fix for ltr

MGEScan · Jun 13, 2015 · 936fef4 · 936fef4
1 parent ba0a003
commit 936fef4
Showing 1 changed file with 3 additions and 2 deletions.
diff --git a/mgescan/ltr/find_ltr_pair.pl b/mgescan/ltr/find_ltr_pair.pl
@@ -13,7 +13,8 @@
 my $tool_matrix = $program_dir."/matrix/EDNAFULL";
 my $tool_pfam = $program_dir."/pfam/";
 my $tool_ltr = $program_dir."/MER/ltr";
-my $tool_trf;
+my $tool_trf = `which trf`;
+chomp $tool_trf;
 #my $tool_emboss;
 #my $tool_hmmer = "/nfs/nfs4/home/wazimoha/softwares/hmmer-3.1b1/src/";
 my $main_dir;           # directory of output data            
@@ -59,7 +60,7 @@
 ##################################################
 # get congifuration from input
 ##################################################
-get_path_conf($conf_file, \$tool_trf);
+#get_path_conf($conf_file, \$tool_trf);
 get_value_conf($value_file, \$MIN_DIST,\$MAX_DIST,\$MIN_LEN_LTR,\$MAX_LEN_LTR,\$LTR_SIM_CONDITION,\$CLUSTER_SIM_CONDITION,\$LEN_CONDITION, );
 
 ##############################################