Install Open Clinica on Linux [OpenClinica 2.5.6 with Oracle 10g XE]

   


OpenClinica is an open source Clinical Data Management system [Can be used as an Electronic Data capture (EDC) solution for clinical trial]

Click here if you want install instructions for OpenClinica with PostgreSql.  

Operating System tested : RHEL 4, Fedora 11 and PCLinuxOS2009

These are roughly the 5 steps to install OpenClinica on Linux :
1.Install Java [Java]
2.Install Tomcat [Java Web Server]
3 Install Oracle 10 g XE [Database]
4.Install OpenClinica 2.5.6 [OpenClinica Package]
5.Some final configurations

And at last some custom settings to suit your requirements in OpenClinica 2.5.6

Download the following :
OpenClinica-2.5.6
jdk-1_5_0_16-linux-i586.bin
apache-tomcat-5.5.27.tar.gz
oracle-xe-univ-10.2.0.1-1.0.i386.rpm

Login with your login account (ritesh in this example):
Once you have downloaded everything required, copy all the files in a folder somewhere in your home (/home/ritesh/ritesh_cdm).

[ritesh@chennai ~]$ cd ritesh_cdm/ change directory
[ritesh@chennai ritesh_cdm]$ ls
apache-tomcat-5.5.27.tar.gz  OpenClinica-2.5.6.tar.gz  jdk-1_5_0_16-linux-i586.bin  oracle-xe-univ-10.2.0.1-1.0.i386.rpm
Verify if all required files are present

Installing Java
 
[ritesh@chennai ritesh_cdm]$ sh jdk-1_5_0_16-linux-i586.bin
Sun Microsystems, Inc. Binary Code License Agreement

for the JAVA 2 PLATFORM STANDARD EDITION DEVELOPMENT KIT 5.0

SUN MICROSYSTEMS, INC. ("SUN") IS WILLING TO LICENSE THE
SOFTWARE IDENTIFIED .........

Do you agree to the above license terms? [yes or no] yes

inflating: jdk1.5.0_16/man/man1/jps.1
inflating: jdk1.5.0_16/man/man1/jsadebugd.1
inflating: jdk1.5.0_16/man/man1/jstack.1
inflating: jdk1.5.0_16/man/man1/jstat.1
inflating: jdk1.5.0_16/man/man1/jstatd.1
inflating: jdk1.5.0_16/man/man1/keytool.1
inflating: jdk1.5.0_16/man/man1/kinit.1
inflating: jdk1.5.0_16/man/man1/klist.1 ............
Creating jdk1.5.0_16/jre/lib/javaws.jar
Creating jdk1.5.0_16/jre/lib/deploy.jar

Done.


[ritesh@chennai ritesh_cdm]$

Start the binary file using sh, and press Ctrl-C or choose to keep on pressing Enter to complete the long license agreement from Sun Microsystems !

When asked for "Do you agree to the above license terms" type yes followed by enter key.

[ritesh@chennai ritesh_cdm]$ su root
Password:
Change to root using su [superuser], because now its time to do some Java settings
[root@chennai ritesh_cdm]# mv jdk1.5.0_16 /usr/local/ move the jdk folder to /usr/local
[root@chennai ritesh_cdm]# cd /usr/local/ change directory
[root@chennai local]# ln -s jdk1.5.0_16 java create symbolic link between jdk and java folders
[root@chennai local]# echo "export JAVA_HOME=/usr/local/java" >> /etc/profile setting JAVA_HOME environment variables.

