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annotate wrapper.sh @ 19:cc270db37d33 draft

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author Mikel Egana Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
date Sat, 06 Oct 2012 21:50:39 +0200
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Mikel Egana Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
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1 #!/bin/sh
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Mikel Egana Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
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Mikel Egana Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
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3 # STDERR wrapper - discards STDERR if command execution was OK.
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Mikel Egana Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
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Mikel Egana Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
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5 #
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Mikel Egana Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
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6 # This script executes a given command line,
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Mikel Egana Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
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7 # while saving the STDERR in a temporary file.
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Mikel Egana Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
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8 #
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9 # When the command is completed, it checks to see if the exit code was zero.
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10 # if so - the command is assumed to have succeeded - the STDERR file is discarded.
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11 # if not - the command is assumed to have failed, and the STDERR file is dumped to the real STDERR
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12 #
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13 #
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14 # Use this wrapper for tools which insist on writting stuff to STDERR
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15 # even if they succeeded -
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16 # which throws galaxy off balance.
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17 #
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18 #
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Mikel Egana Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
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19 # Copyright 2009 (C) by Assaf Gordon
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20 # This file is distributed under the BSD license.
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22 TMPFILE=$(mktemp) || exit 1
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24 "$@" 2> $TMPFILE
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26 EXITCODE=$?
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27 # Exitcode != 0 ?
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28 if [ "$EXITCODE" -ne "0" ]; then
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29 cat $TMPFILE >&2
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30 fi
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31 rm $TMPFILE
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33 exit $EXITCODE