# Find the script we will run.
my $runSppScript = 0;
foreach my $path (split(/:/, $ENV{'PATH'})){
if(-e "$path/run_spp_nodups.R"){
$runSppScript = "$path/run_spp_nodups.R";
last;
}
}
die "###CF Error - could not find phantompeaktools run_spp_nodups.R script" unless($runSppScript);
When I load the module I get this message:
$ module load phantompeakqualtools
The R scripts implemented by this tool can be run directly, e.g.,
run_spp.R <options>
..so wondering if we can just call run_spp_nodups.R directly now instead of $runSppScript?
Thanks again! I added tiny bit to check if the script can be found directly, to avoid iterating through the PATH if it's not needed (4fdf34da9daab2cc7234487a06eb4813bda4a57a)
Great! Do we need this code now?
When I load the module I get this message:
..so wondering if we can just call
run_spp_nodups.R
directly now instead of$runSppScript
?