attribute name change in ensembl: external_gene_id to external_gene_name
Allow empty optional inputs
Add four new copy number tools.
Rewrite MEDIPS tools for R-3.0, and combine into one single tool.
Enable SSL by default in tarball version
Merge pull request #41 from ilarischeinin/master

Four new copy number tools and rewritten MEDIPS
Changed saubset.fastq.R to use seqtk
New index/GTF/genome files
Merge branch 'job_manager'

Conflicts:
	src/main/applications/activemq/activemq.xml
Merge branch 'master' into job_manager