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Nextomics / NextDenovo

Fast and accurate de novo assembler for long reads
GNU General Public License v3.0
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how to run on LSF system? #43

Closed huangyixian123 closed 4 years ago

huangyixian123 commented 4 years ago

Hi! I want to use NextDenovo on my LSF system, but when I set "lsf" on " job_type" of "run.cfg", the system get the following error: drmaa.errors.InternalException: code 1: Please set the environment variable SGE_ROOT. So my questions are:

  1. Does NextDenovo work on lsf system？how to set run.cfg (especially "cluster_options" )?
  2. how to set "SGE_ROOT" or somethings like "LSF_ROOT" of drmaa-python in LSF system? Does drmaa-python work on lsf system? And I found a another tool named lsf-drmaa? Does lsf-drmaa work on NextDenovo? what is the the relationship between drmaa-python and lsf-drmaa？
moold commented 4 years ago

Q1. see ParallelTask for help. Q2. I have no idea about this, because they are third-party packages, only used by NextDenovo, maybe you can ask for help in the issue page of lsf-drmaa or drmaa-python.