Add SOMATIC flag for FreeBayes records

Initial step to address issue #317, but it is not hooked yet to the pipeline
RNA-seq disambiguation parallelisation improvements
add "--no-check-certificate" 

to wget gemini_install.py 

not sure if everyone has the same issue though
Merge pull request #354 from tanglingfung/patch-1

add "--no-check-certificate"
Ensure batch names do not clash with sample names, which causes issues when preparing gemini databases. Fixes #352. Handle non-bgzipped inputs to Gemini database creation, from ensemble calls
RNA-seq disambiguation: Moved to under same cluster config as quantification
Merge pull request #351 from mjafin/master

RNA-seq disambiguation parallelisation improvements
Avoid bgzipping callable region file when no explicit variant regions specified and validation used. Thanks to Severine Catreux
Correctly check batches for naming clashes with descriptions for multi-batch inputs
Improved fix for list/non-list batches that handles non string batch names
Swap samtools view to sambamba view to avoid bug in samtools for SAM inputs without reads. Fixes #346
Reduce memory usage on streaming jobs like marking duplications and realignment to help with memory conflict errors while running alignment post-preparation
Avoid memory usage issues when merging BAM files by reducing samtools sort memory
Enable specifying genome build in template CSV files
Avoid duplicate VCF merge errors when running ensemble calling on batches. Fixes #352
Fix location of disambiguation directory inside sample directory to avoid multisample directory clashes. Fixes #355
Add timing information to the RNA-seq pipeline.
Added information for fixing conda.cli not found issue.

Thanks to Jiantao Shi.
Fix for Cufflinks dropping high-coverage genes.

Set --max-bundle-frags to 2000000, up from the default of
1000000. Thanks to @mjafin for the suggestion and
discussion.  Closes #357.
Update of changes in preparation for the 0.7.8 release.