Bioconductor R/Batch

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For small tests, pre- and post-processing with Bioconductor, you can start an interactive R session on the login nodes. All other Bioconductor jobs have to be submitted through the batch system. You can submit a Bioconductor job (inputfile.R) in batch mode with the following command:

sbatch [Slurm options] --wrap="R --vanilla --slave < inputfile.R > outputfile"

Here you need to replace [Slurm options] with Slurm parameters for the resource requirements of the job. Please find a documentation about the parameters of sbatch on the wiki page about the batch system. In this case, stdout is redirected into "outputfile".