How to install Galaxy-ES to EC2

(Under Construction)
In these steps we assume an installation from scratch without using Globus provisioning.

The main installation issue is related to the tools backend: the exectutable (binary, script, bytecode) that actually performs the tool action. The easiest way is to begin form an Ubuntu 11.10 or above image.
  1. Log in the AWS console and select the EC2 panel (we assume you have an EC2 account) pointing your browser to https://console.aws.amazon.com/ec2
  2. Select your starting image pointing another browser instance to http://uec-images.ubuntu.com/releases/11.10/release/
  3. Double click on the AMI code you prefer taking into account this points:
    1. Choose the best availability zone
    2. Use a micro instance just for experiments
    3. Use an m1.large for personal production and demos
    4. For production consider something of more performing
  4. Follow the on screen instruction
  5. If available, choose a key pair, otherwise create a new one
  6. Assign the VM to a Security Group (be sure you have TCP ports 22 and 8080 opened for the incoming traffic
  7. Launch the VM, wait until it is available, assign a name as Galaxy-ES-Demo
  8. Using an ssh client connects to the machine as the user ubuntu and using the public key downloadable using the Amazon interface
  9. Once you are logged in the VM as the ubuntu user, became root
    sudo -i
  10. Set the locale
    vi /etc/rc.local
  11. Add the following lines before the exit command
    export LANGUAGE=en_US.UTF-8
    export LANG=en_US.UTF-8
    export LC_ALL=en_US.UTF-8
  12. Save the file, quit vi and reboot the machine
    reboot
  13. When the instance is back available, login as root (see step 9)
  14. Update the system
    apt-get update
    apt-get install language-pack-en-base -y
    locale-gen en_US.UTF-8
    dpkg-reconfigure locales
    apt-get upgrade -y
    reboot
  15. Wait for the VM perform the reboot, then log in again and became root
  16. Create a /nfs/ directory
    mkdir /nfs/
    chmod –R 777 /nfs/
  17. Install the required software
    apt-get update
    apt-get install make gcc gfortran openjdk-7-jdk zip apache2 mercurial grads cdo nco netcdf-bin gdal-bin python-numpy python-scipy python-netcdf -y
  18. Unfortunately wgrib2 does not have an aptitude package, so it must be installed in the old fashion
    cd
    mkdir dist
    cd dist
    wget
    http://www.ftp.cpc.ncep.noaa.gov/wd51we/wgrib2/wgrib2.tgz
    tar -xvzf wgrib2.tgz
    cd grib2
    make 2>&1 | tee make.1.log
    cp wgrib2/wgrib2 /usr/bin/
  19. The ubuntu packd version of jython is not up to date to the last version, so we have to install it manually.
    cd
    cd dist
  20. Download the package in http://www.jython.org/downloads.html. Be careful to change the placeholder x.y.z with the actual version numbers
    java -jar nomepackage
  21. Choose defaults. Install in /opt/jython-x.y.z
  22. Create the sourceme for jython
    cat > /opt/jython-x.y.z/surceme << EOF
    #! /bin/bash
    export JYTHON_HOME=/opt/jython-x.y.z
    export PATH=$JYTHON_HOME/bin:$PATH
    export LD_LIBRARY_PATH=$JYTHON_HOME/lib:$LD_LIBRARY_PATH
    EOF
  23. Source the jython environment
    source /opt/jython-x.y.z/sourceme
  24. Install GeoScript (follow the instruction in http://geoscript.org/py/quickstart.html#quickstart)
    cd
    cd dist
    ...
  25. Add the galaxy user. Do not set anything more than the user name.
    adduser galaxy
    su - galaxy
  26. Clone the repository:
  27. Configure Galaxy as Galaxy-ES galaxy-es
    cd galaxy-es
    ./set_earthsystem
  28. Run galaxy-es
    sh ./run.sh
  29. Try it pointing your brwser http://yourpubliciporfqdn:8080
  30. To check if it works correctly, please follow the “FACE-IT enjoy-it” or “The first FACE-IT Galaxy-ES DEMO” section pointing your browser on your machine instead of the testing one.

Comments