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Genomics Virtual Lab (GVL) flavor for CloudBioLinux

About

This is a CloudBioLinux (CBL) flavor intended to be used when building CBL images on the NeCTAR cloud as part of the Genomics Virtual Laboratory.

Installation

To install, first clone CBL from its Git repository (if you have already done that). Then, change into cloudbiolinux/contrib/flavor/ directory and clone this flavor:

$ cd <project_home>
$ git clone https://github.com/chapmanb/cloudbiolinux.git
$ cd cloudbiolinux/contrib/flavor
$ git clone https://github.com/afgane/gvl_flavor.git gvl

The two repositories will be kept separate (depending on the contents of your .gitignore file in the cloudbiolinux repository root directory (i.e., <project_home>), git may mark contrib/flavor/gvl as untracked files, but no need to worry about that - you can add that directory to your .gitignore or leave it as is. However, do not add/commit gvl flavor files into the cloudbiolinux repository).

The reason for having separate repositories is because gvl_flavor code depends on CBL, but CBL code does not depend on the gvl_flavor code. As a result, having these two repositories separate and independently versioned, it allows them to be managed independently (i.e., gvl_flavor can be versioned but does not have to become part of the main CBL source).

Use

The flavor is used as part of invoking CBL scripts. To adjust the settings the flavor defines, edit the following files (all in <project_home>/cloudbiolinux/contrib/flavor/gvl directory):

  • main.yaml - to define the list of meta-packages to be installed
  • packages.yaml - to define the exact list of system packages to be installed (this is in part defined by the list from main.yaml)
  • *-libs.yaml - to define specific language libraries to be installed (this is in part defined by the list from main.yaml)
  • tools.yaml - to define a list of tools and their versions that will be installed as Galaxy-dependencies
  • fabricrc.txt - to define the paths where software should be installed on the remote system

Once all the configuration has been done run the CBL scripts:

$ fab -i <key> -H ubuntu@<IP> -c contrib/flavor/gvl/fabricrc.txt install_biolinux:flavor=gvl

Once all the packages and libraries have been installed, clean the image and then create a snapshot from it via the cloud console:

$ fab -i <key> -H ubuntu@<IP> install_biolinux:target=cleanup