clean up

MGEScan · Feb 12, 2016 · 277b6d8 · 277b6d8
1 parent f99341f
commit 277b6d8
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Showing 2 changed files with 2 additions and 15 deletions.
diff --git a/mgescan/nonltr/hmm/get_phmm.pl b/mgescan/nonltr/hmm/get_phmm.pl
@@ -3,11 +3,6 @@
 use Getopt::Long;
 use Cwd 'abs_path';
 use File::Basename;
-use lib dirname (dirname abs_path $0) . '/lib';
-use Prompt qw(prompt_yn);
-
-my $debug;
-$debug = $ENV{'MGESCAN_DEBUG'};
 
 my $seq; 
 my $phmm_file;
@@ -56,10 +51,6 @@
 	#system("hmmconvert ".$phmm_file." > ".$phmm_file."c");
 	#system("hmmsearch  --noali --domtblout ".$phmm_dir."tbl ".$phmm_file."c ".$pep_file." > /dev/null");
 	my $hmm_command = ("hmmsearch  --noali --domtblout ".$tmpfile." ".$phmm_file."3 ".$pep_file." > /dev/null");
-	print $hmm_command if ($debug);
-	#if ($debug && not prompt_yn("Continue?")) {
-	#	exit;
-	#}
 	system($hmm_command);
 	local $/ = undef;
 	my $hmm_result = <$fh>;
@@ -80,10 +71,6 @@
 	}
 }else{
 	$command = "hmm2search ".$phmm_file." ".$pep_file;
-	print $command if ($debug);
-	#if ($debug && not prompt_yn("Continue?")) {
-	#	exit;
-	#}
 	$hmm_result = `$command`;
 
 	@hmm_results = split(/\n/, $hmm_result);

diff --git a/mgescan/nonltr/hmm/makefile b/mgescan/nonltr/hmm/makefile
@@ -1,11 +1,11 @@
 CC =	gcc
 CFLAGS = -O3 -Wall -w
 SRCS =	util_lib.c hmm_lib.c test_hmm.c
-OBJS = $(SRCS:.c=.o) -lm
+OBJS = $(SRCS:.c=.o)
 MAIN = MGEScan
 
 $(MAIN): $(OBJS) 
-	$(CC) $(CFLAGS) -o $(MAIN) $(OBJS)
+	$(CC) $(CFLAGS) -o $(MAIN) $(OBJS) -lm
 
 .c.o:
 	$(CC) $(CFLAGS) -c $< -o $@