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comparison tools/rtg/galaxy-rtg-snpsim-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 snpfile=$1
13 shift
14 snpoutputdir=$1
15 shift
16
17 # Run the program, send STDERR to temporary file
18 mkdir $snpoutputdir
19 tmpout=$snpoutputdir/snps.vcf
20 $rtg "$@" -s $tmpout -Z 2> $TMP_STDERR
21
22 #check program's exit code
23 if (( $? )); then
24 #echo "$(date) FAIL $@" >>~/galaxy-rtg-wrapper.log
25 #cat $TMP_STDERR >>~/galaxy-rtg-wrapper.log
26 #Program failed, send STDERR to real STDERR
27 cat $TMP_STDERR >&2
28 rm $TMP_STDERR
29 rm -rf $tmpout
30 exit 1
31 fi
32
33 mv $tmpout $snpfile
34
35 #echo "$(date) DONE $@" >>~/galaxy-rtg-wrapper.log
36
37 #Program succeeded, delete STDERR file
38 rm $TMP_STDERR
39 rm -rf $snpoutputdir
40 exit 0