ICGC-TCGA-PanCancer/SeqWare-CGP-SomaticCore — pull request #9 by keiranmraine (2014-10-31 15:48:22+00:00)
Title: Multi tumour - working

This resolves the need for this branch. Will now cope with any number of tumours for a single donor and only pull the control BAM a single time.

Everything has been tested except vcfUpload. Switching testMode to false will pull data from GNOS with the specified server (``gnosServer``) and info from the decider populating

* tumourAliquotIds
* tumourAnalysisIds
* tumourBams
* controlAnalysisId
* controlBam

To activate the upload branch specify ``uploadServer``, some of the other test parameters are available and hopefully clear in the ini file. I'll focus on expanding the readme and docs next.