sci-*/*: remove dead java-ant-2 eclass

profiles/package.mask

@@ -33,10 +33,3 @@
 # Andrew Ammerlaan <andrewammerlaan@gentoo.org> (2024-07-18)
 # Requires java openmpi bindings, no longer packaged.
 sci-biology/BBmap
-
-# Andrew Ammerlaan <andrewammerlaan@gentoo.org> (2024-10-30)
-# Requires removed dev-java/ant-core
-sci-biology/MeV
-sci-biology/SnpEff
-sci-biology/trimmomatic
-sci-biology/trinityrnaseq

sci-biology/BBmap/BBmap-38.87.ebuild

@@ -3,7 +3,7 @@
 
 EAPI=7
 
-inherit java-pkg-2 java-ant-2
+inherit java-pkg-2
 
 DESCRIPTION="Short read aligner, K-mer-based error-correct and normalize, FASTA/Q tool"
 HOMEPAGE="https://sourceforge.net/projects/bbmap/"
@@ -32,7 +32,7 @@ src_prepare(){
 }
 
 src_compile(){
-	ant dist || die
+	eant dist
 }
 
 src_install(){

sci-biology/MeV/MeV-4.8.1.ebuild

@@ -5,12 +5,13 @@ EAPI=7
 
 MY_PV="${PV//./_}"
 
-inherit java-pkg-2 java-ant-2
+inherit java-pkg-2
 
 DESCRIPTION="Multiple experiment Viewer for genomic data analysis"
 HOMEPAGE="https://sourceforge.net/projects/mev-tm4/"
 SRC_URI="https://downloads.sourceforge.net/project/mev-tm4/mev-tm4/MeV%20${PV}/MeV_${MY_PV}_r2727_linux.tar.gz -> ${P}.tar.gz"
 
+S="${WORKDIR}/${PN}_${MY_PV}"
 LICENSE="Artistic-2"
 SLOT="0"
 KEYWORDS="~amd64"
@@ -19,11 +20,8 @@ RDEPEND=">=virtual/jre-1.5:*
 	${DEPEND}"
 DEPEND="${RDEPEND}
 		>=virtual/jdk-1.5:*
-		dev-java/ant-core
 		"
 
-S="${WORKDIR}/${PN}_${MY_PV}"
-
 src_install() {
 	dodoc -r documentation/*
 	rm -r documentation

sci-biology/SnpEff/Manifest

@@ -1,2 +1 @@
-DIST SnpEff-4.3t.html 10041 BLAKE2B fe3f9b3cf2198af8690bd1f7fdda0a718c354f69343280d29b3021aa00a426653079aec738f8e0d0be0856d789526678481c8a255f0d77463e7e7dc2b4aec7a5 SHA512 fba76ce6e9414a610e2ee4247c6fa34601d0b2925cce1c35ffa7fc865ad80684c28e2a23c0f551cf5ee47057f847c5e2ebfaca18d5c47f41722951b192b1fbfb
 DIST snpEff_v4_3t_core.zip 69708122 BLAKE2B c64c68c9923951f086df447b93adf55e5555e545c59e30a2ce2fdef7e9690cf5219aaab112a6dce23ce6ea72d80772f686a7eb5f000d11b28503f792e0df09a7 SHA512 dfb48c2ae6b9b6dc07b02d44ae0b6ee09d235f1abce8e4df9e9bafbe8e9cd00f914f6e83dee7e67fcd7db0369e00c9dbb8f39575a956ddf3c611298d9c8e062f

sci-biology/SnpEff/SnpEff-4.3t.ebuild

@@ -3,14 +3,15 @@
 
 EAPI=7
 
-inherit java-pkg-2 java-ant-2
+inherit java-pkg-2
 
 DESCRIPTION="SnpEff, SnpSift: Annotate SNP changes and predict effect in HGVS-compliant VCF"
 HOMEPAGE="https://pcingola.github.io/SnpEff/"
 SRC_URI="
 	https://downloads.sourceforge.net/project/snpeff/snpEff_v${PV//./_}_core.zip
-	https://pcingola.github.io/SnpEff/index.html -> ${P}.html"
+"
 
+S="${WORKDIR}"
 LICENSE="LGPL-3"
 SLOT="0"
 KEYWORDS="~amd64"
@@ -21,11 +22,9 @@ RDEPEND="
 	dev-java/antlr:*"
 DEPEND="${RDEPEND}
 	>=virtual/jdk-1.7:*
-	dev-java/ant-core"
+"
 BDEPEND="app-arch/unzip"
 
-S="${WORKDIR}"
-
 src_install(){
 	cd .. || die
 	mkdir -p "${ED}"/usr/share || die

sci-biology/fastqc/fastqc-0.11.9.ebuild

@@ -3,7 +3,7 @@
 
 EAPI=8
 
-inherit desktop java-pkg-2 java-ant-2 xdg
+inherit desktop java-pkg-2 xdg
 
 DESCRIPTION="Quality control FASTA/FASTQ sequence files"
 HOMEPAGE="https://www.bioinformatics.babraham.ac.uk/projects/fastqc/"
@@ -24,7 +24,19 @@ DEPEND="
 "
 BDEPEND="media-gfx/imagemagick"
 
