diff --git a/biology/snpeff/Makefile b/biology/snpeff/Makefile
index 3973e9a9a792..81cf1d4f56e1 100644
--- a/biology/snpeff/Makefile
+++ b/biology/snpeff/Makefile
@@ -1,41 +1,42 @@
 PORTNAME=	snpeff
 DISTVERSION=	5.0
 CATEGORIES=	biology java python
 MASTER_SITES=	https://snpeff.blob.core.windows.net/versions/
 DISTNAME=	snpEff_latest_core
+DIST_SUBDIR=	${PORTNAME}-${PORTVERSION}
 
 MAINTAINER=	jwb@FreeBSD.org
 COMMENT=	Genetic variant annotation and effect prediction toolbox
 
 LICENSE=	MIT
 LICENSE_FILE=	${WRKSRC}/LICENSE.md
 
 RUN_DEPENDS=	bash:shells/bash
 
 USES=		python:3.6+ shebangfix zip
 USE_JAVA=	yes
 
 JAVA_VERSION=	12+
 SHEBANG_FILES=	scripts/* scripts/gsa/*
 
 NO_BUILD=	yes
 NO_ARCH=	yes
 WRKSRC=		${WRKDIR}/snpEff
 
 LIBEXEC_DIR=	${PREFIX}/libexec/snpeff
 
+pre-configure:
+	${REINPLACE_CMD} -e 's|%%JAVAJARDIR%%|${JAVAJARDIR}|g' \
+			 -e 's|%%JAVA_HOME%%|${JAVA_HOME}|g' \
+			 ${WRKSRC}/scripts/snpEff ${WRKSRC}/scripts/snpSift
+
 do-install:
 	${MKDIR} ${STAGEDIR}${JAVAJARDIR}/snpeff
 	${MKDIR} ${STAGEDIR}${LIBEXEC_DIR}
 	${INSTALL_SCRIPT} ${WRKSRC}/scripts/snpEff ${STAGEDIR}${PREFIX}/bin
 	${INSTALL_SCRIPT} ${WRKSRC}/scripts/snpSift ${STAGEDIR}${PREFIX}/bin
 	${INSTALL_DATA} ${WRKSRC}/*.jar ${STAGEDIR}${JAVAJARDIR}/snpeff
 	${INSTALL_DATA} ${WRKSRC}/*.config ${STAGEDIR}${JAVAJARDIR}/snpeff
 	cd ${WRKSRC}/scripts && ${COPYTREE_BIN} . ${STAGEDIR}${LIBEXEC_DIR}
 
-pre-configure:
-	${REINPLACE_CMD} -e 's|%%JAVAJARDIR%%|${JAVAJARDIR}|g' \
-			 -e 's|%%PREFIX%%|${PREFIX}|g' \
-			 ${WRKSRC}/scripts/snpEff ${WRKSRC}/scripts/snpSift
-
 .include <bsd.port.mk>
diff --git a/biology/snpeff/distinfo b/biology/snpeff/distinfo
index 895315e4a8c3..decfc79a708d 100644
--- a/biology/snpeff/distinfo
+++ b/biology/snpeff/distinfo
@@ -1,3 +1,3 @@
-TIMESTAMP = 1618353537
-SHA256 (snpEff_latest_core.zip) = 85d907b5dd9e9008a0cf245956e3c9077a31e45f21a1b580d9b98a53fd8dcb9d
-SIZE (snpEff_latest_core.zip) = 45828841
+TIMESTAMP = 1618847647
+SHA256 (snpeff-5.0/snpEff_latest_core.zip) = 85d907b5dd9e9008a0cf245956e3c9077a31e45f21a1b580d9b98a53fd8dcb9d
+SIZE (snpeff-5.0/snpEff_latest_core.zip) = 45828841
diff --git a/biology/snpeff/files/patch-scripts_snpEff b/biology/snpeff/files/patch-scripts_snpEff
index dace484960d7..d15b83ad84e0 100644
--- a/biology/snpeff/files/patch-scripts_snpEff
+++ b/biology/snpeff/files/patch-scripts_snpEff
@@ -1,27 +1,27 @@
---- scripts/snpEff.orig	2021-04-13 22:55:13 UTC
+--- 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=%%PREFIX%%/openjdk12
++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
diff --git a/biology/snpeff/files/patch-scripts_snpSift b/biology/snpeff/files/patch-scripts_snpSift
index 838875a344f8..c76fa3c4fcfd 100644
--- a/biology/snpeff/files/patch-scripts_snpSift
+++ b/biology/snpeff/files/patch-scripts_snpSift
@@ -1,19 +1,19 @@
---- scripts/snpSift.orig	2021-04-13 22:40:00 UTC
+--- scripts/snpSift.orig	2021-04-19 15:55:06 UTC
 +++ scripts/snpSift
 @@ -13,9 +13,9 @@
  # Created by: Brad Chapman
  #---------------------------------------------------------------------------------------------------
  
 -jardir="$(cd "$(dirname "$0")" && cd ".." && pwd -P)"
 +jardir=%%JAVAJARDIR%%/snpeff
-+JAVA_HOME=%%PREFIX%%/openjdk12
++JAVA_HOME=%%JAVA_HOME%%
  
 -java=java
  if [ -e "$JAVA_HOME/bin/java" ]
  then
  	java="$JAVA_HOME/bin/java"
 @@ -44,4 +44,3 @@ if [ "$jvm_mem_opts" == "" ]; then
  fi
  
  exec $java $jvm_mem_opts $jvm_prop_opts -jar ${jardir}/SnpSift.jar $pass_args
 -exit