Commit ebfdc202842b4ec16ac6b3a380b17f2e00ab6b68 - barrnap

Support alternate 'nhmmer' in PATH Torsten Seemann 7 years ago

1 changed file(s) with 10 addition(s) and 6 deletion(s). Raw diff Collapse all Expand all

+10

-6

bin/barrnap less more

8	8	# global variables
9	9
10	10	my $EXE = $FindBin::RealScript;
11		my $VERSION = "0.7";
	11	my $VERSION = "0.8";
12	12	my $DESC = "rapid ribosomal RNA prediction";
13	13	my $AUTHOR = 'Torsten Seemann <torsten.seemann@gmail.com>';
14		my $URL = 'https://github.com/Victorian-Bioinformatics-Consortium/barrnap';
	14	my $URL = 'https://github.com/tseemann/barrnap';
15	15	my $DBDIR = "$FindBin::RealBin/../db";
16	16	my $OPSYS = $^O;
17		my $NHMMER = "$FindBin::RealBin/../binaries/$OPSYS/nhmmer";
	17	my $BINDIR = "$FindBin::RealBin/../binaries/$OPSYS";
18	18
19	19	my %KINGDOM = (map { substr($_,0,1) => $_ } qw(bac arc euk mito));
20	20	my %LENG = (

36	36	msg("Written by $AUTHOR");
37	37	msg("Obtained from $URL");
38	38	msg("Detected operating system: $OPSYS");
39
40		-x $NHMMER or err("No binary for your OS '$OPSYS' is included. If you have one, copy it to $NHMMER.");
	39	msg("Adding $BINDIR to end of PATH");
	40	$ENV{PATH} .= ":$BINDIR";
	41
	42	my($NHMMER) = qx(which -a nhmmer 2> /dev/null);
	43	$NHMMER or err("Could not find 'nhmmer' executable in PATH");
	44	chomp $NHMMER;
41	45	msg("Using HMMER binary: $NHMMER");
42	46
43	47	$threads > 0 or err("Invalid --threads $threads");

47	51	msg("Setting evalue cutoff to $evalue");
48	52
49	53	$lencutoff > 0 or err("Invalid --lencutoff $lencutoff");
50		msg("Will tag genes < $lencutoff of expected length.");
	54	msg("Will tag genes < $lencutoff of expected length.");
51	55
52	56	$reject > 0 or err("Invalid --reject cutoff $reject");
53	57	msg("Will reject genes < $reject of expected length.");