# HG changeset patch
# User alermine
# Date 1352890862 18000
# Node ID 5d392b47717266c35c0b837113abcb01fe9630de
# Parent  0ec82f1785af2731938b39b8e16782df83e3a18c
Uploaded

diff -r 0ec82f1785af -r 5d392b477172 [APliBio]Nebula tools suite/Nebula/FindPeaks/findPeaks_wrapper.sh
--- a/[APliBio]Nebula tools suite/Nebula/FindPeaks/findPeaks_wrapper.sh	Wed Nov 14 05:59:25 2012 -0500
+++ b/[APliBio]Nebula tools suite/Nebula/FindPeaks/findPeaks_wrapper.sh	Wed Nov 14 06:01:02 2012 -0500
@@ -107,7 +107,7 @@
     fi
 
     if [[ $ALIGNER == "sam" && $IFBAM == 0 ]]; then
-       samtools view -S -h $INPUT -b |  $SAMTOOLS_BIN_DIR/samtools sort -m 4000000000 -o - $INPUT.sorted | /bioinfo/local/samtools/samtools view -h - >$INPUT.tmp.sam 2>> $OLOG
+       samtools view -S -h $INPUT -b |  $SAMTOOLS_BIN_DIR/samtools sort -m 4000000000 -o - $INPUT.sorted | samtools view -h - >$INPUT.tmp.sam 2>> $OLOG
     fi
 
     if [[ $ALIGNER == "sam" && $IFBAM == 1 ]]; then