Mercurial > repos > diego > rtg_investigator
comparison tools/rtg/galaxy-rtg-map-wrapper.sh @ 1:8593828f91e7 default tip
Full galaxy wrapper
author | diego |
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date | Sat, 21 Apr 2012 21:36:15 -0400 |
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0:d50638ebd809 | 1:8593828f91e7 |
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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 |