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.
Clean up unit tests: add shell script to run, mark current broken tests #496
When building docker image, put environmental variable updates in /etc/environment #497. Ensure bcbio symlinked into PATH when doing upgrades
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.
Turn off GEMINI for integration tests.

This way you can run the tests without a huge GEMINI install.
Refactor: remove code referring to a lane

The concept of a lane to process is stale in the code, which was creating some
confusing code simply due to naming.  Sometimes it was lanes, lane_items,
samples, data, etc. This keeps 'samples' as a list of those data dictionaries
and removes the lane module.

Thanks to @kern3020 for bringing up the issue and @chapmanb for clarifying
that the code was stale.
Refactor: move command line parsing to bcbio_nextgen.py
More work fixing paths and ld_library_path for docker #497
Merge pull request #501 from curoverse/master

Add arvados-python-client dependency.
Fix for arvados client specification #501
Remove extra slash in continued line
Skip post-annotation with GATK if GATK jar not installed
Isoform level fpkm matrix included in output.

Saved in the upload/project directory as combined.isoform.fpkm.
Fixed downsampling for mutect to use Broad default when max_coverage_depth set to zero