Wednesday, 11 January 2012

Ubuntu LabKey Upgrade Guide

Labkey has pretty thorough installation steps on their website, but just want to document the process using the manual upgrade guide, on Ubuntu 10.04. Guide assumed you are logged in as a local user and downloaded the setup files to your home directory. Also assumed tomcat has been installed through the repositories, which places tomcat binaries in /usr/share/tomcat6, configuration in /etc/tomcat6, labkey logs in /usr/share/tomcat6/logs.

First off, to avoid any issues, stop tomcat.

sudo service tomcat6 stop

Step 1. Untar the tarball

tar zxvf LabKey11.3-*-bin.tar.gz && cd LabKey11.3-*-bin

Step 2. Create a backupdir to move the existing labkey files into

cd /usr/local/labkey
sudo mkdir backup2
sudo mv labkeywebapp/ backup2/
sudo mv modules/ backup2/
sudo cp /etc/tomcat6/Catalina/localhost/labkey.xml backup2/

Step 3. Move the new files into the current directory

sudo cp -rd ~/LabKey11.3-*-bin/labkeywebapp/ ./
sudo cp -rd /home/trent/LabKey11.3-*-bin/modules/ ./

nb: The installation guide also suggest some MS1 and MS2 third party binaries, but I haven't bothered with those. And to avoid any issues, change the owner back to the tomcat user (tomcat6) of the directories just copied across:

sudo chown tomcat6.tomcat6 -R labkeywebapp/ modules/

If not already done, install graphviz

sudo apt-get install graphviz

Step 4. Copy the library files into the lib folder in tomcat, replacing any that already exist.

cd ~/LabKey11.3-*-bin/
sudo cp -i common-lib/* server-lib/* /usr/share/tomcat6/lib/

Step 5. Copy the labkey.xml file to the tomcat cnofiguratino directory

cd ~/LabKey11.3-*-bin
sudo cp -i labkey.xml /etc/tomcat6/Catalina/localhost/labkey.xml

Then it's just a matter of updating the labkey.xml file. Things to update: Point the docBase to the labkeywebapp folder (line 1) <Context docBase="/usr/local/labkey/labkeywebapp" debug="0" reloadable="true" crossContext="true"> Update the username and password in the Resource for the labkey database server Update the mail server configuration Any other resources that may need re-adding e.g. External data sources. Finally, start tomcat

sudo service tomcat6 start

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