Merge branch 'master' of https://github.com/chapmanb/cloudbiolinux
Write output YAML to manifest subdirectory
Add manifest branch as submodule
Add starting place for R software retrieval
Added R packages metadata processing
Merge pull request #44 from hmenager/master

R metadata processing
Initial dump of information from custom installed programs
Merge branch 'master' of github.com:chapmanb/cloudbiolinux
Fix for when R package info does not have homepage information
Update documentation for custom packages to feed into package descriptions
Update manifest for CloudBioLinux release 27 June 2012
Remove submodule link to manifest branch
Manifest configuration files for CloudBioLinux release 27 June 2012
Recursive no longer needed with switch from submodules
Move genome download functionality into importable module. Move setup and hard coding to original data_fabfile. Thanks to @jmchilton. fixes #45
Add custom build target for Artem Tarasov's sambamba
Bug fix for now undefined variable do_additional. Handle None case for empty genomes or genome_indexes in yaml config.
Merge pull request #46 from jmchilton/master

Small genomes.py fixes.
Install latest processing pipeline as part of exome analysis setup
Apply diff for revision ce55ac362fcb from mi-deployment to ec2autorun.py.