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#!/usr/bin/sh
# Find a suitable Java runtime (requires Java >= 21)
if [ -n "$JAVA_HOME" ] && [ -x "$JAVA_HOME/bin/java" ]; then
JAVA_EXEC="$JAVA_HOME/bin/java"
else
JAVA_EXEC="/usr/bin/java"
# If the default java is not >= 21, try to find one under /usr/lib/jvm/
if [ -x "$JAVA_EXEC" ]; then
DEFAULT_VER=$("$JAVA_EXEC" -version 2>&1 | awk -F '"' '/version/ {print $2}' | cut -d. -f1)
if [ -z "$DEFAULT_VER" ] || [ "$DEFAULT_VER" -lt 21 ]; then
for jvm in /usr/lib/jvm/java-*-openjdk /usr/lib/jvm/java-*; do
if [ -x "$jvm/bin/java" ]; then
JVM_VER=$(basename "$jvm" | sed -E 's/java-([0-9]+)-.*/\1/')
case "$JVM_VER" in
[0-9]*)
if [ "$JVM_VER" -ge 21 ]; then
JAVA_EXEC="$jvm/bin/java"
break
fi
;;
esac
fi
done
fi
fi
fi
exec "$JAVA_EXEC" -jar '/usr/share/java/snpEff/snpEff.jar' "${@}"
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