XNAT Ubuntu Install Script for 12.04 LTS

xnat-base-setup.sh

## David A Gutman  dgutman _at_ emory.edu
## This script walks through install an XNAT Ubuntu Virtual Machine for a VMware Host 
## Note:  this script can not be run as a single bash script.
# This is a fork/update of johnpaulett's guest setup script
# https://gist.github.com/johnpaulett/206346

## VMWARE Setup:  I allocated 80GB for the main XNAT partition (using Thin Provisioning)
## Also I set up an additional disk as a standalone partition to actually store all my data
## Presumably you do not want to have your VM image with your database/XNAT/etc in the same VM as 
## storage

##  This assumes a basic Ubuntu 12.04 LTS image has been already set up, and an IP Address and hostname have been generated

## When I first created me VM I used my user ID; after logging on for the first time I created an 'xnat' user
sudo adduser xnat  ## enter default password you want for xnat...
sudo usermod -G sudo xnat  ## add xnat user to sudo... 
## If you installed 12.04 LTS Server andwant a desktop 
#sudo apt-get install ubuntu-desktop
## then logout and log back in as xnat user

############# Make sure latest packages are installed and install vm tools ####
sudo apt-get update && sudo apt-get -y dist-upgrade 
## rebooted to update to the latest kernel
#sudo reboot

sudo apt-get install open-vm-tools


## I created a separate partition  where I will place all my main xnat images and archives
## I do not want to include the data in the same VM/snapshot as the XNAT database so I can keep them separated
## I am using nfs and mounting the partition from another machine
# I created an ext4 partition on /dev/sdb1

## I edited the /etc/fstab file and added the following line
###   /dev/sdb1 /Library ext4 defaults,nobootwait 0 1
## the /dev/sdb1 would vary depending on how the extra storage is located and if it's NFS or local disk, etc...
sudo nano /etc/fstab  # add line from above
sudo mkdir /Library
sudo mount -a
sudo chown xnat:xnat /Library   ##otherwise xnat user can't read/write files to this location
df #run "df" to see if /dev/sdb1 actually mounted..

##### INSTALL DEPENDENCIES FOR XNAT ##################
#### Current list of prerequisites are listed here  https://wiki.xnat.org/display/XNAT16/Prerequisites

## Install dependencies
## first add the PPA that adds the Oracle Java SDK 
sudo apt-get purge openjdk*  ##good not to have multiple java versinos
sudo add-apt-repository ppa:webupd8team/java 
sudo apt-get update
sudo apt-get install oracle-java7-installer


############# Setup database user (xnat) and also a database  #####
sudo -u postgres createuser -S -D -R -P xnat
## will prompt you for  password-- WRITE IT DOWN!!!
sudo -u postgres createdb -O xnat xnat

## Modify configuration files  --- I set these up before tomcat and other package installs
# to make sure everything uses the same version fo java
echo "localhost:*:xnat:xnat:xnat" >> ~/.pgpass
chmod 600 ~/.pgpass
echo "export JAVA_HOME=/usr/lib/jvm/java-7-oracle/" >> ~/.bashrc
echo "export XNAT_HOME=/home/xnat/xnat/" >> ~/.bashrc
echo "export XDAT_HOME=/home/xnat/xnat/" >> ~/.bashrc
echo "export TOMCAT_HOME=/home/xnat/tomcat/" >> ~/.bashrc
echo "PATH=$PATH:$XNAT_HOME/bin" >> ~/.bashrc
#### NEED TO CLARIFY IF XDAT_HOME OR XNAT_HOME is the environment variable
source ~/.bashrc


sudo apt-get -y install openssh-server mercurial postgresql tomcat7 tomcat7-user postfix mailutils ntp nfs-common
##I set up postfix using a smarthost and provided the smtp server my university uses
## Clean the apt cache to save diskspace
sudo apt-get -y autoremove && sudo apt-get clean


##################### SET UP TOMCAT ################
## Remove primary Tomcat init script
## http://www.debuntu.org/how-to-manage-services-with-update-rc.d
sudo update-rc.d -f tomcat7 remove

## Install Tomcat local instance
cd ~
tomcat7-instance-create tomcat

## Get Tomcat to start on boot   ##### NOT WORKING NEED TO FIX #######
CRONFILE=/tmp/xnat-cron
echo "export JAVA_HOME=/usr/lib/jvm/java-7-oracle/" > $CRONFILE
echo "@reboot /home/xnat/tomcat/bin/startup.sh" >> $CRONFILE
crontab $CRONFILE
^^^^ NOT WORKING!!! ^^^

#### Now that the DB is setup and I added environment variables, I can try and install xnat proper #####

### Download the lateset XNAT version ...http://www.xnat.org/download-xnat.html ###
# can get the latest version i.e. ftp://ftp.nrg.wustl.edu/pub/xnat/xnat_1_6_1.tar.gz after reading license
#wget ftp://ftp.nrg.wustl.edu/pub/xnat/xnat_1_6_1.tar.gz
#OR you can install from source and follow the instructions from here...
#https://wiki.xnat.org/display/XNAT16/Build+XNAT+from+Source+Repository
# Checkout code  (mercurial must be installed as per above)

hg clone http://hg.xnat.org/xnat_builder_1_6dev xnat
# also get pipeline manager
cd xnat
hg clone http://hg.xnat.org/pipeline_1_6dev pipeline

############## CONFIGURE XNAT for your system setup #############

#Property information is located at:
#https://wiki.xnat.org/display/XNAT16/XNAT+1.6+Installation+Guide
#Build.properties is located in ~/xnat/build.properties.sample
cd ~/xnat
cp build.properties.sample build.properties
#Edit build.properties with your favorite editor, vim, nano, gedit, etc
#Don't forget to edit the maven.appserver.home--- I missed this one the first time and the URL

## Run the build
./bin/setup.sh 
psql -h localhost -U xnat -d xnat_db -f deployments/xnat/sql/xnat.sql 
cd deployments/xnat/
StoreXML -location security/security.xml -allowDataDeletion true
cd ../..

#The setup script (step 4) created a WAR file in XNAT_HOME/deployments/PROJECT_NAME/target/.
#This WAR file can be copied to the #webapps directory of your Tomcat server, and will be deployed when the server starts up.
# also can 
#cd to ~/xnat
bin/update.sh -Ddeploy=true

### BELOW IS OPTIONAL BUT IS HOW You would customize your site
## Customize the deployment
SITEVM=projects/xnat/src/templates/screens/site_description.vm
echo "<b>XNAT Virtual Machine Demo</b><br />" > $SITEVM
bin/quick-deploy-templates.sh


## Start tomcat (only need to do it once, cron will start on boot)
~/tomcat/bin/startup.sh

## default user id is admin/admin and you can configure things the first time you conenct