17 files changed, 17 insertions, 35 deletions

diff --git a/biology/artemis/Makefile b/biology/artemis/Makefile
index 484da75e1f9e..133680020cde 100644
--- a/biology/artemis/Makefile
+++ b/biology/artemis/Makefile
@@ -13,11 +13,10 @@ LICENSE_FILE=	${WRKSRC}/LICENSE
 
 RUN_DEPENDS=	bash:shells/bash
 
-USES=		gmake shebangfix
+USES=		gmake java shebangfix
 USE_GITHUB=	yes
 GH_ACCOUNT=	sanger-pathogens
 SHEBANG_FILES=	act art bamview dnaplotter test/*.sh etc/go_associations.pl
-USE_JAVA=	yes
 ALL_TARGET=	jar
 NO_ARCH=	yes
 
diff --git a/biology/bbmap/Makefile b/biology/bbmap/Makefile
index 2c09e28065fa..6807f87f5f5f 100644
--- a/biology/bbmap/Makefile
+++ b/biology/bbmap/Makefile
@@ -15,8 +15,7 @@ RUN_DEPENDS=	bash:shells/bash \
 		pigz:archivers/pigz \
 		pbzip2:archivers/pbzip2
 
-USES=		shebangfix
-USE_JAVA=	yes
+USES=		java shebangfix
 
 SHEBANG_FILES=	${WRKSRC}/*.sh
 
diff --git a/biology/canu/Makefile b/biology/canu/Makefile
index fbb12f8794cf..639805da74aa 100644
--- a/biology/canu/Makefile
+++ b/biology/canu/Makefile
@@ -18,10 +18,8 @@ NOT_FOR_ARCHS_REASON=	Requires 64-bit processor
 LIB_DEPENDS=	libboost_regex.so:devel/boost-libs
 RUN_DEPENDS=	gnuplot:math/gnuplot
 
-USES=		compiler:c++11-lang gmake localbase perl5 tar:xz
+USES=		compiler:c++11-lang gmake java localbase perl5 tar:xz
 USE_CXXSTD=	c++14
-USE_JAVA=	8+
-JAVA_RUN=	yes
 
 # Upstream Makefile compiles directly into ${DESTDIR}${PREFIX} rather than
 # using a separate install target.
diff --git a/biology/cytoscape/Makefile b/biology/cytoscape/Makefile
index 16f1bf26ac6e..034f62515bcf 100644
--- a/biology/cytoscape/Makefile
+++ b/biology/cytoscape/Makefile
@@ -20,9 +20,8 @@ BUILD_DEPENDS=	maven363>0:devel/maven363 \
 		bash:shells/bash
 RUN_DEPENDS=	bash:shells/bash
 
-USES=		shebangfix
+USES=		java shebangfix
 SHEBANG_FILES=	gui-distribution/assembly/src/main/bin/cytoscape.sh
-USE_JAVA=	yes
 USE_GITHUB=	yes
 GH_TUPLE=	${PORTNAME}:${PORTNAME}-parent:${DISTVERSION}:p/parent \
 		${PORTNAME}:${PORTNAME}-api:${DISTVERSION}:a/api \
diff --git a/biology/ddocent/Makefile b/biology/ddocent/Makefile
index 735eba8216d7..2ba33475e6e7 100644
--- a/biology/ddocent/Makefile
+++ b/biology/ddocent/Makefile
@@ -32,8 +32,7 @@ RUN_DEPENDS=	mawk>=0:lang/mawk \
 		freebayes:biology/freebayes \
 		fastp:biology/fastp
 
-USES=		perl5 python shebangfix
-USE_JAVA=	yes
+USES=		java perl5 python shebangfix
 USE_GITHUB=	yes
 
