ~/unjar
unzip $CATALINA_HOME/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 $CATALINA_HOME/webapps/wsrf/WEB-INF/lib
cp ~/unjar/caDNAcopy.jar .
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Starting Bioconductor Services
See the 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 (skip if only using caDNAcopy)
cd /usr/local/bioconductor/caDNAcopy
nohup ant start-worker &
- Start up R worker for caCGHcall (skip if only using caCGHcall)
cd /usr/local/bioconductor/caCGHcall
nohup ant start-worker &
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These shell scripts can be used to automate the launch of Bioconductor. If these are used to automatically start the Bioconductor services at system startup, ensure that all environment variables (as listed in sections above) are already defined. All three scripts should be placed in the same directory and must be set to be executable (chmod a+x
). Also note that these scripts are intended to be used with the common logging setup that is described in #Setting Up Common Logging.
start-worker.sh
Code Block #!/bin/bash # WORKERTYPE=$1 WORKERID=$2 # Run worker echo "Starting $WORKERTYPE worker ($WORKERID)..." cd /usr/local/bioconductor/$WORKERTYPE ant start-worker | sed -u "s/\[java\]/\[$WORKERTYPE $WORKERID\]/"
start-bio.sh
Code Block #!/bin/bash # LOGFILE=/usr/local/bioconductor/logs/bioconductor-combined.log THISDIR=`dirname $0` # Run Tomcat echo Starting Tomcat... $CATALINA_HOME/bin/startup.sh # Run ActiveMQ echo Starting ActiveMQ... $JMS_HOME/bin/activemq start & sleep 10 # Run caDNAcopy workers nohup $THISDIR/start-worker.sh caDNAcopy 1 >> $LOGFILE & nohup $THISDIR/start-worker.sh caDNAcopy 2 >> $LOGFILE & # Run caCGHcall workers nohup $THISDIR/start-worker.sh caCGHcall 1 >> $LOGFILE & nohup $THISDIR/start-worker.sh caCGHcall 2 >> $LOGFILE &
stop-bio.sh
Code Block #!/bin/bash # # Stop ActiveMQ $JMS_HOME/bin/activemq stop & # Stop Tomcat $CATALINA_HOME/bin/shutdown.sh # Stop caDNAcopy/caCGHcall workers ### They stop themselves when ActiveMQ shuts down
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mkdir /usr/local/bioconductor/logs
- Edit /usr/local/activemq/conf/log4j.properties
- Change "log4j.rootLogger=INFO, stdout" to "log4j.rootLogger=INFO, out"
- Change "log4j.appender.out.file=${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-dnacopy.log
ln -s /usr/local/bioconductor/caCGHcall/nohup.out ./rworker-cghcall.log
ln -s $CATALINA_HOME/logs/catalina.out ./tomcat.log
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