Rename seq-comp to misc in MicroarrayModule
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
New parameter defaults for NGS copy number segmentation tool.
Merge remote-tracking branch 'upstream/master'
Merge remote-tracking branch 'origin/master' into trait