I am trying to run SICER (version 0.0.1) in galaxy to call peaks using the 
galaxy interface browser. My workflow is as follows. First I uploaded BAM files 
of my ChIP tag and input tag data, I then convert these to SAM files with the 
SAMtools tool, and then convert the SAM files to intervals using the SAM to 
interval tool. Finally I convert the interval files to BED6 format using the 
convert format tab in the attributes of each file. At every step the tools work 

Finally I go to run SICER on the ChIP tag and input BED6 files I've made but 
after starting successfully I shortly get the following error:

"An error occurred running this job: Traceback (most recent call last): File 
"/galaxy/home/g2main/galaxy_main/tools/peak_calling/sicer_wrapper.py", line 
156, in if __name__=="__main__": __main__() File 
"/galaxy/home/g2main/galaxy_main/tools/peak_calling/sicer_wrapper.py", li"

This is all I can see of the error message. I've tried several times now but it 
still gives the same error. Am I doing something wrong? How do I get SICER to 
work in galaxy?


Peter Thompson, PhD Candidate

Department of Medical Genetics

Life Sciences Centre, UBC

Vancouver, BC CANADA V6T 1Z3
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