 SHEBANG_FILES=	dDocent scripts/*.sh scripts/*.pl scripts/dDocent_filters
diff --git a/biology/erminej/Makefile b/biology/erminej/Makefile
index 69b22e7884fb..a35aadc33429 100644
--- a/biology/erminej/Makefile
+++ b/biology/erminej/Makefile
@@ -11,8 +11,7 @@ WWW=		https://erminej.msl.ubc.ca/
 LICENSE=	APACHE20
 LICENSE_FILE=	${WRKSRC}/LICENSE.txt
 
-USES=		zip
-USE_JAVA=	yes
+USES=		java zip
 
 WRKSRC=		${WRKDIR}/ermineJ-${DISTVERSION}
 NO_BUILD=	yes
diff --git a/biology/fastqc/Makefile b/biology/fastqc/Makefile
index 05f6306c7ec0..7e95d2e95de5 100644
--- a/biology/fastqc/Makefile
+++ b/biology/fastqc/Makefile
@@ -11,8 +11,7 @@ WWW=		https://www.bioinformatics.babraham.ac.uk/projects/fastqc/
 LICENSE=	GPLv3
 LICENSE_FILE=	${WRKSRC}/LICENSE.txt
 
-USES=		zip perl5 shebangfix
-USE_JAVA=	yes
+USES=		java zip perl5 shebangfix
 USE_PERL5=	run
 
 SHEBANG_FILES=	fastqc
diff --git a/biology/figtree/Makefile b/biology/figtree/Makefile
index 9dd72f07d044..27746c7a58b2 100644
--- a/biology/figtree/Makefile
+++ b/biology/figtree/Makefile
@@ -10,8 +10,7 @@ WWW=		http://tree.bio.ed.ac.uk/software/figtree/
 
 LICENSE=	GPLv2
 
-USE_JAVA=	yes
-USE_ANT=	yes
+USES=		java:ant
 JAVA_VERSION=	17 # Java 8 fails on aarch64: Internal Error (assembler_aarch64.hpp:237) ...
 
 USE_GITHUB=	yes
diff --git a/biology/gatk/Makefile b/biology/gatk/Makefile
index 512cb3b71723..2bcf2b0647e3 100644
--- a/biology/gatk/Makefile
+++ b/biology/gatk/Makefile
@@ -16,9 +16,7 @@ RUN_DEPENDS=	${LOCALBASE}/lib/libfml.so:biology/fermi-lite \
 		gkl>0:biology/gkl \
 		mummer>0:biology/mummer
 
-USES=		gettext-runtime python:test
-USE_JAVA=	yes
-
+USES=		gettext-runtime java python:test
 JAVA_VERSION=	17 # Java 8 fails on aarch64: Internal Error (assembler_aarch64.hpp:237), pid=76025, tid=0x000000000006e359 guarantee(val < (1U << nbits)) failed: Field too big for insn
 
 USE_GITHUB=	yes
diff --git a/biology/gkl/Makefile b/biology/gkl/Makefile
index 84b614afb7d1..7c4c025158c6 100644
--- a/biology/gkl/Makefile
+++ b/biology/gkl/Makefile
@@ -13,8 +13,7 @@ LICENSE_FILE=	${WRKSRC}/LICENSE
 BUILD_DEPENDS=	gmake:devel/gmake
 LIB_DEPENDS=	libisal.so:devel/isa-l
 
-USES=		cmake:noninja localbase:ldflags
-USE_JAVA=	yes
+USES=		cmake:noninja java localbase:ldflags
 USE_LDCONFIG=	yes
 
 USE_GITHUB=	yes
diff --git a/biology/igv/Makefile b/biology/igv/Makefile
index 5790923a7571..23711af1cf41 100644
--- a/biology/igv/Makefile
+++ b/biology/igv/Makefile
@@ -19,8 +19,7 @@ BUILD_DEPENDS=	openjfx14>0:java/openjfx14 \
 		gradle:devel/gradle6
 RUN_DEPENDS=	openjfx14>0:java/openjfx14
 
