Mercurial > repos > diego > rtg_investigator
diff 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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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tools/rtg/galaxy-rtg-map-wrapper.sh Sat Apr 21 21:36:15 2012 -0400 @@ -0,0 +1,50 @@ +#!/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