OpenClinica Quick Install on Fedora

Note: this has been used only for testing a newer OS in preparation for expected features of Red Hat Enterprise Linux 6 (OpenJDK, Tomcat6, postgresql 8.3). We are not using Fedora in production. See OpenClinica for Red Hat Enterprise Linux 5 Update 3 (EL5.3) install.

This "quickstart" guide is a condensed version of the verbose instructions found in the OpenClinica download at install-docs/linux/install.txt. It should allow you to get OpenClinica installed on a fully updated install of in a short amount of time.

1. Download and install software.

1a. Install prerequisite software

# install Java separately first because there are multiple options (Sun, IBM, BEA)
yum -y install java-1.6.0-openjdk-devel 
yum -y install postgresql-server tomcat6-admin-webapps 

rpm -q java-1.6.0-openjdk-devel  postgresql tomcat6
# java-1.6.0-openjdk-devel-
# postgresql-8.3.7-1.fc11.i586
# tomcat6-6.0.18-9.2.fc11.noarch

1b. Download and extract OpenClinica for Linux

First we'll set up links so that both Red Hat's default OS tools and OpenClinica install.txt instructions will work. In short the downloads will live in /usr/local/oc/ while the live webapp and data will be visible as /usr/local/tomcat/ but really live in /var/lib/tomcat5/ per Linux Standard Base (LSB).

mkdir /var/lib/tomcat6/
chown tomcat:tomcat /var/lib/tomcat6/
ln -s /var/lib/tomcat6/ /usr/share/tomcat6
ln -s /usr/share/tomcat6 /usr/local/tomcat
mkdir /usr/local/oc

Next Register at and get OpenClinica 2.5.4 (02/17/2009), or browse for the latest version at the OpenClinica Downloads website.

Upload your OpenClinica-*.tar.gz download to /usr/local/oc/ on your EL5 host with a command like rsync -vaz OpenClinica-*.tar.gz $RHEL_HOST:/usr/local/oc/.

Now, on your host, decompress the download :

cd /usr/local/oc
tar zxvf OpenClinica-*.tar.gz 

Make sure you only have one /usr/local/oc/OpenClinica-* directory or some of the commands below will fail. If you have older versions of OpenClinica you can move them to an oldversions/ directory.

2. Setup software

2a. PostgreSQL

Prepare a strong password to use for the db user and run the following:

/etc/init.d/postgresql start
chkconfig postgresql on
# change localhost access type to "md5" 
sed -i 's;          ident sameuser;          md5;' /var/lib/pgsql/data/pg_hba.conf
# switch to postgres user       
su - postgres
  createuser --no-superuser --no-createrole --no-createdb --pwprompt clinica
  # type a strong password and note it!
  createdb openclinica 
  psql -d openclinica -f /usr/local/oc/OpenClinica-*/config/database/PostgreSQL/*/install/create_database_*_tables_with_data.sql
/etc/init.d/postgresql restart
# test the connection from the command line -- type your strong password 
psql --user clinica --host openclinica

2b. Tomcat

Below are several small Tomcat configuration changes, bugfixes, and workarounds:

# set tomcat to start automatically on boot
chkconfig tomcat6 on

# install postgresql JDBC driver per OpenClinica instructions
cp /usr/local/oc/OpenClinica-*/config/libraries/postgresql-8.1-405.jdbc3.jar /usr/local/tomcat/lib/

By default, Tomcat is not configured for encrypted (HTTPS) requests. If you want to pass requests through an Apache httpd server, see ApacheConfig for details. Alternatively you can configure Tomcat to serve SSL requests by editing /etc/tomcat/server.xml. First uncomment the Connector port="8443" section, then create a keystore with a self-signed certificate for Tomcat:

keytool -genkey -alias tomcat -keyalg RSA -dname "cn=Mark Jones, ou=JavaSoft, o=Sun, c=US" -storepass changeit -keypass changeit
mv /root/.keystore /usr/local/tomcat/

service tomcat6 start
# verify it is now running
netstat -anp |grep 8443
# tcp        0      0 :::8443                     :::*                        LISTEN      581/java            

2c. OpenClinica Deployment

# pre-deploy the WAR; we will edit some files before restarting Tomcat
cp /usr/local/oc/OpenClinica-*/distribution/OpenClinica.war /usr/local/tomcat/webapps 

Lastly, in /usr/local/tomcat/conf/Catalina/localhost/OpenClinica.xml change the JDBCRealm and SQLPostgres password lines for the "clinica" user to your db password and then run

# change OpenClinica settings
sed -i 's;;smtpHost=localhost;' /usr/local/tomcat/webapps/OpenClinica/properties/
sed -i 's;adminEmail=.*;adminEmail=you@your.domain;' /usr/local/tomcat/webapps/OpenClinica/properties/
/etc/init.d/tomcat5 restart

Now go to https://localhost:8443/OpenClinica/MainMenu (root/12345678) and enjoy! If you cannot log in, check the log files in /usr/local/tomcat/logs/ for details.

Last modified 10 years ago Last modified on 05/08/09 13:42:54