From d58beeee56d2ee9b6b4f0f7eb2396d0337aa85fb Mon Sep 17 00:00:00 2001
From: Heng Li <lh3@me.com>
Date: Wed, 19 Nov 2014 12:38:55 -0500
Subject: [PATCH] smarter about path finding

---
 bwakit/run-bwamem | 1 +
 1 file changed, 1 insertion(+)

diff --git a/bwakit/run-bwamem b/bwakit/run-bwamem
index 4c75de9..1b40be2 100755
--- a/bwakit/run-bwamem
+++ b/bwakit/run-bwamem
@@ -55,6 +55,7 @@ my $idx = $ARGV[0];
 
 my $exepath = $0 =~/^\S+\/[^\/\s]+/? $0 : &which($0);
 my $root = $0 =~/^(\S+)\/[^\/\s]+/? $1 : undef;
+$root = $exepath =~/^(\S+)\/[^\/\s]+/? $1 : undef if !defined($root);
 die "ERROR: failed to locate the 'bwa.kit' directory\n" if !defined($root);
 
 die("ERROR: failed to locate the BWA index. Please run '$root/bwa index -p $idx ref.fa'.\n")