chipster/chipster — pull request #33 by ilarischeinin (2014-03-28 09:06:49+00:00)
Title: Update all copy number tools to R-3.0 and add method QDNAseq for CNA-seq.

All copy number tools have been updated to R-3.0 and to use "library scripts", which handle construction and deconstruction of more complicated R objects from flat tables that can be presented in the Chipster user interface. QDNAseq method has also been implemented for CNA-seq.

Requirements (all for R-3.0):
- Install package QDNAseq from http://bioconductor.org/packages/devel/bioc/html/QDNAseq.html
- Install package WECCA from https://www.dropbox.com/s/98ohl908z0dkvrl/WECCA_0.40.tar.gz (currently installed version is outdated)
- Install package png from CRAN
- Under tools, create directory QDNAseq, which should contain the nine files available at https://bitbucket.org/ccagc/qdnaseq/downloads (directory MPScall can be deleted)

Other:
- In addition to MPScall, directories CanGEM and DGV (all under tools) are also no longer needed and can be deleted.