Merge branch 'master' of https://github.com/chapmanb/cloudbiolinux
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.
Apply diff for revision 3fa397c3929c from mi-deployment to ec2autorun.py.
Apply diff for revision 16381c282a3f from mi-deployment to ec2autorun.py.
Merge pull request #47 from jmchilton/openstack_fixes

Merge recent changes to mi-deployment/ec2autorun.py
Change cloudman default to use cloudbiolinux auto run instead of mi-deployment's.
Check that nxserver config directory exists before trying to write to it. Trying to install cloudbiolinux with a stripped down package list caused problems without this check.
Upgrade versions for GATK-lite and Picard
Work toward intergrating more of mi-deployment and galaxy-vm-launcher
into CloudBioLinux and making it more configurable. See the following
file for a summary of what has been done and what is left to do:

contrib/cloudman/development_checklist.md
Enhancements to nginx configuration. Refactor modules stuff to allow easy addition of new modules (LDAP for instance can now be configured, off by default). Allow user to specify a nginx.conf file (with nginx_conf_path) or template (with nginx_conf_template_path).
Add jemboss
Merge branch 'master' of github.com:chapmanb/cloudbiolinux