WISH: makeClusterFunctionsTorque("<brew string>")

[HenrikBengtsson]

If makeClusterFunctionsTorque() et al. would accept a brew string as input (as an alternative to a pathname as now), one could make .BatchJobs.R self contained (one file instead of two is easier to keep track off and share), e.g.

cluster.functions <- makeClusterFunctionsTorque('
## Job name
#PBS -N <%= job.name %>

## Merge standard error and output:
#PBS -j oe

## Direct streams to our logfile:
#PBS -o <%= log.file %>

## Resources needed:
<% if (length(resources) > 0) {
  opts <- unlist(resources, use.names=TRUE)
  opts <- sprintf("%s=%s", names(opts), opts)
  opts <- paste(opts, collapse=",") %>
#PBS -l <%= opts %>
<% } %>

## Run R:
Rscript --verbose "<%= rscript %>"
')

staged.queries <- TRUE

[mllg]

We agreed on a feature freeze of BatchJobs and will probably only do maintenance release from now on.

If you are feeling adventurous, you can give the (still unofficial) successor of BatchJobs/BatchExperiments a try (https://github.com/mllg/batchtools). I've already added a string option for the ClusterFunction constructors there.

[HenrikBengtsson]

@mllg, interesting and surprising.

May I suggest that you create a separate issue clarifying this and why, and what you're plans are, ETAs etc? I can see there will be some concerns and you might want to provide a place for folks to raise and discuss them.