Getting Started

Getting Started

Cancer Genome Collaboratory is built using Openstack, which is an open-source cloud solution with extensive documentation provided on the official site.

For your convenience, we offer these short instructions that you should follow in order to start a new instance, while also recommending you read the official user guide to familiarize with more advanced functionalities.


    First please open in your browser and login using the credentials provided.

    A screenshot of Cancer Genome Collaboratory Console

    Before launching a virtual machine, you have to accomplish a number of steps.

    1. Create a SSH key-pair by going to the Compute tab, Access & Security, Key Pairs:

      A screenshot of the create a SHH key-pair window.
    2. Customize your security groups with rules allowing access to your instance, by going to the Compute tab, Access & Security, Security Groups.

      A screenshot of the create security group window.

      Pick a descriptive name and group similar rules together. For example, have a group allowing restricted access to SSH and Mysql from your organization’s IP space, and one security group more open for public access to a web application. There is a limit of 10 security groups a project can have, so it is a good idea to plan the security groups/rules before hand. Openstack allows security groups editing after the instance has started, so additional changes can be made later if the exact requirements are not clearly defined.

    3. Decide on the flavor needed when launching the instance from the Compute, Instances tab:

      A screenshot of the luanch instance window.
    4. Choose the source image to be used (Ubuntu Precise, Trusty, Centos, Debian)

      A screenshot of the luanch instance window with the source image selected.
    5. Choose the SSH and security group(s) you previously created.

      A screenshot of the access and security tab of the luanch instance window with the SSH and security groups selected.
    6. Choose the network that your instance will connect to.

      A screenshot of the network tab of the launch instance window.
    7. Optionally, customize your instance after it has launched using the options available in the Post-Creation tab.

      A screenshot of the post-creation tab of the luanch instance window.

      Finally, click the Launch button. It will take a few minutes for the instance to start, depending on how large the base image you chose was, and if it was already cached or not on the physical server where the VM will be scheduled to start.


    Associate a floating/public IP address.

    By default, the VM will receive a private IP that is only reachable from inside your virtual network (other VMs connected to the same network).

    Because public IPv4 addresses are limited and there is an inherent security risk when connecting to the Internet, it is recommended to associate a floating/public IP address only to a single VM and use that one as an access server into your cloud environment.

    A screenshot of associating a floating/public IP address.

    SSH into your instance.

    When you started the VM and specified the name of your key pair, its public part was automatically added to the default user’s “~/.ssh/authorized_keys” file, which will allow you SSH access into it.

    From your laptop, first change the permissions for the private SSH key, so your SSH client doesn’t complain when you will try to use the key:

    chmod 400 path_to_private_key

    Then, using the desired SSH client application, run:

    ssh -i path_to_private_key ubuntu@142.1.177.X

    Customize your virtual machine, upgrade the package index and existing packages, and it’s especially important to apply all the security updates available.

In order to access and analyze ICGC data on the Collaboratory, please follow the user guide provided that has step-by-step instructions.