Hi, 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 successfully.
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? Thanks, Peter Thompson, PhD Candidate Department of Medical Genetics Life Sciences Centre, UBC Vancouver, BC CANADA V6T 1Z3
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