HCC Mutations Workflow on Local Galaxy Instance

[moritz1]

Hello Ladies and Gentlemen,

I am Moritz Juchler from University Heidelberg. For my Bachelor thesis I have to setup Galaxy to find SNP's in genomes from hcc patients. I have a 64-bit openSuse 11.3 server on which I installed Galaxy locally, since we have a) very large files (>30GB per patient) and b) the data is protection sensitive.
I have to run this pipeline:
http://www.nature.com/ng/journal/v44...ng.2256-S1.pdf (page 2)
from this paper:

http://www.nature.com/ng/journal/v44/n6/pdf/ng.2256.pdf

I have some paired end data from patients, and I want to reproduce the pipeline as similar as possible. I have this so far:

https://main.g2.bx.psu.edu/u/mj--/w/ngs

I would be glad to even do 2-3 steps, I wont need much more for my thesis. But I find it so hard to find any information about what to do in Galaxy in practice.

The first step in the workflow of the paper I included are the statistics on page 1 of the supplements, but those aren't necessary (?). So the first step I have to do after the alignment and the sam to bam conversion and the dedupe is the first step on page 2 of the supplements:
"Variant calling Tumor"
Which tool in Galaxy do I have to use in order to do this and the following steps? Any hints, links to papers or answers are welcome I asked the Galaxy Users Mailing list 1 week ago but unfortunately I didnt get any answers.

Best
Moritz