New parameter defaults for NGS copy number segmentation tool.
Merge remote-tracking branch 'upstream/master'
Merge remote-tracking branch 'upstream/master'
Merge remote-tracking branch 'upstream/master'
Making Microarrays/Utilities/Extract samples from dataset less sensitive about phenodata column names.

When reading in the phenodata, by default R will check that column names are valid R variable names (e.g. cannot contain spaces or start with a number). As the user interface allows users to create illegal column names in phenodata (like containing spaces), this can break tools that have a METACOLUMN_SEL parameter, as the column names in the phenodata read into R will no longer be the same as was displayed in the user interface. This can be fixed by adding check.names=FALSE to the R command reading in the phenodata (of each and every tool), or alternatively by preventing creation of illegal column names in the phenodata in the user interface.
Merge remote-tracking branch 'upstream/master'
Merge remote-tracking branch 'upstream/master'
Bugfix for CNA / Count overlapping CNVs when parameter genome.build is set to the previous build NCBI36.
Merge remote-tracking branch 'upstream/master'
Merge pull request #29 from ilarischeinin/master

Phenodata column names that are not valid R variable names
Bugfix for plotting from tool Copy number aberrations / Group tests for called copy number data. When data from chromosomes X/Y was present, the lines between chromosomes were drawn at wrong places.
Merge remote-tracking branch 'upstream/master'
Merge pull request #30 from ilarischeinin/master

Small bug fix to one copy number tool
Require java 1.7+ in chipster.jnlp
Clean up jnlp and chipster launch page
Merge branch 'master' of https://github.com/chipster/chipster.git
Merge branch 'master' into data_beta