diff --git a/tools/phenotype_association/ldtools_wrapper.sh b/tools/phenotype_association/ldtools_wrapper.sh index 331d01bf025..d4788bf2d73 100755 --- a/tools/phenotype_association/ldtools_wrapper.sh +++ b/tools/phenotype_association/ldtools_wrapper.sh @@ -5,7 +5,7 @@ set -e -SCRIPT_DIR=$(dirname $0) +SCRIPT_DIR=$(dirname "$0") ## pagetag options input= @@ -46,16 +46,7 @@ do done ## run pagetag -python $SCRIPT_DIR/pagetag.py --rsquare $rsquare --freq $freq "$input" snps.txt neighborhood.txt -if [ $? -ne 0 ]; then - echo "failed: pagetag.py --rsquare $rsquare --freq $freq \"$input\" snps.txt neighborhood.txt" - exit 1 -fi - -## run sentag -python $SCRIPT_DIR/senatag.py neighborhood.txt snps.txt > "$output" -if [ $? -ne 0 ]; then - echo "failed: senatag.py neighborhood.txt snps.txt" - exit 1 -fi +python "$SCRIPT_DIR/pagetag.py" --rsquare $rsquare --freq $freq "$input" snps.txt neighborhood.txt +## run senatag +python "$SCRIPT_DIR/senatag.py" neighborhood.txt snps.txt > "$output"