Remove unnecessary source in venvburrito setup. Do not default to cloudbiolinux edition to avoid insallation of cloud components on local systems. Fixes #99
Automatically determine java home from alternatives on debian systems. Fixes #100
Upgraded picard to 1.96.
Structural variant detection tools: lumpy and delly
Merge branch 'master' of github.com:chapmanb/cloudbiolinux
Added Control-FREEC to bio_nextgen.

This is a CNV caller: http://bioinfo-out.curie.fr/projects/freec/
Add stdout_index to versioncheck to allow finding programs with non-standard version location in the version line
Update freebayes installation to check version. Avoid currently problematic autoversion code in GitHub
Merge branch 'master' of github.com:chapmanb/cloudbiolinux
Added version checking to freec installation.
Avoid graphical window popups for checking presence of tracer and beast. #102
Avoid paging in anaconda installation with smaller terminal fixes. Thanks to @andersje. Fixes #101
Preferentially use anaconda python if present even when PATH has not been resourced during localhost builds from .bashrc. Fixes #104
Provide versioned downloads for RNA-seq transcript information. Add latest download for GRCh37 from @roryk
Revert freebayes version to one not causing core dumps on population calling
Ensure gemini installer download removes older scripts from previous runs. Fixes #105
Add required pre-release flag in new pip versions > 1.4.0 to get seal from pypi. seal only has development releases. Fixes #106
Remove requirement for GATK protected until testing with 2.7.1 is complete
bcbio.variation release v0.1.0
Fix for older fabric not having warn_only function in fabric.api module.