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Automated deployment for Galaxy and the BioInvestigatorIndex (BII) to support the Stem Cell Discovery Engine.

Galaxy and BII Installation


  • Install Python (version 2.6 or better, not Python 3)

  • Build libraries and install Python library pre-requisites

      cd ~/hsph/projects/scde_deploy
      python setup.py build && sudo python setup.py install
  • Edit config/scde.yaml to specify system directories and passwords


  • Run Fabric script for deployment:

    fab -f ~/hsph/projects/scde_deploy/scde_fabfile.py -H your_remote_host install_scde

    You can also install only BII:

    fab -f ~/hsph/projects/scde_deploy/scde_fabfile.py -H your_remote_host install_bii

    Or use the script to start servers:

    fab -f ~/hsph/projects/scde_deploy/scde_fabfile.py -H your_remote_host install_bii

Vagrant testing

Pre-deployment testing uses a local virtual machine managed with Vagrant:

  • Install VirtualBox and Vagrant

  • Install CloudBioLinux box with Vagrant. Creates a Vagrantfile for configuring and running the virtual machine

      mkdir tmp/vagrant/galaxy_bii
      cd tmp/vagrant/galaxy_bii
      vagrant box add biolinux_centos_20110412 https://s3.amazonaws.com/chapmanb/biolinux_centos_20110412.box
      vagrant init biolinux_centos_20110412
  • Allow web access to your machine from a port on your computer. Edit the Vagrantfile to forward port 80 from the machine to 8082 on your local computer:

      config.vm.forward_port "http", 80, 8082
  • Start the virtual machine:

      cd tmp/vagrant/galaxy_bii
      vagrant up
  • Run fabric script to install dependencies, BII and Galaxy; all servers are started in screen sessions:

      cd tmp/vagrant/galaxy_bii
      fab -f ~/hsph/projects/scde_deploy/scde_fabfile.py -H vagrant install_scde
  • Browse BII and Galaxy:

ISA-Tab record management

  • Directories of ISA-Tab metadata, raw and derived data files are stored in Amazon S3 buckets for reliable backup

  • Edit config/isatab_studies.yaml to specify public and private datasets that should be downloaded.

  • Download data from S3 bucket and install into BII

     fab -f scde_data_fabfile.py -H localhost scde_data

Integrate BII data with Galaxy

On BII/Galaxy machine, run script to parse ISA-Tab and prepare associated data libraries in Galaxy for raw and derived data:

   python2.6 scripts/bii_datasets_to_galaxy.py config/scde.yaml config/isatab_studies.yaml