Compiling Supernova

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

Steps

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:

   #!/bin/bash
   #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
   
   cd $PBS_O_WORKDIR
   supernova testrun --id=tiny
   

6. If the run succeeded, the supernova_test.out should contain, at the end, text that looks similar to:

   Outputs:
   - 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