Loading modules for deeptools and phantomqualpeaktools

[ewels]

Great! Do we need this code now?

# 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?

[ewels]

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)

Phil