Merge pull request #7 from mariogiov/fix_test_pipeline

Fix bug in test_pipeline.py relating to change in programs._get_versions...
Merge pull request #8 from chapmanb/master

Merge from Brad upstream
Changed pipeline/config_utils.py to expand shell variables into paths (specifically for snpEff)
Custom filtering of FreeBayes with bcbio.variation, falling back on standard hard filters
Merge pull request #101 from mariogiov/master

Expand shell variables into paths in config_utils.py
Update Miniconda download to latest released version. Fixes #100
Merge branch 'master' of github.com:chapmanb/bcbio-nextgen