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CloudBioLinux: configure virtual (or real) machines with tools for biological analyses

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Octocat-spinner-32 cloudbio
Octocat-spinner-32 config
Octocat-spinner-32 contrib
Octocat-spinner-32 doc
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Octocat-spinner-32 manifest
Octocat-spinner-32 test
Octocat-spinner-32 utils
Octocat-spinner-32 .gitignore
Octocat-spinner-32 MANIFEST.in
Octocat-spinner-32 README.md
Octocat-spinner-32 contributors.mkd
Octocat-spinner-32 data_fabfile.py
Octocat-spinner-32 fabfile.py
Octocat-spinner-32 setup.py
README.md

CloudBioLinux is a build and deployment system which installs a large selection of Bioinformatics and machine learning libraries on a bare virtual machine (VM) image, freshly installed PC, or in the Cloud. All that is required is a login with ssh (secure shell) into a fresh base install of Linux. The CloudBiolinux scripts will login and install software remotely - followed by system configuration.

By default CloudBioLinux includes a large suite of tools and libraries, largely pulled from the package management system provided by the image. In addition to the default configuration, other software configurations are supported through, so called, 'editions' and 'flavors'. An edition is a named base install, e.g. CloudBioLinux for Ubuntu. Such an Edition reflects shared installation properties between different projects. Flavors support overriding base packages for specific installations. With a Flavor a derivative of a base Edition can be designed. For example a single web server cound be implemented as a Flavor on top of the 'Minimal' Debian edition. CloudBioLinux installs packages through multiple mechanisms, including the default distribution installer, native installers, and libraries for Perl, R, Python, JAVA and Ruby, as well as installers for special data resources.

CloudBioLinux is designed as a single install route for both VMs on the desktop, such as VirtualBox, and cloud providers, such as Amazon EC2, Openstack, where you start with a bare bones system and bootstrap a running instance. You can even create a minimalistic private cloud on top of XEN or Linux KVM, just plain, or with Eucalyptus. CloudBioLinux included software packages are fully customizable, and different flavours of CloudBioLinux can be configured.

CloudBioLinux provides a Fabric build file, written in Python. There is little need to understand Python, though, as most configuration is done through configuration files. Other scripting languages can be added too. Package selection is through YAML files in the ./config directory.

Using an instance

CloudBioLinux has ready-made images for Amazon EC2 and VirtualBox. Also a repository of biological data is available.

It should be noted, at least 13GB free space is required on the disk.

Amazon

See the 'Getting Started with CloudBioLinux' guide on the CloudBioLinux website for a detailed description. The short version for users familiar with Amazon is:

  • Login to the Amazon EC2 console.
  • Click Launch Instance, and choose the latest CloudBioLinux AMI from the website in the community AMI section (search for 'biolinux').
  • After launching the instance, find the host details of your running instance from the Instances section.
  • Connect to your machine via ssh or VNC (using the Amazon PEM keys)

To use bioligical data provided on Amazon, you need to use CloudBioLinux tools and fabric:

Using CloudBioLinux tools and fabric

Installation

  1. On your (local) machine, install Fabric:

    sudo apt-get install python-setuptools python-dev
    sudo easy_install fabric pyyaml
    
  2. Retrieve the cloudbiolinux code base:

    git clone git://github.com/chapmanb/cloudbiolinux.git
    cd cloudbiolinux
    

Biological data

We manage a repository of useful public biological data on an Amazon S3 bucket. Currently this includes whole genomes pre-indexed for a number of popular aligners. Downloading and installing these saves a ton of time over running the indexing steps yourself, and eases running next-generation analyses on cloud machines.

A Fabric build script is provided to install this data on your local machine. A biodata configuration file in YAML format, config/biodata.yaml, specifies the genomes of interest and the aligner indexes to use. The config/fabricrc.txt file specifies details about the system and where to install the data.

The basic commandline is:

fab -f data_fabfile.py -H your_machine install_data_s3

and you can pass in custom biodata and fabricrc files with:

fab -f data_fabfile.py -H your_machine -c your_fabricrc.txt install_data_s3:your_biodata.yaml

In addition to downloading and preparing the data, the script will integrate these files with a Galaxy instance by updating appropriate Galaxy configuration files. This makes it useful for installing data to a local or cloud-based Galaxy server.

VirtualBox with vagrant

Vagrant allows easy deploying and connecting to VirtualBox images. The setup is ideal for runnig CloudBioLinux on a desktop computer. Install VirtualBox 4.0 and vagrant. Then add the pre-built CloudLinux VirtualBox images and start it up:

    vagrant box add biolinux_version https://s3.amazonaws.com/chapmanb/biolinux_version.box
    mkdir tmp/biolinux
    cd tmp/biolinux
    vagrant init biolinux_version

(note with vagrant you need disk space - at least 3x the image size). The created ./Vagrantfile can be edited to get a full GUI, extra RAM, and a local IP address. Next, fire up the image with

    vagrant up

Once you have a running virtual machine with CloudBioLinux, connect to it with:

    vagrant ssh

no passwords needed! Get root with

    sudo bash

Through Vagrant additional facilities are available, such as a shared network drive. It is also possible to tweak the image (e.g. RAM/CPU settings, and getting the all important guest additions) by firing up virtualbox itself. For more information, see the BioLinux Vagrant documentation, as well as the documentation on the Vagrant website.

Building an image from scratch using CloudBioLinux

CloudBioLinux can be built for any virtualized platform, as long as the target VM is Linux, with an ssh command line.

Amazon

A bare Linux image launched in Amazon EC2 is configured from another machine, i.e. your local desktop, using ssh and cloudbiolinux. See the Installation section for installing CloudBioLinux with fabric.

