Install Open Clinica on Linux (OpenClinica 2.5.6 with Oracle 10g XE)
by Ritesh
Posted on September 18, 2010 at 9:00 PM
OpenClinica is an open source Clinical Data Management system (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 |
| [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 |
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. |
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Next >>> Installing Oracle 10g Express Edition |
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