Preparing OpenClinica Package
 
[root@chennai local]# exit as user - navigate back to the folder
[ritesh@chennai ritesh_cdm]$ tar -xzvf OpenClinica-2.5.6.tar.gz
OpenClinica-2.5.6/install-docs/
OpenClinica-2.5.6/install-docs/windows/
OpenClinica-2.5.6/install-docs/linux/
OpenClinica-2.5.6/distribution/OpenClinica.war
OpenClinica-2.5.6/LICENSE.txt
OpenClinica-2.5.6/README.txt
....................
OpenClinica-2.5.6/config/libraries/ojdbc14-10g.jar
OpenClinica-2.5.6/config/libraries/postgresql-8.1-405.jdbc3.jar
Untar OpenClinica
[ritesh@chennai ritesh_cdm]$ su root
Password:
Change to root using su [superuser], because we need to create folders to keep open clinica files
[root@chennai ritesh_cdm]# mkdir /usr/local/oc create a folder oc in /usr/local
[root@chennai ritesh_cdm]# mv OpenClinica-2.5.6 /usr/local/oc/ Move unpacked Open Clinica folder to newly created oc folder

Installing Apache Tomcat Server
 
[root@chennai ritesh_cdm]# /usr/sbin/adduser tomcat create tomcat user
[root@chennai ritesh_cdm]# /usr/sbin/groupadd developers create group developers
[root@chennai ritesh_cdm]# gpasswd -a tomcat developers
Adding user tomcat to group developers
add tomcat to developers
[root@chennai ritesh_cdm]# mv /home/ritesh/ritesh_cdm/apache-tomcat-5.5.27.tar.gz /home/tomcat/ move tomcat tar file to tomcat users home directory
[root@chennai ritesh_cdm]# su tomcat change to tomcat user
[tomcat@chennai ritesh_cdm]$ cd /home/tomcat navigate to tomcat home directory
[tomcat@chennai ~]$ tar -zxvf apache-tomcat-5.5.27.tar.gz
apache-tomcat-5.5.27/webapps/tomcat-docs/config/globalresources.html
apache-tomcat-5.5.27/webapps/tomcat-docs/config/host.html
apache-tomcat-5.5.27/webapps/tomcat-docs/config/http.html
apache-tomcat-5.5.27/webapps/tomcat-docs/config/index.html
apache-tomcat-5.5.27/webapps/tomcat-docs/config/loader.html
apache-tomcat-5.5.27/webapps/tomcat-docs/config/manager.html
apache-tomcat-5.5.27/webapps/tomcat-docs/config/printer/ajp.html
apache-tomcat-5.5.27/webapps/tomcat-docs/config/printer/context.html
apache-tomcat-5.5.27/webapps/tomcat-docs/config/printer/engine.html .....
.........................
apache-tomcat-5.5.27/webapps/webdav/tomcat-power.gif
apache-tomcat-5.5.27/webapps/webdav/tomcat.gif

[tomcat@chennai ~]$
untar apache tomcat
[tomcat@chennai ~]$ exit change user to root
[root@chennai ~]# mv /home/tomcat/apache-tomcat-5.5.27 /usr/local/ shift the unpacked tomcat folder to /usr/local
[root@chennai ~]# cd /usr/local get inside /usr/local
[tomcat@chennai local]# ln -s apache-tomcat-5.5.27 tomcat create symbolic link between apache and tomcat folders
[tomcat@chennai local]# echo "export CATALINA_HOME=/usr/local/tomcat" >> /etc/profile setting CATALINA_HOME environment variables.
[root@chennai local]# cp /usr/local/oc/OpenClinica-2.5.6/install-docs/linux/tomcatd /etc/init.d/ Copy tomcat daemon to init.d folder
[root@chennai local]# cd /etc/init.d get inside init.d folder
[root@chennai local]# chmod 755 tomcatd assign privileges to tomcatd
[root@chennai local]# /sbin/chkconfig --del tomcatd remove any previous chkconfig managed service for tomcat (if any)
[root@chennai local]# /sbin/chkconfig --add tomcatd set tomcatd to run as service

Restart Computer and type http://localhost:8080 to verify if tomcat is working

Next step would be to install Oracle 10g XE, which is quite a straight forward installation.

 

Next >>> Installing Oracle 10g Express Edition
 

For more tutorials click here
 
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