Cleanly handle varscan cleaning case when line previously removed. #491
Produce validation CSV files for structural variant calls, avoiding comparisons in excluded low complexity regions. Avoid pre-calculating merging in complex regions which reduced sensitivity.
fix for issue #494
chanjo integration
Clean up unit tests: add shell script to run, mark current broken tests #496
issue #249 - chanjo integration
Merge branch 'dev' - chanjo integration
Merge remote-tracking branch 'upstream/master'
When building docker image, put environmental variable updates in /etc/environment #497. Ensure bcbio symlinked into PATH when doing upgrades
Merge remote-tracking branch 'upstream/master'
polish fix for issue #494. add unit test
moved chanjo test stub to test directory
renamed variable based on code review
specify version for chanjo
Merge branch 'master' of https://github.com/kern3020/bcbio-nextgen
extended notes on how to run a stub pipeline for chanjo
Add arvados-python-client dependency.
Add slides from BOSC and GCC conference talks
Add slides from BOSC and GCC conference talks
Find post_process-sample.yaml properly

Previous code was looking in data/ instead of data/automated.