From a462b5e1e7c9015774846a4c20535458cd3bc659 Mon Sep 17 00:00:00 2001 From: weisburd Date: Mon, 3 May 2010 17:07:21 +0000 Subject: [PATCH] Changed a default path git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3291 348d0f76-0448-11de-a6fe-93d51630548a --- python/genomicAnnotatorScripts/GenerateTranscriptToInfo.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/python/genomicAnnotatorScripts/GenerateTranscriptToInfo.py b/python/genomicAnnotatorScripts/GenerateTranscriptToInfo.py index 087c552ed..2dba17882 100755 --- a/python/genomicAnnotatorScripts/GenerateTranscriptToInfo.py +++ b/python/genomicAnnotatorScripts/GenerateTranscriptToInfo.py @@ -16,7 +16,7 @@ NOTE: This script must be run in the top level dir of your GATK checkout area. parser = OptionParser( description=description, usage="usage: %prog [options] ", formatter=IndentedHelpFormatterWithNL()) -parser.add_option("-d", "--refgene-directory", metavar="DIR", dest="refgene_dir", help="Specifies the directory that contains refGene-converted.txt", default="/humgen/gsa-hpprojects/GATK/data/Annotations/refseq/raw/") +parser.add_option("-d", "--refgene-directory", metavar="DIR", dest="refgene_dir", help="Specifies the directory that contains refGene-converted.txt", default="/humgen/gsa-hpprojects/GATK/data/Annotations/refseq/hg18_b36/raw/") parser.add_option("-p", "--print", dest="output", action="store_true", default=False, help="Only print the commands to standard out, don't actually execute them yet.") parser.add_option("-e", "--execute", dest="execute", action="store_true", default=False, help="Executes the commands. This flag acts as a confirmation that you want to proceed with launching the processes.")