Compiling Supernova

Author:Brant C. Faircloth
Copyright:This documentation is available under a Creative Commons (CC-BY) license.


  1. On whatever HPC system you are using (should be QB2 or another HPC system w/ a high RAM queue), download the code for supernova. As of writing this protocol, the current stable version is 2.1.

  2. Navigate to a location on that system where you have sufficient space to unzip the software package. 10X handily provides their software with everything you need, so the unzipped package is rather large (~5 GB).

  3. Unzip the sofware package:

    tar -xzvf supernova-2.1.1.tar.gz
  4. In ~/.bashrc (or similar) or for the current session, update the $PATH to include the directory where we unpacked the supernova software:

    export PATH=/home/brant/project/shared/bin/supernova-2.1.1/:$PATH
  5. Everything should be good to go, now. You can test the software installation using a submission script like the following:

    #PBS -q workq
    #PBS -A <allocation>
    #PBS -l walltime=02:00:00
    #PBS -l nodes=1:ppn=20
    #PBS -V
    #PBS -N supernova_test
    #PBS -o supernova_test.out
    #PBS -e supernova_test.err
    export PATH=/home/brant/project/shared/bin/supernova-2.1.1/:$PATH
    supernova testrun --id=tiny
  6. If the run succeeded, the supernova_test.out should contain, at the end, text that looks similar to:

    - Run summary:        /home/brant/work/supernova-assembly/tiny/outs/summary.csv
    - Run report:         /home/brant/work/supernova-assembly/tiny/outs/report.txt
    - Raw assembly files: /home/brant/work/supernova-assembly/tiny/outs/assembly
    Running onfinish handler...
    Waiting 6 seconds for UI to do final refresh.
    Pipestance completed successfully!
    Saving pipestance info to tiny/tiny.mri.tgz