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Bioconductor / BiocParallel

Bioconductor facilities for parallel evaluation
https://bioconductor.org/packages/BiocParallel
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Template file for Slurm job submission #222

Closed mitmurakami closed 1 year ago

mitmurakami commented 1 year ago

Hello,

I have trouble understanding the template file given in a vignettes example, as little explanation is given (Section 4.3.2). The <% ... %> portion of the file seems like JSP scriptlet, but how do they get executed in bash script? I cannot find anything like this anywhere on the internet search. I want to separate the error output and log output files, but the example handles both as "log.file" - what is this keyword do? Is it in R or in JSP?

mtmorgan commented 1 year ago

The templates are from the batchtools package https://cran.r-project.org/package=batchtools. From the vignette the <% ... %> code come from use of the 'brew' package for template instantiation; it is not 'JSP'.

For the specific question about log versus output, it looks like the key line is https://github.com/mllg/batchtools/blob/63a6f812927f6dc78595abbffac0f6bc9651f67a/inst/templates/slurm-simple.tmpl#L27 and the solution would edit this template to use a different file for log versus output.