 |
Page History
Overview
caIntegrator provides the capability to perform level 3 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 or both of these tools can be installed either on a separate server from caIntegrator or on the same server. Be aware that the R processing associated with caDNAcopy and/or caCGHcall can be very CPU and memory intensive. Also, the current installation instructions only support installation on Linux platforms. Recommended configurations are given at the bottom.
Prerequisites
The following software packages must be installed prior to beginning the instructions:
- Java Development Kit (JDK) 1.6.x
- Ensure that JAVA_HOME is defined, preferably in the user or system profile
- Ensure that $JAVA_HOME/bin is in PATH
- Ant 1.7.x
- Ensure that ANT_HOME is defined, preferably in the user or system .profile
- Ensure that $ANT_HOME/bin is in PATH
- Tomcat 5.5.x
- Instructions assume Tomcat is configured to run on port 8080, if you are using another port, please substitute it into later instructions
- Ensure that CATALINA_HOME is set
- Tomcat may be autostarted or started as part of the Bioconductor launch script (provided later in these instructions)
Install Dependent Packages
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 them follow.
Globus 4.0.3
Installed at
...
/usr/local/ws-core-4.0.3
...
- Download
...
- from
...
...
- Unpack tar file into /usr/local/ws-core.4.0.3
...
- Ensure that GLOBUS_LOCATION is set to /usr/local/ws-core-4.0.3
...
Apache Axis 1.4
Installs files into $CATALINA_HOME
...
- 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)
...
- You
...
- can
...
- test
...
- Axis
...
- installation
...
- at
...
...
ActiveMQ 4.0.2
...
Installed
...
at
...
/usr/local/incubator-activemq-4.0.2
...
- Download
...
- from
...
- http://people.apache.org/repository/incubator-activemq/distributions/incubator-activemq-4.0.2.tar.gz
...
- 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"/>"
...
- Make
...
- main
...
- binary
...
- executable
...
- chmod
...
- 755
...
- $JMS_HOME/bin/activemq
...
- ActiveMQ
...
- may
...
- be
...
- autostarted
...
- or
...
- started
...
- as
...
- part
...
- of
...
- the
...
- Bioconductor
...
- launch
...
- script
...
- (provided
...
- later
...
- in
...
- these
...
- instructions)
...
R
...
2.9.0
...
Installed
...
at
...
/usr/local/R-2.9.0
...
- Download
...
- from
...
...
- Unpack
...
- tar
...
- file
...
- in
...
- home
...
- directory
...
- Configure,
...
- build,
...
- and
...
- install
...
- cd
...
- R-2.9.0
...
- ./configure
...
- --enable-R-shlib
...
- --with-readline=no
...
- --with-x=no
...
- Fix
...
- src/modules/Makefile
...
- as
...
- follows
...
- (fix
...
- is
...
- from
...
...
- )
...
- Change
...
- lines
...
- that
...
- read:
...
Code Block
...
for d in "$(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
...
- 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")
...
- 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)
...
- $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
...
Installs
...
into
...
R_HOME
...
- cd
...
- to
...
- your
...
- home
...
- directory
...
- svn
...
- checkout
...
...
- cd
...
- bioconductor/trunk/services/caDNAcopy/R
...
- $R_HOME/bin/R
...
- CMD
...
- INSTALL
...
- caDNAcopy
...
caDNAcopy
...
RWebService
...
Installs
...
into
...
/usr/local/bioconductor/caDNAcopy
...
- cd
...
- /usr/local/bioconductor
...
- $R_HOME/bin/R
...
- At
...
- the
...
- R
...
- prompts:
...
- library(RWebServices)
...
- unpackAntScript("caDNAcopy")
...
- q()
...
- 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
- the test
...
- Check
...
- any
...
- failures
...
- in
...
- test/output.
...
- Ignore
...
- failures
...
- that
...
- say
...
- "expected
...
- 79,
...
- got
...
- 80"
...
caDNAcopy
...
Grid
...
Service
...
Installs
...
into
...
$CATALINA_HOME
...
- Download
...
- Bioconductor-caGrid-Services.tar.gz
...
- from
...
...
- Unpack
...
- tar
...
- file
...
- in
...
- home
...
- directory
...
- Build
...
- and
...
- deploy
...
- caDNAcopy
...
- grid
...
- service
...
- cd
...
- caGrid/CaDNAcopy
...
- 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
...
- 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
...
- .
...
- Optionally,
...
- fix
...
- timeout
...
- value
...
- in
...
- R
...
- worker
...
- to
...
- be
...
- 2
...
- hours
...
- instead
...
- of
...
- 60
...
- seconds
...
- Edit
...
- $R_HOME/lib64/R/library/RWebServices/scripts/RWebServicesTuning.properties
...
- Change
...
- to:
...
- jms.timeout=7200000
...
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.
...
caCGHcall
...
Base
...
Code
...
Installs
...
into
...
R_HOME
...
- cd
...
- to
...
- your
...
- home
...
- directory
...
- svn
...
- checkout
...
...
- cd
...
- bioconductor/branches/caIntegrator/services/caCGHcall/R
...
- $R_HOME/bin/R
...
- CMD
...
- INSTALL
...
- caCGHcall
...
caCGHcall
...
RWebService
...
Installs
...
into
...
/usr/local/bioconductor/caCGHcall
...
- cd
...
- /usr/local/bioconductor
...
- $R_HOME/bin/R
...
- At
...
- the
...
- R
...
- prompts:
- library(RWebServices)
...
- unpackAntScript("caCGHcall")
...
- q()
...
- cd
...
- caCGHcall
...
- 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
...
- Download
...
- Bioconductor-caGrid-Services.tar.gz
...
- from
...
...
- Unpack tar file in home directory
- Build and deploy caDNAcopy grid service
- cd caGrid/CaDNAcopy
- 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
...
- 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
...
- .
- Optionally,
...
- fix
...
- timeout
...
- value
...
- in
...
- R
...
- worker
...
- to
...
- be
...
- 2
...
- hours
...
- instead
...
- of
...
- 60
...
- seconds
- Edit $R_HOME/lib64/R/library/RWebServices/scripts/RWebServicesTuning.properties
...
- Change to:
...
- jms.timeout=7200000
...
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.
Starting Bioconductor Services
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
...
- (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.
...
- 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 $CATALINA_HOME/bin/shutdown.sh # Stop caDNAcopy/caCGHcall workers ### They stop themselves when ActiveMQ shuts down
...
Setting up common logging
One disadvantage to having multiple separate processes for Bioconductor is that each process creates a separate log file by default. By using the following steps, the log files for Tomcat, ActiveMQ, and caDNAcopy/caCGHcall are placed into a single directory (/usr/local/bioconductor/logs).
...
If
...
the
...
scripts
...
in
...
the
...
above
...
section
...
are
...
used,
...
it
...
further
...
improves
...
logging
...
by
...
placing
...
all
...
messages
...
into
...
a
...
single
...
log
...
file
...
(/usr/local/bioconductor/logs/bioconductor-combined.log).
...
- mkdir
...
- /usr/local/bioconductor/logs
...
- Edit
...
- /usr/local/activemq/conf/log4j.properties
...
- Change
...
- "log4j.rootLogger=INFO,
...
- stdout"
...
- to
...
- "log4j.rootLogger=INFO,
...
- out"
...
- Change
...
- "log4j.appender.out.file=${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
