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