Unify align and align_pipe to avoid artificial distinction between processes. Move bwa aln versus bwa mem checks internal to bwa instead of exposing them.
Added picard as a used program.
Merge branch 'master' of github.com:chapmanb/bcbio-nextgen
Fix minimum required version for HTSeq
Merge branch 'master' of github.com:chapmanb/bcbio-nextgen
docker build: ensure environmental variables set even in non-interactive environments. Additional space cleanup for smaller image sizes