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Fix ldtools if tool path contains spaces

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This commit is contained in:
Nicola Soranzo
2025-09-10 02:14:50 +01:00
parent 922bbdc741
commit 0abc2f7d97
1 changed files with 4 additions and 13 deletions
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tools/phenotype_association/ldtools_wrapper.sh
+4 -13
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@@ -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"