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comparison tools/rtg/galaxy-rtg-map-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 paired=$1
13 shift
14 outputfile=$1
15 shift
16 if [ $paired == "paired" ]; then
17 outputfile2=$1
18 fi
19 shift
20 outputdir=$1
21 shift
22
23 # Run the program, send STDERR to temporary file
24 tmpout=$outputdir/tmpout$$
25 $rtg "$@" -o $tmpout --legacy-cigars 2> $TMP_STDERR
26
27 #check program's exit code
28 if (( $? )); then
29 #echo "$(date) FAIL $@" >>~/galaxy-rtg-wrapper.log
30 #cat $TMP_STDERR >>~/galaxy-rtg-wrapper.log
31 #Program failed, send STDERR to real STDERR
32 cat $TMP_STDERR >&2
33 rm $TMP_STDERR
34 rm -rf $tmpout
35 exit 1
36 fi
37
38 if [ -f $tmpout/mated.sam.gz ]; then
39 mv $tmpout/mated.sam.gz $outputfile
40 [ "$outputfile2" ] && mv $tmpout/unmated.sam.gz $outputfile2
41 else
42 mv $tmpout/alignments.sam.gz $outputfile
43 fi
44
45 #echo "$(date) DONE $@" >>~/galaxy-rtg-wrapper.log
46
47 #Program succeeded, delete STDERR file
48 rm $TMP_STDERR
49 rm -rf $tmpout
50 exit 0