Merge pull request #265 from mjafin/master

Added gathering of SGE information from command line
Provide command line interface to run a single distributed function. Work towards enabling docker encapsulation
Merge branch 'master' of github.com:chapmanb/bcbio-nextgen
Ensure java memory passed to snpEff commandline call when direct jar access used. Thanks to Jeff Kittrell
Fix grammatical error that bothers me every time I see it
Merge pull request #266 from mariogiov/fix_grammatical_error

Fix grammatical error that bothers me every time I see it
Provide lazy/soft imports for secondary non-core dependencies used in processing to allow use of bcbio-nextgen as a library. conda build script for bcbio-nextgen
add min_read_length to ALGORITHM_KEYS
Merge pull request #267 from porterjamesj/patch-5

add min_read_length to ALGORITHM_KEYS
Removed B run trimming.
Remove B run  trimming.
Finalize removal of old brun trimming: removes supplemental code that is no longer used. Plug min_read_length into read_through_trimming. Add documentation. #267
Add documentation and expansion of Ensemble calling to TODO list. Fixes #268
Update docker file to ensure leninent permissions on /usr/local directory to allow updates in place. Ensure loaded values from YAML files get mapped to strings for comparisons
Enable running docker tests without installed bcbio-nextgen and only bcbio-nextgen-vm and docker
skip decompressing fastq.gz if it's already been done.
Provide empty default for tag when not specified. #258
Co-opt currently usused profile argument to allow tagging of bcbio runs to help differentiate them on busy clusters. #258
Use 1Gb/core base memory usage if no memory specified instead of enforcing 2Gb. Fixes #271
Merge branch 'master' of github.com:chapmanb/bcbio-nextgen