Added option of reporting gene_name instead of gene_id in htseq count files.
Added annotated_combined.counts to output.

This is annotated with the gene_symbol for supported organisms
(human, mouse, rat, others are possible though) using the mygene
package.
Added gathering of SGE information from command line
Merge branch 'master' of https://github.com/chapmanb/bcbio-nextgen
Merge branch 'count-file-annotation'
Reverted count files back to using gene_id solely
Merge branch 'master' of https://github.com/chapmanb/bcbio-nextgen
Revert files to match upstream
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