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changeset 2:5d392b477172 draft

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Uploaded
author alermine
date Wed, 14 Nov 2012 06:01:02 -0500
parents 0ec82f1785af
children 1c699789d6d3
files [APliBio]Nebula tools suite/Nebula/FindPeaks/findPeaks_wrapper.sh
diffstat 1 files changed, 1 insertions(+), 1 deletions(-) [+]
line wrap: on
line diff
--- 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