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.