# HG changeset patch
# User stef
# Date 1410427019 14400
# Node ID 4d30096403143cacee5f1b114cbd7e1873ba35aa
# Parent  9285f791716dadd55e22e2781cec5fb27bc22598
Uploaded

diff -r 9285f791716d -r 4d3009640314 falco.sh
--- a/falco.sh	Thu Sep 11 05:11:11 2014 -0400
+++ b/falco.sh	Thu Sep 11 05:16:59 2014 -0400
@@ -75,20 +75,20 @@
 ## running analysis
 ## ----------
 echo "Starting VcAn"
-$TOOLDIR/falco_new/amplicon-VcAn-TSACP.sh $bam_file $bam_base
+$TOOLDIR/falco/amplicon-VcAn-TSACP.sh $bam_file $bam_base
 #$TOOLDIR/falco/amplicon-AlVcAn-TSACP.sh ## this contains more
 
 echo "Starting amplicon-Report"
-$TOOLDIR/falco_new/amplicon-Report.sh $bam_base
+$TOOLDIR/falco/amplicon-Report.sh $bam_base
 
 echo "Starting QC"
-$TOOLDIR/falco_new/amplicon-QC.sh $bam_file
+$TOOLDIR/falco/amplicon-QC.sh $bam_file
 
 #echo "Starting plots.R"
 #$TOOLDIR/falco/misc/plots.R $bam_base.qc.ann.txt $bam_base.qc.targets.txt $bam_base.pdf
 
 echo "Starting mkHtmlReport"
-$TOOLDIR/falco_new/misc/mkHtmlReport.pl ./ ./
+$TOOLDIR/falco/misc/mkHtmlReport.pl ./ ./