1. Thanks, I'll try this out, after you reavealed me which version I should use :)
, 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?
which runs fine ONLINE AT USE GALAXY 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 here is my 3rd question: How to solve this error? I didnt find anything online.