From 8144866e5b00ec84b075a5f71ce16415e0868154 Mon Sep 17 00:00:00 2001
From: Lee Katz - Aspen <gzu2@cdc.gov>
Date: Wed, 4 May 2016 14:14:46 -0400
Subject: [PATCH] removed ridiculous symlinks in main project directory; made
 tree.dnd symlink

---
 scripts/launch_set.pl | 7 ++-----
 1 file changed, 2 insertions(+), 5 deletions(-)

diff --git a/scripts/launch_set.pl b/scripts/launch_set.pl
index a1b8012..a3fec71 100755
--- a/scripts/launch_set.pl
+++ b/scripts/launch_set.pl
@@ -183,11 +183,8 @@ sub main{
   # Find the output files
   my $absDir=rel2abs($$settings{msadir}); # save the abs. path
   my $outPrefix="$project/out"; # consistent output naming
-  symlink("$absDir/out.RAxML_bipartitions","$outPrefix.dnd") if(-e "$absDir/out.RAxML_bipartitions");
-  symlink("$absDir/out.filteredMatrix.tsv","$outPrefix.matrix.tsv") if(-e "$absDir/out.filteredMatrix.tsv");
-  symlink("$absDir/out.informative.fasta","$outPrefix.fasta") if(-e "$absDir/out.informative.fasta");
-  symlink("$$settings{msadir}/out.pairwise.tsv","$outPrefix.pairwise.tallskinny.tsv") if(-e "$absDir/out.pairwise.tsv");
-  symlink("$$settings{msadir}/out.pairwiseMatrix.tsv","$outPrefix.pairwise.matrix.tsv") if(-e "$absDir/out.pairwiseMatrix.tsv");
+
+  symlink("out.RAxML_bipartitions","$$settings{msadir}/tree.dnd");
 
   my $stopTimestamp=time();
   logmsg "Finished at ".strftime("\%F \%T",localtime());