-USES=		gettext-runtime
-USE_JAVA=	yes
+USES=		gettext-runtime java
 
 USE_GITHUB=	yes
 GH_ACCOUNT=	igvteam
diff --git a/biology/jalview/Makefile b/biology/jalview/Makefile
index 5b1a44b7f8bc..ee85f65f4a46 100644
--- a/biology/jalview/Makefile
+++ b/biology/jalview/Makefile
@@ -15,7 +15,7 @@ LICENSE_FILE=	${WRKSRC}/LICENSE
 
 BUILD_DEPENDS=	gradle761:devel/gradle761
 
-USE_JAVA=	yes
+USES=		java
 JAVA_VERSION=	11
 
 WRKSRC=		${WRKDIR}/${PORTNAME}
diff --git a/biology/picard-tools/Makefile b/biology/picard-tools/Makefile
index bc736acc4cb5..6e24a141e0ac 100644
--- a/biology/picard-tools/Makefile
+++ b/biology/picard-tools/Makefile
@@ -14,8 +14,7 @@ LICENSE=	MIT
 
 RUN_DEPENDS=	samtools:biology/samtools
 
-USE_JAVA=	8+
-JAVA_RUN=	yes
+USES=		java
 
 CONFLICTS_INSTALL=	picard # bin/picard
 
diff --git a/biology/readseq/Makefile b/biology/readseq/Makefile
index af5dafdf3af8..e8faf68f0ae8 100644
--- a/biology/readseq/Makefile
+++ b/biology/readseq/Makefile
@@ -13,7 +13,7 @@ WWW=		https://sourceforge.net/projects/readseq
 
 LICENSE=	PD
 
-USE_JAVA=	yes
+USES=	java
 NO_BUILD=	yes
 SUB_FILES=	readseq
 PLIST_FILES=	bin/readseq share/java/classes/readseq.jar
diff --git a/biology/snpeff/Makefile b/biology/snpeff/Makefile
index 778d62c8fca3..79a90a231703 100644
--- a/biology/snpeff/Makefile
+++ b/biology/snpeff/Makefile
@@ -14,8 +14,7 @@ LICENSE_FILE=	${WRKSRC}/LICENSE.md
 
 RUN_DEPENDS=	bash:shells/bash
 
-USES=		python shebangfix zip
-USE_JAVA=	yes
+USES=		java python shebangfix zip
 
 JAVA_VERSION=	17+
 SHEBANG_FILES=	scripts/* scripts/gsa/*
diff --git a/biology/sra-tools/Makefile b/biology/sra-tools/Makefile
index c774f64a5159..8ffd6b236fe5 100644
--- a/biology/sra-tools/Makefile
+++ b/biology/sra-tools/Makefile
@@ -18,10 +18,9 @@ ONLY_FOR_ARCHS_REASON=	Upstream explicitly supports specific platforms
 BUILD_DEPENDS=	bash:shells/bash
 RUN_DEPENDS=	hdf5>0:science/hdf5
 
-USES=		bison cmake shebangfix
+USES=		bison cmake java shebangfix
 USE_GITHUB=	yes
 USE_LDCONFIG=	${PREFIX}/lib64
-USE_JAVA=	yes
 
 # Builds with earlier versions, but ngs-doc plist differs if jdk17 is present
 JAVA_VERSION=	17+
diff --git a/biology/trimmomatic/Makefile b/biology/trimmomatic/Makefile
index e382fe63dbd2..01948fedc4f4 100644
--- a/biology/trimmomatic/Makefile
+++ b/biology/trimmomatic/Makefile
@@ -11,10 +11,8 @@ WWW=		http://www.usadellab.org/cms/?page=trimmomatic
 LICENSE=	GPLv3
 LICENSE_FILE=	${WRKSRC}/LICENSE
 
-USES=		zip
-USE_JAVA=	yes
+USES=		java zip
 
-JAVA_RUN=	yes
 NO_BUILD=	yes
 NO_ARCH=	yes