Upgrade bwa and samtools to latest releases
Build targets for bamutil, tabix, grabix. Fix S3 genome upload command. Handle empty packages or libraries in configuration files
Fix for empty packages fix, thanks to @jmchilton
Proteomics: Updates geared toward actually properly installing OpenMS from source.
Proteomics: Upgrade TPP to 4.6.2, OpenMS 1.10.0 (actually compiled now instead using the apt-only packaging).
Galaxy Tools: Allow specification in YAML tools file of environment variables that will be inserted into env.sh.

The following tool entry for Augustus demonstrates setting the version, setting multiple dirs in env.sh specified path, and these new environment variables (in this case AUGUSTUS_CONFIG_PATH will be set to /path/to/tools/augustus/2.7/config):

    applications:
      augustus:
      - version: "2.7"
        bin_dirs:
        - bin
        - scripts
        env_vars:
          AUGUSTUS_CONFIG_PATH: $system_install/config
Galaxy Tools: Updates/improvements for augustus Galaxy tool install.
Proteomics: Add a required library for galaxyp flavor.
Implement stronger check for correct distribution when targetting Ubuntu or Debian (i.e. make sure dist_name is correct).

I hosed a precise VM a few weeks ago because quantal was being targetted and I have a collaborator who just did the same. This should prevent that.
Merge pull request #71 from jmchilton/stronger_check

Ensure dist_name is correct.
Move to latest CRAM release. Fixes chapmanb/bcbio-nextgen#4
Ignore distribution checks for specialized usage of CloudBioLinux like installing libraries or custom packages
Update to latest bcbio.variation
Correctly load CloudBioLinux editions and flavors for distribution checks when doing data loading, fixes chapmanb/bcbio-nextgen#6 Thanks to @cbergman
Provide samtools build that is safe on systems lacking ncurses. Thanks to @arq5x
Correctly test for samtools being present on the system before installing
Remove potentially truncated previously downloaded files for biodata extraction. closes chapmanb/bcbio-nextgen#7
Move to latest versions of novoalign and novosort: V3
Remove gatk gsalib installation approach until we can make into a proper R package. closes chapmanb/bcbio-nextgen#8
Progress towards running local commands without using ssh, directly on filesystem. Generalize run and exists functions and apply to tabix and grabix as testing examples. Partial improvements for arq5x/gemini#110