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#!/bin/sh
#
# Script to submit a SGE job that will run an alignment and
# merge the results using goby using goby
#
ALIGN=`qsub -terse -N %SGE_JOB_NAME%-align goby-align.qsub`
echo $ALIGN
# if the align job is an array job then the id returned
# is of the form N.I-J:K where N is the job id and the
# I,J,K are the array indices and step value
# we only care about the job id (N)
ALIGN=${ALIGN%%.*}
echo $ALIGN
# Merge results from the alignment
MERGE=`qsub -hold_jid $ALIGN -terse goby-merge.qsub`
echo $MERGE
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