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
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