Version 13 (modified by 11 years ago) (diff) | ,
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OpenClinica Quick Install on Red Hat
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 Open
`Clinica installed on a fully updated install of Red Hat Enterprise Linux 5 Update 3 (EL5.3) in a short amount of time.
Note: For Sun Java, you may need to add the channel "RHEL Supplementary (v. 5)" in the RHN web interface, or separately install and configure a JDK as described in the OpenClinica instructions. We prefer to use standard RHEL components when possible to take advantage of Red Hat's security/QA process. EL5.3's version of postgres is slightly older than in the Open
Clinica recommendations, but Red Hat backports updates. We have not encountered any issues.
1. Download and install software.
1a. Install prequisite software on RHEL 5.3.
# install Java separately first because there are multiple options (Sun, IBM, BEA) yum -y install java-1.6.0-sun-devel yum -y install postgresql-server tomcat5-admin-webapps rpm -q tomcat5 postgresql java-1.6.0-sun # As of 2009 Mar 19 # tomcat5-5.5.23-0jpp.7.el5_2.1 # postgresql-8.1.11-1.el5_1.1 # java-1.6.0-sun-1.6.0.12-1jpp.3.el5
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/tomcat5/openclinica.data chown tomcat:tomcat /var/lib/tomcat5/openclinica.data ln -s /var/lib/tomcat5/openclinica.data /usr/share/tomcat5 ln -s /usr/share/tomcat5 /usr/local/tomcat mkdir /usr/local/oc
Next Register at OpenClinca.org 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 EL5 host, decompress the download :
cd /usr/local/oc tar zxvf OpenClinica-*.tar.gz
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;127.0.0.1/32 ident sameuser;127.0.0.1/32 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 exit /etc/init.d/postgresql restart # test the connection from localhost psql --user clinica --host localhost openclinica
2b. Tomcat
By default, Tomcat is not configured for encrypted (HTTPS) requests. First
uncomment the Connector port="8443"
section in /etc/tomcat/server.xml
to configure SSL. For more information, see http://tomcat.apache.org/tomcat-5.5-doc/ssl-howto.html
# 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/ # small configuration, bugfixes, and workarounds cp /usr/local/oc/OpenClinica-*/config/libraries/postgresql-8.1-405.jdbc3.jar /usr/local/tomcat/common/lib/ # Bug: https://bugzilla.redhat.com/show_bug.cgi?id=217630 wget https://staff.washington.edu/joshuadf/java/naming-factory-dbcp.jar -O /var/lib/tomcat5/common/lib/naming-factory-dbcp.jar # Open``Clinica is only compatible with Sun Java``Mail http://java.sun.com/products/javamail/ wget https://staff.washington.edu/joshuadf/java/mail.jar -O /usr/share/java/mail.jar /usr/sbin/alternatives --install /usr/share/java/javamail.jar javamail /usr/share/java/mail.jar 4289 /usr/sbin/alternatives --set javamail /usr/share/java/mail.jar # set tomcat to start automatically on boot and start it now chkconfig tomcat5 on service tomcat5 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=mail.example.com;smtpHost=localhost;' /usr/local/tomcat/webapps/OpenClinica/properties/datainfo.properties sed -i 's;adminEmail=.*;adminEmail=you@your.domain;' /usr/local/tomcat/webapps/OpenClinica/properties/datainfo.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.