Merge branch 'master' of https://github.com/chapmanb/cloudbiolinux
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
Inclued updated Bio-Linux packages
Merge branch 'cloudbiolinux/master' into mi-deployment
Disable galaxy tool installs by default.
Allow whitespace in URL in _fetch_and_unpack.
Fix typo in install_bfast in applications.py.
Work on harmonizing cloudbio/galaxy/applications.py with the CBL custom applications framework and existing install procedures (reusing macs, bowtie, bfast, bwa, samtools, ucsc tools, abyss, velvet, and emboss). Rewrote @_if_not_installed to look at tool config directories instead of the default path if installing as Galaxy dependency. Implemented ability to have multiple versions of a tool.
Migrated Galaxy freebayes, lastz, perm, and mosiak code to use matching bits in bio_nextgen.py.