--- scripts/snpEff.orig	2021-04-19 15:55:06 UTC
+++ scripts/snpEff
@@ -13,9 +13,10 @@
 # Created by: Brad Chapman
 #---------------------------------------------------------------------------------------------------
 
-jardir="$(cd "$(dirname "$0")" && cd ".." && pwd -P)"
+jardir=%%JAVAJARDIR%%/snpeff
+userdir=~/snpEff
+JAVA_HOME=%%JAVA_HOME%%
 
-java=java
 if [ -e "$JAVA_HOME/bin/java" ]
 then
 	java="$JAVA_HOME/bin/java"
@@ -43,8 +44,9 @@ if [ "$jvm_mem_opts" == "" ]; then
     jvm_mem_opts="$default_jvm_mem_opts"
 fi
 if [[ "$pass_args" != "" && ! "$pass_args" =~ "-c " ]]; then
-    pass_args="$pass_args -c ${jardir}/snpEff.config"
+    pass_args="$pass_args -c ${userdir}/snpEff.config"
 fi
 
+mkdir -p ~/snpEff
+cp ${jardir}/*.config ~/snpEff
 exec $java $jvm_mem_opts $jvm_prop_opts -jar ${jardir}/snpEff.jar $pass_args
-exit