Install Open Clinica on Linux (OpenClinica 2.5.6 in PostgreSQL)
by Ritesh
Posted on September 18, 2010 at 4:00 PM
OpenClinica is an open source Clinical Data Management system (Electronic Data capture (EDC) solution for clinical trial)
Note :
The windows installation is quite straight forward, but for Linux be prepared
with some more patience. If everything goes fine its your luck else be prepared
to try reading lots of Linux blogs till you succeed. I have tried to address few
commonly encountered issues with solutions while installing PostgreSQL.
If you don't want to use PostgreSQL then OpenClinica supports Oracle 10g as
well. Oracle 10g Express edition (Oracle 10g XE) is available free to download
from Oracle website. Click here if you want install instructions for
OpenClinica with Oracle 10g XE.
| 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 PostgreSQL [Database] [To install in oracle
click here]
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 |
| postgresql-8.2.9.tar.gz |
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 postgresql-8.2.9.tar.gz |
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 |
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 >>> Installing PostgreSql |
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