--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/phylogenies/phylobayes33_wrapper.pl	Tue Mar 11 12:19:13 2014 -0700
@@ -0,0 +1,23 @@
+#!/usr/bin/perl
+
+my $phylobayes_path = '/home/galaxy/pkgs/phylobayes3.3b/exe_lin64/pb';
+my $readPB_path = '/home/galaxy/pkgs/phylobayes3.3b/exe_lin64/readpb';
+
+my $fileName = $ARGV[0];
+my $nchainInput = $ARGV[1];
+my $cycle_bp_trace_comp = $ARGV[2];
+my $discrepancies_threshold = $ARGV[3];
+my $effective_size_floor = $ARGV[4];
+my $jobName = "dataset";
+
+my $burnin = $ARGV[5];
+my $sampleInterval = $ARGV[6];
+
+my $run1 = qx/$phylobayes_path -d $fileName -nchain $nchainInput $cycle_bp_trace_comp $discrepancies_threshold $effective_size_floor $jobName 2>errorlog/;
+print $run1;
+
+my $list = qx/ls -l/;
+print $list;
+
+my $run2 = qx/$readPB_path -x $burnin $sampleInterval $jobName 2>errorlog/;
+print $run2;