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comparison tools/rtg/galaxy-rtg-snpintersect-wrapper.sh @ 1:8593828f91e7 default tip

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Full galaxy wrapper
author diego
date Sat, 21 Apr 2012 21:36:15 -0400
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0:d50638ebd809 1:8593828f91e7
1 #!/bin/sh
2
3 DIR="$( cd "$( dirname "$0" )" && pwd )"
4 source $DIR/rtg-galaxy.cfg
5
6 # Temporary storage for STDERR
7 TMP_STDERR=$(mktemp) || exit 1
8
9 #echo "$(date) START $@" >>~/galaxy-rtg-wrapper.log
10 # Run the program, send STDERR to temporary file
11 $rtg snpintersect "$@" 2> $TMP_STDERR
12
13 #check program's exit code
14 if (( $? )); then
15 #echo "$(date) FAIL $@" >>~/galaxy-rtg-wrapper.log
16 #cat $TMP_STDERR >>~/galaxy-rtg-wrapper.log
17 #Program failed, send STDERR to real STDERR
18 cat $TMP_STDERR >&2
19 rm $TMP_STDERR
20 exit 1
21 fi
22 #echo "$(date) DONE $@" >>~/galaxy-rtg-wrapper.log
23
24 #Program succeeded, delete STDERR file
25 rm $TMP_STDERR
26 exit 0