Submitting jobs to the MSU HPC queue

In Processing another sample with TopHat and HTSeq, we showed you a shell script, which was a way of telling the computer to do multiple things in a row. We discussed several advantages to scripting –

1. It automates long-running processes;
2. It tracks what you did, and you can edit it (to modify analyses) and also copy it (to do a family of analyses);
3. You can also provide it as part of your Methods in your paper;

There is also a fourth advantage, or really a necessity, to scripting: it’s how you use the MSU HPC to run your computation. Briefly, to run a job on the HPC, you create a shell script and then run ‘qsub’.

Here are four scripts (plus a common library script) that you could use to run some analyses on the HPC. To run, do something like this:

module load powertools
getexample RNAseq-model

mkdir ~/rnaseq
mkdir ~/rnaseq/script
cd ~/rnaseq/script
ln -fs ~/RNAseq-model/data/*.fastq .

curl -O http://2014-msu-rnaseq.readthedocs.org/en/latest/_static/subset/env.sh
curl -O http://2014-msu-rnaseq.readthedocs.org/en/latest/_static/subset/process-1.sh
curl -O http://2014-msu-rnaseq.readthedocs.org/en/latest/_static/subset/process-2.sh
curl -O http://2014-msu-rnaseq.readthedocs.org/en/latest/_static/subset/process-3.sh
curl -O http://2014-msu-rnaseq.readthedocs.org/en/latest/_static/subset/process-4.sh

qsub process-1.sh
qsub process-2.sh
qsub process-3.sh
qsub process-4.sh

You can use ‘qstat | grep <username>’ to check on your jobs’ status.

Next: Miscellaneous advice

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