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chef/cookbooks
puppet/modules
README.md
biodata.yaml
chef_recipes.yaml
custom.yaml
fabricrc.txt
haskell-libs.yaml
main.yaml
node_extra.json
packages-debian.yaml
packages-homebrew.yaml
packages-nix.yaml
packages-scientificlinux.yaml
packages-yum.yaml
packages.yaml
perl-libs.yaml
puppet_classes.yaml
python-libs.yaml
r-libs.yaml
ruby-libs.yaml

README.md

This directory contains details of the software installed with CloudBioLinux. This is the right place to dig around if you are interested in adding packages to the image, or would like to get an overview of what is installed. The configuration files are written in easily readable YAML format.

  • main.yaml -- High level category view of packages and libraries that are installed with CloudBioLinux.

  • packages.yaml -- A full list of operating system packages that are included, organized by category. The names are standard Ubuntu APT package names.

  • custom.yaml -- Installed software that is not included in the standard package repository. These are often specialized biological packages that have not yet been cleanly packaged. Actual installation code is in the custom sub-directory.

  • python-libs.yaml, r-libs.yaml, perl-libs.yaml, ruby-libs.yaml,-- Libraries installed for a number of programming languages. These are installed by the language specific library managers (easy_install for Python, cpan for Perl, gem for Ruby).