From 570f8ffc94c594073762adcc584ad16aeaaf54e6 Mon Sep 17 00:00:00 2001
From: kohleman <kohleman>
Date: Wed, 28 Oct 2009 11:13:53 +0000
Subject: [PATCH] - parallel usage: starts one process for each lane - Number
of tile is now a mandatory parameter
SVN: 13108
---
deep_sequencing_unit/source/bash/cif2txt.sh | 10 +++++-----
1 file changed, 5 insertions(+), 5 deletions(-)
diff --git a/deep_sequencing_unit/source/bash/cif2txt.sh b/deep_sequencing_unit/source/bash/cif2txt.sh
index 7599516f064..942ffcc7b3f 100755
--- a/deep_sequencing_unit/source/bash/cif2txt.sh
+++ b/deep_sequencing_unit/source/bash/cif2txt.sh
@@ -21,13 +21,13 @@
INTENSITY_FOLDER=$1
CYCLES=$2
+NUMBER_OF_TILES=$3
NUMBER_OF_LANES=8
-NUMBER_OF_TILES=100
#INT_NSE_DIR=$1/int_nse
PRG=`basename $0`
-USAGE="Usage: ${PRG} <Path_to_Intensity_Folder> <Number_of_Cycles> \n\nEXAMPLE: ${PRG} /array0/Runs/090720_42HUDAAXX/Data/Intensities/ 38"
+USAGE="Usage: ${PRG} <Path_to_Intensity_Folder> <Number_of_Cycles> \n\nEXAMPLE: ${PRG} /array0/Runs/090720_42HUDAAXX/Data/Intensities/ 38 120"
-if [ -z "${INTENSITY_FOLDER}" -o -z "${CYCLES}" ]
+if [ -z "${INTENSITY_FOLDER}" -o -z "${CYCLES}" -o -z "${NUMBER_OF_TILES}" ]
then
echo -e "${USAGE}"
exit 1
@@ -41,8 +41,8 @@ for (( l = 1; l <= $NUMBER_OF_LANES; l++ )); do
for (( t = 1; t <= $NUMBER_OF_TILES; t++ )); do
echo Lane $l Tile $t;
# Convert Signal cif to int
- /dsf/GAPipeline/bin/cifToTxt -l $l -t $t -n $CYCLES -i $INTENSITY_FOLDER -o $INTENSITY_FOLDER -c none
+ /dsf/GAPipeline/bin/cifToTxt -l $l -t $t -n $CYCLES -i $INTENSITY_FOLDER -o $INTENSITY_FOLDER -c none &
# Convert Noise cnf to nse (additional -N)
- /dsf/GAPipeline/bin/cifToTxt -N -l $l -t $t -n $CYCLES -i $INTENSITY_FOLDER -o $INTENSITY_FOLDER -c none
+ /dsf/GAPipeline/bin/cifToTxt -N -l $l -t $t -n $CYCLES -i $INTENSITY_FOLDER -o $INTENSITY_FOLDER -c none &
done
done
--
GitLab