Mercurial > repos > diego > rtg_investigator
view 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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#!/bin/sh DIR="$( cd "$( dirname "$0" )" && pwd )" source $DIR/rtg-galaxy.cfg # Temporary storage for STDERR # Temporary storage for mapping output TMP_STDERR=$(mktemp) || exit 1 #echo "$(date) START $@" >>~/galaxy-rtg-wrapper.log paired=$1 shift outputfile=$1 shift if [ $paired == "paired" ]; then outputfile2=$1 fi shift outputdir=$1 shift # Run the program, send STDERR to temporary file tmpout=$outputdir/tmpout$$ $rtg "$@" -o $tmpout --legacy-cigars 2> $TMP_STDERR #check program's exit code if (( $? )); then #echo "$(date) FAIL $@" >>~/galaxy-rtg-wrapper.log #cat $TMP_STDERR >>~/galaxy-rtg-wrapper.log #Program failed, send STDERR to real STDERR cat $TMP_STDERR >&2 rm $TMP_STDERR rm -rf $tmpout exit 1 fi if [ -f $tmpout/mated.sam.gz ]; then mv $tmpout/mated.sam.gz $outputfile [ "$outputfile2" ] && mv $tmpout/unmated.sam.gz $outputfile2 else mv $tmpout/alignments.sam.gz $outputfile fi #echo "$(date) DONE $@" >>~/galaxy-rtg-wrapper.log #Program succeeded, delete STDERR file rm $TMP_STDERR rm -rf $tmpout exit 0