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. |
Overview
caIntegrator provides the capability to perform segmentation and
Overview
caIntegrator provides the capability to perform level 3 Should "level 3" be defined? copy number analysis using either caDNAcopy or caCGHcall. Both of these tools are part of the Bioconductor suite and are implemented as caGrid services wrapping the R Bioconductor code. One You can install one or both of these tools can be installed either on a separate server from caIntegrator or on the same server.
Warning | ||
---|---|---|
| ||
Be aware that the The R processing associated with caDNAcopy and/or caCGHcall can be very CPU and memory intensive. |
...
The caIntegrator Bioconductor installation also depends on several other packages that may not be installed on your system. Summaries of these packages and how to install directions for installing them follow.
Globus 4.0.3
Installed Installs at /usr/local/ws-core-4.0.3
...
- Download
- Unpack tar file in home directory.
- Move axis-1_4/webapps/axis directory to $CATALINA_HOME/webapps.
- Stop and restart Tomcat ($CATALINA_HOME/bin/shutdown.sh; $CATALINA_HOME/bin/startup.sh).
- Test your Axis installation by visiting http://YOUR-HOSTNAME:8080/axis/happyaxis.jsp (be sure to substitute the name of your machine in the URL).
ActiveMQ 4.0.2
Installed Installs at /usr/local/incubator-activemq-4.0.2
- Download
- Unpack tar file into /usr/local/incubator-activemq-4.0.2
- Ensure that JMS_HOME is set to /usr/local/incubator-activemq-4.0.2
- Edit file $JMS_HOME/conf/activemq.xml
- Change line that reads "
<broker useJmx="true">
" to "<broker useJmx="true" persistent="false">
" - Replace line that reads "
<transportConnector name="default" uri="tcp://localhost:61616" discoveryUri="multicast://default"/>
" with "<transportConnector name="default" uri="tcp://localhost:61616"/>
". - Comment out or remove line that reads "
<networkConnector name="default" uri="multicast://default"/>
".
- Change line that reads "
- Make main binary executable.
chmod 755 $JMS_HOME/bin/activemq
ActiveMQ can be autostarted or started as part of the Bioconductor launch script (provided later in these instructions)
R 2.9.0
Installed Installs at /usr/local/R-2.9.0
- Download
- Unpack tar file in home directory
- Configure, build, and install
cd R-2.9.0
./configure --enable-R-shlib --with-readline=no --with-x=no
- Fix src/modules/Makefile as follows (fix is from http://tolstoy.newcastle.edu.au/R/e6/devel/09/04/1434.html)
Change lines that read:
Code Block
for d in "$(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
Dependent R packages (RCurl, SJava, RWebServices, RUnit, DNAcopy)
Installs files into $R_HOME
$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 per Bioconductor Installation Guide page 10)Need link#* , 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.
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
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 Installs into R_HOME
cd ~
(- This is your home directory
svn checkout
httphttps://gforgencisvn.nci.nih.gov/svnrootsvn/bioconductor/branches/caIntegratorcd
bioconductor/trunkcaIntegrator/services/caDNAcopy/R
$R_HOME/bin/R CMD INSTALL
caDNAcopy
caDNAcopy RWebService
...
caDNAcopy
caDNAcopy RWebService
Installs into /usr/local/bioconductor/caDNAcopy
cd /usr/local
...
- library(RWebServices)
- unpackAntScript("caDNAcopy")
- q()
...
/bioconductor
$R_HOME/
...
bin/R
...
- Change to: jms.timeout=7200000
...
- 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
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, 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):
Check any failures in test/output. Ignore failures that say "expected 79, got 80"
caDNAcopy Grid Service
Installs into $CATALINA_HOME
- Download
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
- Download Bioconductor-caGrid-Services.tar.gz from https://gforge.nci.nih.gov/docman/view.php/175/19977/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 .
Install caCGHcall
This section installs the caCGHcall grid service in three pieces: base code, R web service, and caGrid service. You may can skip this section if you are only using caDNAcopy.
caCGHcall Base Code
Installs into R_HOME
cd ~
...
- This is your home directory
...
svn checkout
...
[https://
...
ncisvn.nci.nih.gov/
...
svn/
...
bioconductor/branches/caIntegrator
cd caIntegrator/services/caCGHcall/R
$R_HOME/bin/R CMD INSTALL caCGHcall
caCGHcall RWebService
...
RWebService
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
.
- . 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
...
- the 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
- , you must shut it down before using the following command):
...
- :
$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"
...
- Build and deploy caCGHcall grid service.
cd ~/caIntegrator/
services/
caCGHcall/
caGrid/caCGHcall
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 to $CATALINA_HOME/webapps/wsrf/WEB-INF/lib
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 #Optional Imporvements, you can find optional scripts that can automate the startup and shutdown of all processes.
Starting Bioconductor Services
As per See the Bioconductor Installation Guide page 11: link?.
- 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 &
Optional Improvements
Scripts to
...
Startup/
...
Shutdown Bioconductor
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, please 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 the section following this one #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 $CATALINA_HOME/bin/shutdown.sh # Stop caDNAcopy/caCGHcall workers ### They stop themselves when ActiveMQ shuts down
Setting
...
Up Common Logging
One disadvantage to having multiple separate processes for Bioconductor is that each process creates a separate log file by default. By using the following steps, the log files for Tomcat, ActiveMQ, and caDNAcopy/caCGHcall are placed into a single directory (, /usr/local/bioconductor/
logs)log
. If the scripts in the above section #Optional Improvements are used, it further improves logging by placing all messages into a single log file (, /usr/local/bioconductor/logs/bioconductor-combined.log
).
mkdir /usr/local/bioconductor/logs
- Edit /usr/local/activemq/conf/log4j.properties
- Change "log4j.rootLogger=INFO, stdout" to "log4j.rootLogger=INFO, out"
- Change "log4j.appender.out.file=${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-dnacopy.log
ln -s /usr/local/bioconductor/caCGHcall/nohup.out ./rworker-cghcall.log
ln -s $CATALINA_HOME/logs/catalina.out ./tomcat.log
Include Page | ||||
---|---|---|---|---|
|