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CloudBioLinux Deployer CloudMan QuickStart

As far as I can determine there is no current documentation on how to build CloudMan instances from scratch. Thus I am collecting my unofficial notes on how to do this here - spefically using the CloudBioLinux deployer.

You will need to navigate the AWS management console and obtain the following information.

  • Your AWS Access ID and secret key (access_id, secret_key)
  • Ubuntu EBS-backed AMI ID to target. This writeup was tested with ami-9b85eef2 (12.04.2 (64-bit) in us-east-1)
  • Image size to use (e.g. m1-small)
  • Availibity zone (e.g. us-east-1)
  • You will need to setup a bucket to store your snaps file, here you will need the bucket name.
  • You will need to setup two volumes in your target availibity zone, one for Galaxy tools and data (perhaps 20Gb for testing) and one for galaxyIndices. Here you will need the volume ids.
  • Generate a private a key (e.g. galaxy1.pem) and copy it into keys directory (or anywhere really), also note the keypair_name corresponding to the key.

Create a directory (e.g. /home/mary/marys_cloudman_bucket_contents). Copy the files from an existing CloudMan bucket here (e.g. http://s3.amazonaws.com /cloudman-dev).

It is not really important how you download these files, but one quick option is to use s3cmd tool:

% sudo apt-get install s3cmd  # Or your OS's package manager
% mkdir /home/mary/marys_cloudman_bucket_contents
% s3cmd -r get s3://cloudman-dev /home/mary/marys_cloudman_bucket_contents

Here you can replace the CloudMan source (i.e. cm.tar.gz) or any of these files to match the customized setup you would like. In particular you are going to want to create a custom snaps.yaml file. Here is a simple outline that we will fill out as we good.

version: 1
clouds:
  - name: amazon
    regions:
    - deployments:
      - name: GalaxyCloud
        filesystems:
        - name: galaxy
          roles: galaxyTools,galaxyData
          snap_id: snap-XXXXXXXXXXX
          mount_point: /mnt/galaxy
        - name: galaxyIndices
          roles: galaxyIndices
          snap_id: snap-XXXXXXXXXXXX
          mount_point: /mnt/galaxyIndices
        default_mi: ami-XXXXXXXXXXXXX
        bucket: marys_cloudman_bucket
      name: us-east-1

Immediately this template can be updated to reflect the bucket created above and the availibity zone you are targetting. We can update teh snap_id's and the default_mi after creating them.

Copy and modify settings-sample-cm.yaml to settings.yaml:

% git clone git://github.com/chapmanb/cloudbiolinux.git
% cd cloudbiolinux/deploy
% cp settings-sample-cm.yaml settings.yaml
% vim settings.yaml # or your favorite editor

Carefully scan through settings.yaml and change the properties marked as requiring change. The word UPDATE in the comments indicates properties of special interest that either don't have reasonable defaults or have reasonable defaults but that I have deemed highly likely to be overridden.

Now you can use the CloudBioLinux deployer to launch an image, attach volumes, install biolinux, take needed snapshots, and package the whole thing up:

% ./deploy.sh --action=launch
% ./deploy.sh --action=attach_volumes
% ./deploy.sh --action=install_biolinux --flavor=cloudman/cloudman_and_galaxy
% ./deploy.sh --action=snapshot_volumes
% ./deploy.sh --action=detach_volumes
% ./deploy.sh --action=package

If at any point in the above process you need to interactively inspect the state of the instance being configured you can do this via the following command:

% ./deploy.sh --action=ssh

Once a CloudMan AMI has been created, update snaps.yaml in your bucket directory (e.g. /home/mary/marys_cloudman_bucket_contents) to reflect the snap_ids and AMI created. These should all be available via the AWS management console or by reviewing the output of the steps above.

Finally, you can upload your new bucket and launch a test CloudMan instance:

% ./deploy.sh --action=sync_cloudman_bucket
% ./deploy.sh --action=cloudman_launch

Customizing

The above example uses the cloudman/cloudman_and_galaxy CloudBioLinux flavor, but there are additional flavors of CloudBioLinux available. Please consult this page and choose the most appropriate flavor:

Customizing Galaxy

Installing a customized Galaxy is as simple as overriding the galaxy_repository variable in the fabricrc_overrides section of the settings.yaml.

Customizing Tools

Out of the box, CloudBioLinux can be configured to install dozens of bioinformatic packages out of the box and adding additional packages is fairly straight forward. One simply need to create a CloudBioLinux flavor that configures which such packages are installed and specify that flavor (either in the command-line as shown above or in settings.yaml).

Your custom flavor should include the cloudman packages. If your flavor additionally includes galaxy (as the flavor cloudman_and_galaxy shown above) packages and install_tool_dependencies is set to True in settings.yaml - CloudBioLinux will setup a tool dependencies directory for Galaxy. This allows multiple versions of an application to be installed in isolation.

When enabled, the list of tools and versions that is installed can be found in cloudbiolinux/contrib/flavor/cloudman/tools.yaml <https://github.com/chapmanb/cloudbiolinux/blob/master/contrib/flavor/cloudman/tools.yaml>. One can modify that file directly or specify an entirely new file by setting the galaxy_tools_conf property in the fabric_overrides section of settings.yaml.

Customizing CloudMan

CloudMan is downloaded from the bucket you specify and installed at system startup. Hence one can simply place a customized version of CloudMan (tarred up and named cm.tar.gz) in the bucket.

If cloudman_repository, bucket_source, and bucket_default are set in the cloudman section of settings.yaml, then one can execute the following command to quickly tar up the local copy of CloudMan (in cloudman_repository) and update your target bucket.

% ./deploy.sh --action=bundle_cloudman --action=sync_cloudman_bucket