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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 $DIR/rtg-galaxy.cfg
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5
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6 # Temporary storage for STDERR
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7 TMP_STDERR=$(mktemp) || exit 1
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8
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9 #echo "$(date) START $@" >>~/galaxy-rtg-wrapper.log
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10 # Run the program, send STDERR to temporary file
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11 $rtg "$@" 2> $TMP_STDERR
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12
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13 #check program's exit code
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14 if (( $? )); then
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15 #echo "$(date) FAIL $@" >>~/galaxy-rtg-wrapper.log
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16 #cat $TMP_STDERR >>~/galaxy-rtg-wrapper.log
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17 #Program failed, send STDERR to real STDERR
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18 cat $TMP_STDERR >&2
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19 rm $TMP_STDERR
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20 exit 1
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21 fi
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22 #echo "$(date) DONE $@" >>~/galaxy-rtg-wrapper.log
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23
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24 #Program succeeded, delete STDERR file
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25 rm $TMP_STDERR
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26 exit 0
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