From 8f4fbf29a75c2c9d88c36f3962447d22a7244c9e Mon Sep 17 00:00:00 2001
From: kshakir <kshakir@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Sun, 7 Mar 2010 04:19:01 +0000
Subject: [PATCH] Band-Aid: changed the pointers from mike's home directory to
 a checkout of the last know working revision r7169 in my directory.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2946 348d0f76-0448-11de-a6fe-93d51630548a
---
 perl/maf_annotation/annotate_single_maf.pl | 8 +++++---
 1 file changed, 5 insertions(+), 3 deletions(-)

diff --git a/perl/maf_annotation/annotate_single_maf.pl b/perl/maf_annotation/annotate_single_maf.pl
index 34ef65b36..eaf29f406 100755
--- a/perl/maf_annotation/annotate_single_maf.pl
+++ b/perl/maf_annotation/annotate_single_maf.pl
@@ -7,10 +7,12 @@ if (scalar(@ARGV) != 1) {
 
 my ($maf) = @ARGV;
 
+# TODO: Have a common checkout of https://svn/CancerGenomeAnalysis
+# or a compiled version of this matlab program like Firehose uses.
 my $cmd = "matlab <<STOP\n" .
-          "addpath /home/radon00/lawrence/CancerGenomeAnalysis/trunk/matlab/mike" . "\n" .
-          "addpath /home/radon00/lawrence/CancerGenomeAnalysis/trunk/matlab/seq" . "\n" .
-          "addpath /home/radon00/lawrence/CancerGenomeAnalysis/trunk/matlab" . "\n" .
+          "addpath /humgen/gsa-hphome1/kshakir/src/cga_matlab_r7169/mike" . "\n" .
+          "addpath /humgen/gsa-hphome1/kshakir/src/cga_matlab_r7169/seq" . "\n" .
+          "addpath /humgen/gsa-hphome1/kshakir/src/cga_matlab_r7169" . "\n" .
           "annotate_maflite('$maf', '$maf.annotated')" . "\n" .
           "quit" . "\n" .
           "STOP" . "\n";