Any cloudbiolinux distribution can be used, including Ubuntu, Debian Linux and CentOS.

  1. Go to the cloudbiolinux source and edit the config/fabricrc.txt, to match the system you plan to install on. Specifically, distribution and dist_name parameters specify details about the type of target.

  2. Start an Amazon EC2 base instance and retrieve it's DNS hostname:

  1. From your local machine, have CloudBioLinux install your Amazon instance:

    fab -f fabfile.py -H hostname -u username -i private_key_file install_biolinux
    
  2. When finished, use the Amazon console to create an AMI. Thereafter make it public so it can be used by others.

Virtualbox

See the VirtualBox and Vagrant documentation for details on creating a local virtual machine from scratch with CloudBioLinux.

OpenStack

OpenStack is a promising platform for Cloud computing. CloudBioLinux support for OpenStack is planned.

XEN/KVM/Eucalyptus private Cloud

As long as there is an 'ssh' entry to an running VM, CloudBioLinux can install itself.

For more on private Cloud and CloudBioLinux see ./doc/private_cloud.md.

Technical details for using build scripts

Targets for local builds

The Fabric build files are useful for automating installation of scientific software on local systems as well as Amazon cloud servers. There are a number of build targets that can be used to install a subset of the total available packages.

The main build command is used as described above, but the host can point to a local machine or any server on your network:

  fab -f fabfile.py -H localhost -c config/fabricrc.txt install_biolinux

The config/fabricrc.txt configuration file specifies install directories and other server specific details.

With this basic command, you can substitute install_biolinux with serveral more specific targets:

  • install_biolinux:packages -- Install all of the defined system packages.
  • install_biolinux:libraries -- Install all libraries for various programming languages.
  • install_libraries:language -- Install libraries for a specific language.
  • install_biolinux:custom -- Install all custom programs.
  • install_custom:your_package_name -- Install a specific custom program.

Custom package installs

The custom directory contains installation instructions for programs that are not available from standard package repositories. These instructions are written in Python using the Fabric remote deployment tool and can also be used for installing individual packages locally on your machine. To do this, run:

  fab -f fabfile.py -H localhost install_custom:your_package_name

To build and install your_package_name on the local machine. We welcome additional custom bioinformatics package definitions for inclusion in CloudBioLinux. custom/shared.py contains a number of higher level functions which make it easier to write installation instructions.

Using flavors

A Flavor is a specialization of an installation edition. A flavor can filter on packages and add packages and other software. To use a flavor, pass it in on the command line, e.g.

  fab -f fabfile.py -H localhost install_biolinux:flavor=my_flavor

And, like with the other options, a flavor can also be defined in the config file. A command line parameter, however, is preferred.

Rolling your own

BioLinux normally creates a full system for Bioinformatics. The tools provided here to create such an environment are rather generic. So, if you want to install packages on any system, be it desktop, server or VM, the BioLinux tool set can be used to role your own. The first step it to us install_biolinux with a named package list, e.g.

  fab -f fabfile.py -H localhost install_biolinux:packagelist=./contrib/minimal/main.yaml

where install_biolinux is the fab entry point to a non-specific install, starting from the package list in the passed in packagelist. For more information see the section 'Rolling your own' in the BioLinux vagrant documentation in ./doc/vagrant.md.

EC2 quickstart

This provides a quick cheat sheet of commands for getting up and running on EC2 using Amazon's command line tools.

Initial set up

The first time using EC2, you'll need to install the toolkit and credentials for connecting on your local machine, following the getting started guide.

Login to your Amazon EC2 account and go to Security Credentials/X.509. Create a new certificate and download the public cert-*.pem and private pk-*.pem files. Put these in ~.ec2.

Install the ec2 api tools, which require java.

Set up .zshrc/.bashrc:

   export EC2_PRIVATE_KEY=~/.ec2/pk-UBH43XTAWVNQMIZRAV3RP5IIBAPBIFVP.pem
   export EC2_CERT=~/.ec2/cert-UBH43XTAWVNQMIZRAV3RP5IIBAPBIFVP.pem
   export AWS_ACCESS_KEY_ID=<your access key>
   export AWS_SECRET_ACCESS_KEY=<your secret access key>

To test, you should be able to run the command:

   % ec2-describe-regions

Now generate a privatekey for logging in:

   % ec2-add-keypair yourmachine-keypair

This will produce an RSA private key. You should copy and paste this to your .ec2 directory for future use:

   % vim ~/.ec2/id-yourmachine.keypair
   % chmod 600 ~/.ec2/id-yourmachine.keypair

Allow ssh and web access to your instances:

   % ec2-authorize default -p 22
   % ec2-authorize default -p 80

Starting an instance

Each time you'd like to use EC2, you need to create a remote instance to work with; the AWS console is useful for managing this process.

When building from scratch with Alestic images, you will need to increase the size of the root filesystem to fit all of the CloudBioLinux data and libraries. This is done by starting the instance from the commandline with:

   % ec2-run-instances ami-1aad5273 -k kunkel-keypair -t m1.large
                       -b /dev/sda1=:20
   % ec2-describe-instances i-0ca39764

On Ubuntu 10.04, you then need to ssh into the instance and resize the filesystem with:

   % sudo resize2fs /dev/sda1

On 11.04 the resize happens automatically and this is not required.

Testing

BioLinux comes with an integration testing frame work - currently based on Vagrant. Try:

    cd test
    ./testing_vagrant --help

Target VMs can be listed with

    ./testing_vagrant --list

Build a minimal VM

    ./testing_vagrant Minimal

Documentation

Additional documentation can be found in the ./doc directory in the BioLinux source tree.

LICENSE

The code is freely available under the MIT license.

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