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chef/cookbooks Globus integration. Add meta-package and flavor for installing globus… Jun 17, 2013
puppet/modules Initial work LWR integration. Jun 25, 2013
README.md Add links to configuration files; thanks to Ross Whetten Feb 16, 2012
biodata.yaml Add viral references to hg19/GRCh37 Feb 8, 2017
chef_recipes.yaml Globus integration. Add meta-package and flavor for installing globus… Jun 17, 2013
custom.yaml Remove custom GEMINI build, replaced by conda. Fixes #211 Dec 5, 2015
fabricrc.txt Initial cleanups of editions Jul 15, 2014
haskell-libs.yaml A comment about flowsim, failing on Lucid Feb 22, 2012
main.yaml Additional cleanups to manage removal of editions Jul 15, 2014
node_extra.json Globus integration. Add meta-package and flavor for installing globus… Jun 17, 2013
packages-debian.yaml Remap debian packages not available from latest ubuntu list. Thanks t… Dec 7, 2012
packages-homebrew.yaml Packages for metasv support + Biointerchange Aug 7, 2015
packages-nix.yaml Disable default use of Nix Packages Oct 12, 2011
packages-scientificlinux.yaml Fill in some missing gaps between Ubuntu and CentOS/SL (base R). Add … Aug 6, 2013
packages-yum.yaml Update installation on CentOS 7, testing bcbio on bare Docker machine… Jul 3, 2015
packages.yaml Millstone flavor Jul 23, 2015
perl-libs.yaml Mega patch of fixes to get installation working cleanly on localhost … Aug 8, 2013
puppet_classes.yaml Initial work LWR integration. Jun 25, 2013
python-libs.yaml Install current setuptools at beginning of python libraries. Avoids e… Dec 22, 2014
r-libs.yaml updated yaml; sacCer2 => sacCer3 Jun 11, 2014
ruby-libs.yaml Mega patch of fixes to get installation working cleanly on localhost … Aug 8, 2013

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).