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1
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1 #!/bin/bash
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2
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3
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4 while getopts "f:c:m:o:s:u:p:" optionName; do
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5 case "$optionName" in
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6
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7 f) CHIPFILE="$OPTARG";;
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8 c) CONTROLFILE="$OPTARG";;
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9 m) MINVAL="$OPTARG";;
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10 s) MAXVAL="$OPTARG";;
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11 o) OUTPUT="$OPTARG";;
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12 u) OUTSTAT="$OPTARG";;
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13 p) PDF="$OPTARG";;
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14
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15 esac
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16 done
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17
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18 local_path=/usr/bin/ChIPQC
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19 R_PATH='Rscript --slave '
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20
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21 echo "$R_PATH $local_path/ChIPQC.R --args $MINVAL $MAXVAL $CHIPFILE $CONTROLFILE $OUTPUT $OUTSTAT $PDF"
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22 $R_PATH $local_path/ChIPQC.R --args $MINVAL $MAXVAL $CHIPFILE $CONTROLFILE $OUTPUT $OUTSTAT $PDF
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23
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