Allow running of gemini externally without needing explicit program version information
Merge pull request #252 from mjafin/master

qcsummary.py modified to report disambiguation statistics.
v0.7.6
Remove unused import.
Fix for single end reads and STAR.
Fix issues with uploading to Galaxy, avoiding upload of directories. Improve documentation. Fixes #255
Remove old deprecated functionality: celery distributed processing, original variant pipeline and support for algorithm/custom_algorithms in bcbio_system.yaml
Provide lower memory defaults for picard processing to match GATK and ensure that picard requirements used during bam post-alignment preparation
Keep mako as requirement until next release
Ensure parsed configuration has empty algorithm directory if not present
Document curl and libcurl-devel requirement for isolated installations. Fixes #256
Initial oncofuse support.

Implemented by (@tanglingfung) Paul Tang (tanglingfung@gmail.com).
Unit test data is from @aebruno's nice FUSIM package:
https://github.com/aebruno/fusim

The unit test needs to be pointed to the bcbio_system YAML file
and hg19 must be installed for this to work.
Set unit test genome for fusion mode to hg19.
Cleanup of commented out code.
Add merging of multiple lanes on todo list. Fixes #259
Download snpEff databases using wget directly to handle proxy issues. chapmanb/bcbio-nextgen-vm#1
Add back compatible algorithm section to configuration to support 0.7.6 release. Thanks to Jeff Kittrell
Add back compatible algorithm section to configuration to support 0.7.6 release. Thanks to Jeff Kittrell
Enable docker style updates using standard bcbio_nextgen.py upgrade command. Remove install/upgrade functionality from web server.
DNA-seq disambiguation enabled