tranSMART (GPL) Installation

mountainromeInternet and Web Development

Oct 31, 2013 (3 years and 7 months ago)

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1


tranSMART
(GPL)
Installation


1.

Setup
user
environment

Create
an operating system user
appuser

and set its home directory to
/home/appuser
.

2.

JDK Installation




Download and install the latest
JDK 1.6

to the directory
/usr/local

and this JDK is
used for
i2b2, tranSMART,
GenePattern server

and SOLR


3.

Tomcat Installation


Download
the latest stable Tomcat 6.0.XX release and
unzip it under
/usr/local

folder
.
T
he Tomcat Application Server’s home directory
should look like this


/usr/local/tomcata
-
6.0.XX

where XX is the latest minor tomcat release number.


Start Tomcat:


/usr/local/tomcat
-
6.0.XX
/bin/shutdown.sh


Stop Tomcat:


/usr/local/tomcat
-
6.0.XX
/bin/startup.sh



4.

I2b2 1.6

I
nstallation



Download or copy JBoss with pre
-
compiled i2b2
1.6
package,
jboss
-
4.2.2
.GA
.jar
, and
then unzip it under
/usr/local
. So the JBoss Application Server’s home directory
becomes

/usr/local/

jboss
-
4.2.2
.GA
.


Modify configuration files under the directory
/usr/local/

jboss
-
4.2.2.GA/server/default/i2b2

and
the following
files under
/usr/local/

jboss
-
4.2.2.GA/server/default/deploy

as needed
:



crc
-
ds.xml



crc
-
jms
-
ds.xml



ont
-
ds.xml



work
-
ds.xml

Start
JBoss
:

2



/usr/local/
jboss
-
4.2.2.GA
/bin/
run
.sh


b 0.0.0.0&


Stop
JBoss
:


/usr/local/
jboss
-
4.2.2.GA
/bin/s
hutdown
.sh

-
S



5.

SOLR I
nstallation

and Configuration

Download or copy a pre
-
configured SOLR packages,
SOLR
-
3.1.0.jar
, and unzip this
package to
/home/appuser

directory as the user
appuser
, and SOLR will reside in
/home/appuser/

solr
-
3.1.0
.

After unzipped, you need change the

database connection string as needed in
/home/appuser/solr
-
3.1.0/example/solr/conf/

data
-
config.xml
.

Start SOLR by entering:

cd /home/appuser/solr
-
3.1.0/example

java
-
jar start.jar &


Remove any current indexes and recreate new indexes by retrieving the i
nformation from
the database by entering:


wget http:
//localhost:8983/solr/dataimport?command=full
-
import


6.

R I
nstallation




Download/
Install g77 Fortran compiler, the readline development libraries, the X11 development
libraries and the Cario

development libraries:

#
yum install gcc
-
gfortran

#
yum install readline
-
devel

#
yum update libX11

#
yum install libX11
-
devel

#
yum install libXt
-
devel

#
yum install tk
-
devel

#
yum install cario
-
devel




Download/install the latest R from
http://www.r
-
project.org
:



wget
http://cran.r
-
project.org/src/base/R
-
2/R
-
2.14.1.tar.gz


3




Configure/install R



tar xvf R
-
2.14.1.tar.gz


cd

R
-
2.14.1

./configure

prefix=/usr/local/R

enable
-
R
-
shlib

make

make install




Install R packages


The following R packages are used by tranSMART’s Data Association Tool functions and need
to be installed:



>
install.packages(
"Rserve"
)


>
install.packages(
"Cairo"
)

>
install.packages(
"MASS"
)

>
install.packages(
"stringr"
)

>
install.packages(
"ggplot2"
)

>
install.packages(
"plyr"
)

>install.packages(“reshape2”)

>
install.packages(
"gplots
"
)


>
install.packages(
"data.table
"
)


>
source("http://bioconductor.org/biocLite.R")


>
biocLite("impute")


>
install.packages("WGCNA")


>
source("http://bioconductor.org/biocLite.R")


>
biocLite("
multtest
")




Start Rserver


Enter R and then type:


>
library(Rserve)

>
Rserve()


Or using the following command:

/usr/local/R/lib64/R/bin/R CMD
/home/oracle/R/x86_64
-
unknown
-
linux
-
gnu
-
library/2.13/Rserve/libs
//Rserve
-
bin.so >> rout.log 2>&1




Validation R installation


Check if all required R packages are installed using:

>library()


After
R and R packages are installed. Create a R script with "te
stCairo.R":

4


library(ggplot2)

library(Cairo)

qplot(wt, mpg, data=mtcars)+geom_abline(intercept=20)

#ggsave(
"TEST.png"
)

CairoPNG(
"TEST.png"
, width=4, height=4)


Run the script:

R CMD BATCH ./testCairo.R


7.

Optional
-

GenePattern Server I
nstallation


Download
or copy

pre
-
built GenePattern package,
gp
-
3.2.3.jar

and unzip it to the
directory /home/appuser as
/home/appuse/gp
-
3.2.3
.

Modify
/home/appuser/gp
-
3.2.3/resources/genepattern.properties

accordingly.

Also the file /
usr/local/tomcat
-
5.5.27/webapps/gp
/WEB
-
INF/web.xml

needs to be
configured too.

8.

Optional
-

PLINK Installation


Download PLINK from the URL:
http://pngu.mgh.harvard.edu/~purcell/plink/download.shtml#downl
oad

using the
command:


wget http://pngu.mgh.harvard.edu/~purcell/plink/dist/plink
-
1.07
-
x86_64.zip


and then unzip to /usr/local.

9.

Schemas
Import


The following schemas are needed for tranSMART application:




i2b2hive



i2b2metadata



i2b2demodata



i2b2sampledata



i2b2demodata



i2b2pm



biomart



biomart_user



beapp

5




searchapp


The following schemas are needed for ETL work:




tm_cz



tm_lz



tm_wz


Before importing those schemas, the following tablespaces should be created:




biomart



transmart



deapp



i2b2_data


tranSMART required schemas with limited public dataset can be imported from Oracle
11g’s
expdp dump file
. The commandwill be like:


sqlldr <username/password> dumpfile=<dumpfile name>
logfile=<logfile name>
schemas= i2b2hive, i2b2metdata,
i2b2sampledata,
i2b2demodata, i2b2workdata,
i2b2workdata,biomart,biomart_user,deapp,searchapp,tm_cz,tm_lz,tm_
wz



10.

tranSMART Installation

Create a
transmart.war

file and drop it under
/usr/local/tomcat
-
6.0.XX
/webapps

directory, and then restart Tomcat.

11.

tranSMART
configuration


Download or copy
tranSMARTConfig.jar

file and unzip it under
/home/appuser
.

You should be able to find tranSMART’s external configuration files,
Config.groovy
,

DataSource.groovy

and
RModulesConfig.groovy

from
/home/appuser/.grails/transmartA
ppConfig
.


Modify configuration files as needed.


12.

Validation


6


Before try to access tranSMART UI, please make sure the following servers
or services
are up and running:




Tomcat



JBoss



SOLR



Rserve



Oracle Server


Also you should make sure
that JDK 6 is used by

all containers

and

Rserve are running
by appuser.

Please make sure that /usr/local/tomcat
-
6.0.XX

and /usr/local/jboss
-
4.2.2.GA are owned
by appuser.