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1 #!/bin/sh
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2
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3 DIR="$( cd "$( dirname "$0" )" && pwd )"
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4 source $DIR/rtg-galaxy.cfg
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5
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6 # Temporary storage for STDERR
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7 # Temporary storage for mapping output
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8 TMP_STDERR=$(mktemp) || exit 1
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9
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10 #echo "$(date) START $@" >>~/galaxy-rtg-wrapper.log
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11
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12 outputfile=$1
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13 shift
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14 outputdir=$1
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15 shift
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16
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17 # Run the program, send STDERR to temporary file
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18 tmpout=$outputdir/tmpout$$
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19 $rtg "$@" -Z -o $tmpout 2> $TMP_STDERR
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20
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21 #check program's exit code
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22 if (( $? )); then
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23 #echo "$(date) FAIL $@" >>~/galaxy-rtg-wrapper.log
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24 #cat $TMP_STDERR >>~/galaxy-rtg-wrapper.log
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25 #Program failed, send STDERR to real STDERR
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26 cat $TMP_STDERR >&2
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27 rm $TMP_STDERR
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28 rm -rf $tmpout
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29 exit 1
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30 fi
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31
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32 mv $tmpout/alignments.txt $outputfile
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33
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34 #echo "$(date) DONE $@" >>~/galaxy-rtg-wrapper.log
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35
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36 #Program succeeded, delete STDERR file
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37 rm $TMP_STDERR
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38 rm -rf $tmpout
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39 exit 0
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