BiocParallel:::.batchtoolsClusterAvailable() mistakes Torque for SGE

[HenrikBengtsson]

Not sure whether or not false positives are expected or not, but on a Torque/PBS cluster, BiocParallel:::.batchtoolsClusterAvailable("sge") returns TRUE (with BiocParallel 1.25.1):

> sapply(c("sge", "slurm", "lsf", "openlava", "torque"), BiocParallel:::.batchtoolsClusterAvailable)
     sge    slurm      lsf openlava   torque 
    TRUE    FALSE    FALSE    FALSE     TRUE 

Vice versa, on an SGE cluster, BiocParallel:::.batchtoolsClusterAvailable("torque") returns TRUE:

> sapply(c("sge", "slurm", "lsf", "openlava", "torque"), BiocParallel:::.batchtoolsClusterAvailable)
     sge    slurm      lsf openlava   torque 
    TRUE    FALSE    FALSE    FALSE     TRUE 

The problem seems to be that both SGE and Torque got qstat and qselect commands;

BiocParallel/R/BatchtoolsParam-class.R

Lines 41 to 60 in d762d9e

	.batchtoolsClusterAvailable <-
	function(cluster)
	{
	switch(
	cluster,
	socket = TRUE,
	multicore = .Platform$OS.type != "windows",
	interactive = TRUE,
	sge = suppressWarnings(system2("qstat", stderr=NULL, stdout=NULL) != 127L),
	slurm = suppressWarnings(system2("squeue", stderr=NULL, stdout=NULL) != 127L),
	lsf = suppressWarnings(system2("bjobs", stderr=NULL, stdout=NULL) != 127L),
	openlava = suppressWarnings(system2("bjobs", stderr=NULL, stdout=NULL) != 127L),
	torque = suppressWarnings(system2("qselect", stderr=NULL, stdout=NULL) != 127L),
	.stop(
	"unsupported cluster type '", cluster, "'; ",
	"supported types (when available):\n",
	" ", paste0("'", .BATCHTOOLS_CLUSTERS, "'", collapse = ", ")
	)
	)
	}