Annotations / Add genomic locations to data: fixed sort order and changed a column name from 'chr' to 'chromosome' to make compatible with other scripts.
Merge remote-tracking branch 'upstream/master'
Merge remote-tracking branch 'upstream/master'
Added a new parameter (significance level) to copy number segmentation tools.
Count overlapping CNVs updated to use the new Database of Genomic Variants ( http://dgv.tcag.ca/dgv/app/home ).
Merge remote-tracking branch 'upstream/master'
Changed default parameter value for CNA-seq segmentation tool.
Merge remote-tracking branch 'upstream/master'
Merge remote-tracking branch 'upstream/master'
Merge remote-tracking branch 'upstream/master'
Paramter descriptions changed in BlastN
threads to bowtie, bowtie2, tophat, tophat2 & cufflinks
Merge branch 'master' of https://github.com/chipster/chipster.git
Merge pull request #28 from ilarischeinin/master

Added a new parameter to the segmentation tools for microarrays and NGS data. (These tools are otherwise identical, but the default value for this new parameter is different.)

Tool common/R-2.15/acgh-count-overlapping-cnvs.R has been updated to use the updated version of Database of Genomic Variants. The new tool downloads files directly from their web site, but previously these have been stored in tools/DGV. If local files are preferred, the URLs listed in the code should be downloaded, lines using remote URLs commended out, lines reading local files updated for new file names and uncommented.

Small change to output format of tool microarray/R-2.12/add-locations-to-data.R: name of output column "chr" changed to "chromosome" to be more consistent with other tools.
Merge branch 'master' of https://github.com/chipster/chipster.git
Remove tools/FREEC_Linux64 in update-exec.sh and install-chipster.sh
Merge branch 'master' into data_beta