# HG changeset patch
# User dereeper
# Date 1624551334 0
# Node ID 70b7a5270968937c2188bdb359f7e8e3a683a5da
# Parent  bbb2c473664c993aba9b66443c7371502aaf5b9d
Uploaded

diff -r bbb2c473664c -r 70b7a5270968 PGAP-1.2.1/PGAP.pl
--- a/PGAP-1.2.1/PGAP.pl	Thu Jun 24 15:08:13 2021 +0000
+++ b/PGAP-1.2.1/PGAP.pl	Thu Jun 24 16:15:34 2021 +0000
@@ -2,24 +2,32 @@
 use strict;
 use warnings;
 use Getopt::Long;
+use File::Basename;
+
+use lib dirname(__FILE__);
 
 ### programs from BLAST
-my $formatdb="formatdb";
-my $blastall="blastall";
+my $formatdb=`which formatdb`;
+chomp($formatdb);
+
+my $blastall=`which blastall`;
+chomp($blastall);
 
 ### programs from mcl
-my $mcl="mcl";
+my $mcl=`which mcl`;
+chomp($mcl);
 
 ### programs from mafft
-my $mafft="mafft";
+my $mafft=`which mafft`;
+chomp($mafft);
 
 ### programs from PHYLIP
-my $seqboot="seqboot";
-my $neighbor="neighbor";
-my $consense="consense";
-my $dnaml="dnaml";
-my $dnadist="dnadist";
-my $dnapars="dnapars";
+my $seqboot=`which seqboot`;chomp($seqboot);
+my $neighbor=`which neighbor`;chomp($neighbor);
+my $consense=`which consense`;chomp($consense);
+my $dnaml=`which dnaml`;chomp($dnaml);
+my $dnadist=`which dnadist`;chomp($dnadist);
+my $dnapars=`which dnapars`;chomp($dnapars);
 
 my $count_tree=0;