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NeCTAR flavor for CBL

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 do not already have it). 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/nectar_flavor.git nectar

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/nectar as untracked files, but no need to worry about that - you can add that directory to your .gitignore or leave it as it. However, do not add/commit those files into the cloudbiolinux repostory).

The reason for having separate repositories is because nectar_flavor code depends on CBL, but CBL code does not depend on the nectar_flavor code. As a result, having these two repositories separate and independently versioned, it allows them to be managed independenty (i.e., nectar_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/nectar directory):

  • main.yaml - to define the list of meta-packages to be installed
  • packages.yaml - to define the exact list of packages to be installed (this is in part defined by the list from main.yaml)
  • fabricrc_nectar.txt - to define the paths of where stuff should be installed on the remote system

Once all the configuration has been done, run the CBL scripts. The invocation of these scritps may depend a bit on what you are trying to achieve, but should look something like this (take a look at the CBL documentation for more about the available scripts and options):

$ fab -f fabfile.py -u ubuntu -i <key> -H <IP> \
  -c ./contrib/flavor/nectar/fabricrc_nectar.txt \
  install_biolinux:target=packages,packagelist=./contrib/flavor/nectar/main.yaml,\
  flavor=nectar,pkg_config_file_path=./contrib/flavor/nectar/packages.yaml