including RACS location in testing fn msg
including RACS location in testing fn msg
#!/bin/bash
# unit testing (integrity tests) for the pipeline
#
# script containing a series of integrity checks: internal and external dependencies of the pipeline
# determine where the scripts are located
scriptsDIR=`dirname $0`
# load auxiliary fns
. $scriptsDIR/auxFns.sh --source-only
main() {
# integrity checks
echo "*** CHECKING RACS pipeline INTERNAL INTEGRITY..."
for i in `cat $scriptsDIR/../test/lst`; do
#echo $i;
checkIntegrityPipeline ../$i;
done
# external dependencies
echo "*** CHECKING EXTERNAL DEPENDENCIES with auxiliary software: BWA, SAMTOOLS & RSCRIPT..."
# checking requirements for the ORF part of the RACS pipeline
checkTools bwa samtools
# checking requirements for the intergenic part of the RACS pipeline
checkTools samtools Rscript
}
if [ "${1}" != "--source-only" ]; then
main "${@}"
fi
#########