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/n6/extref/ng.2256-S1.pdf

1. Which version of BWA should I use? The current gives me the EoF error and the 0.5.9. gives me "missing argument -I"

2. Originally I had this workflow to start with https://main.g2.bx.psu.edu/u/mj--/w/ngs

, but I at the sam-to-bam conversion I get the "sequences are not currently available for specified build" error when using "locally cached" and I can't figure out how to use the reference file hg19.fa without actually uploading it to Galaxy, because I do not have enough space on the filesystem where the Galaxy distribution is placed ( /home). The genedata are all on /genedata. So my question here is: How to use the hg19.fa file placed on another filesystem then the galaxydist?

3. Thus I searched the web and found this workaround: https://main.g2.bx.psu.edu/u/mj--/w/sample-workflow-whole-exome-sequencing

which runs fine ONLINE at usegalaxy but produces this error in my local instance

Dataset generation errors

Dataset 18: Filter SAM on data 7

Tool execution generated the following error message:

Traceback (most recent call last):
  File "/home/trr/galaxy-dist/tools/samtools/sam_bitwise_flag_filter.py", line 148, in <module>
    if __name__ == "__main__": main()

  File "/home/trr/galaxy-dist/tools/samtools/sam_bitwise_flag_filter.py", line 137, in main
    flags = int( fields[flag_col] )
IndexError: list index out of range

So thats my 3rd question: How to solve this error? I didnt find anything online.

Best

Moritz