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  • Adam English
    Adam English
    2013-12-31

    Hey Andrew,

    You are correct that the "Jelly.py assembly Protocol.xml" will load the predicted gap-size parameter for each gap assembly. The only work around I can think of would be for you to fill in dummy parameters for the cluster command in your Protocol.xml (echo '${CMD}' ${JOBNAME} ${STDOUT} ${STDERR}) and set your nJobs to 1. Then, inside of assembly/ you'll find assembly_chunk0.sh that will have each command that needs to be executed for each Gap.

    --
    ~/Adam English