|Author:||Brant C. Faircloth|
|Copyright:||This documentation is available under a Creative Commons (CC-BY) license.|
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.
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).
Unzip the sofware package:
tar -xzvf supernova-2.1.1.tar.gz
~/.bashrc(or similar) or for the current session, update the
$PATHto include the directory where we unpacked the supernova software:
Everything should be good to go, now. You can test the software installation using a submission script like the following:
#!/bin/bash #PBS -q workq #PBS -A <allocation> #PBS -l walltime=02:00:00 #PBS -l nodes=1:ppn=20 #PBS -V #PBS -N supernova_test #PBS -o supernova_test.out #PBS -e supernova_test.err export PATH=/home/brant/project/shared/bin/supernova-2.1.1/:$PATH cd $PBS_O_WORKDIR supernova testrun --id=tiny
If the run succeeded, the
supernova_test.outshould 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