Page History
Include Page | ||||
---|---|---|---|---|
|
Page info | ||||
---|---|---|---|---|
|
...
Include Page |
---|
...
|
...
|
...
This document provides instructions for installing caIntegrator Bioconductor.
Topics in this document include:
Table of Contents | ||
---|---|---|
|
Info | ||
---|---|---|
| ||
Text in this document formatted as monoface bold type indicates Unix or R commands you should type, as indicated, at the command line. |
...
- 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
...
$R_HOME/bin/R
- At the R prompts:
source("http://www.bioconductor.org/biocLite.R")
biocLite()
biocLite("RCurl")
biocLite("SJava")
biocLite("RWebServices")
biocLite("RUnit")
biocLite("DNAcopy")
biocLite("CGHcall")
q()
- 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
- Build and test SJava/RWebServices installation (as described in Customizing and Deploying Web and Grid Services, following these steps.
$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.
...
cd ~
- This is your home directory
svn checkout
httphttps://gforgencisvn.nci.nih.gov/svnrootsvn/bioconductor./branches/caIntegratorcd bioconductorcaIntegrator/trunk/services/caDNAcopy/R
$R_HOME/bin/R CMD INSTALL caDNAcopy
...
cd /usr/local/bioconductor
$R_HOME/bin/R
At the R prompts:library(RWebServices)
unpackAntScript("caDNAcopy")
q()
- Optionally, fix the 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
.
- Edit $R_HOME/lib64/R/library/RWebServices/scripts/RWebServicesTuning.properties. Change to:
cd caDNAcopy
ant map-package -Dpkg=caDNAcopy
ant unpack-package -Dpkg=caDNAcopy
ant precompile
- Optionally, test RWebService (as per Bioconductor Installation Guide, page 11) , following these steps.
- Start up Tomcat (If Tomcat is already running, you must shut it down before using the following command):
$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
- Start up Tomcat (If Tomcat is already running, you must shut it down before using the following command):
...
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 $CATALINA_HOME/webapps/wsrf/WEB-INF/lib{*
}
- Optionally, fix the timeout value in
caDNAcopy.jar
to be 2 hours instead of 60 seconds.mkdir ~/unjar; cd ~/unjar
unzip /usr/local/tomcat-5.5.27-8080$CATALINA_HOME/webapps/wsrf/WEB-INF/lib/caDNAcopy.jar
- Edit org/bioconductor/rserviceJms/services/caDNAcopy/RWebServices4java.properties. Change to:
jms.timeout=7200000
- {
*}zip zip -r caDNAcopy.jar **
cd /usr/local/tomcat-5.5.27-8080$CATALINA_HOME/webapps/wsrf/WEB-INF/lib
cp ~/unjar/caDNAcopy.jar .
...
cd ~
- This is your home directory
svn checkout
http[https://gforgencisvn.nci.nih.gov/svnrootsvn/bioconductor
cd bioconductor/branches/caIntegrator
cd caIntegrator/services/caCGHcall/R
$R_HOME/bin/R CMD INSTALL 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
.
- Edit $R_HOME/lib64/R/library/RWebServices/scripts/RWebServicesTuning.properties. Change to:
cd caCGHcall
- Change the queue name for caCGHcall so it does not conflict with caDNAcopy, by editing RWebServicesTuning.properties. Change to:
jms.queue=CGHC
. ant map-package -Dpkg=caCGHcall
ant unpack-package -Dpkg=caCGHcall
ant precompile
- Optionally, test RWebService (as per the Bioconductor Installation Guide page 11the RWebService, following these steps.
- Start up Tomcat (If Tomcat is already running, you must shut it down before using the following command):
$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
- Start up Tomcat (If Tomcat is already running, you must shut it down before using the following command):
...
- Build and deploy caCGHcall grid service.
cd /usr/local/bioconductor/caCGHcall
~/caIntegrator/services/caCGHcall/caGrid/caCGHcall
ant -Dno.deployment.validation=true ant 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 to $CATALINA_HOME/webapps/wsrf/WEB-INF/lib
Launch Bioconductor Services
...
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 &
...
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 $CATALINA_HOME/bin/shutdown.sh # Stop caDNAcopy/caCGHcall workers ### They stop themselves when ActiveMQ shuts down
...
mkdir /usr/local/bioconductor/logs
- Edit /usr/local/activemq/conf/log4j.properties
- Change "log4j.rootLogger=INFO, stdout" to "log4j.rootLogger=INFO, out"
- Change "log4j.appender.out.file=${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
Include Page | ||||
---|---|---|---|---|
|