-EANT_BUILD_TARGET="build"
+src_prepare() {
+	sed -i -E 's/<property name="source" value="[0-9.]+" \/>//g' build.xml || die
+	sed -i -E 's/<property name="target" value="[0-9.]+" \/>//g' build.xml || die
+	sed -i 's/source="${source}"//g' build.xml || die
+	sed -i 's/target="${target}"//g' build.xml || die
+	default
+}
+
+src_compile() {
+	eant build \
+		-Dant.build.javac.source="$(java-pkg_get-source)" \
+		-Dant.build.javac.target="$(java-pkg_get-target)"
+}
 
 src_install(){
 	insinto "opt/${PN}"

sci-biology/genomeview-bin/genomeview-bin-2450.ebuild

@@ -3,7 +3,7 @@
 
 EAPI=7
 
-inherit java-pkg-opt-2 java-ant-2
+inherit java-pkg-opt-2
 
 DESCRIPTION="Genome browser and annotation tool"
 HOMEPAGE="https://genomeview.sourceforge.net"

sci-biology/imagej/imagej-1.54i-r1.ebuild

@@ -3,7 +3,7 @@
 
 EAPI=8
 
-inherit java-pkg-2 java-ant-2 desktop
+inherit java-pkg-2 desktop
 
 MY_PN="ij"
 IJ_PV="154" #plugins now available for 154
@@ -65,14 +65,19 @@ src_prepare() {
 	if ! use debug ; then
 		sed -i 's: debug="on">: debug="off">:' "${S}"/build.xml || die
 	fi
+	sed -i -E 's/source="[0-9.]+"//g' build.xml || die
+	sed -i -E 's/target="[0-9.]+"//g' build.xml || die
+
 	default
 }
 
 src_compile() {
 	local antflags="build"
 	use doc && antflags="${antflags} javadocs"
 
-	ant ${antflags} || die  "ant build failed"
+	eant ${antflags} \
+		-Dant.build.javac.source="$(java-pkg_get-source)" \
+		-Dant.build.javac.target="$(java-pkg_get-target)"
 
 	# Max memory usage depends on available memory and CPU type
 	MEM=$(grep MemTotal /proc/meminfo | cut -d':' -f2 | grep -o [0-9]*)

sci-biology/imagej/imagej-9999.ebuild

@@ -3,7 +3,7 @@
 
 EAPI=8
 
-inherit java-pkg-2 java-ant-2 desktop
+inherit java-pkg-2 desktop
 
 MY_PN="ij"
 IJ_PV="154" #plugins now available for 154
@@ -65,14 +65,18 @@ src_prepare() {
 	if ! use debug ; then
 		sed -i 's: debug="on">: debug="off">:' "${S}"/build.xml || die
 	fi
+	sed -i -E 's/source="[0-9.]+"//g' build.xml || die
+	sed -i -E 's/target="[0-9.]+"//g' build.xml || die
 	default
 }
 
 src_compile() {
 	local antflags="build"
 	use doc && antflags="${antflags} javadocs"
 
-	ant ${antflags} || die  "ant build failed"
+	eant ${antflags} \
+		-Dant.build.javac.source="$(java-pkg_get-source)" \
+		-Dant.build.javac.target="$(java-pkg_get-target)"
 
 	# Max memory usage depends on available memory and CPU type
 	MEM=$(grep MemTotal /proc/meminfo | cut -d':' -f2 | grep -o [0-9]*)

sci-biology/jtreeview-bin/jtreeview-bin-1.2.0.ebuild

@@ -3,7 +3,7 @@
 
 EAPI=7
 
-inherit java-pkg-2 java-ant-2 perl-module
+inherit java-pkg-2 perl-module
 
 S="${WORKDIR}"/TreeView-1.1.6r4-bin
 

sci-biology/trimmomatic/trimmomatic-0.39.ebuild

@@ -3,7 +3,7 @@
 
 EAPI=7
 
-inherit java-pkg-2 java-ant-2
+inherit java-pkg-2
 
 DESCRIPTION="Illumina adapter trimming tool"
 HOMEPAGE="http://www.usadellab.org/cms/?page=trimmomatic"
@@ -17,14 +17,21 @@ LICENSE="GPL-3"
 SLOT="0"
 KEYWORDS="~amd64"
 
-DEPEND=">=virtual/jdk-1.6:*
-	dev-java/ant-core
+DEPEND=">=virtual/jdk-1.7:*
 	app-arch/unzip"
-RDEPEND=">=virtual/jre-1.6:*"
+RDEPEND=">=virtual/jre-1.7:*"
 
-# somehow fails to build with oracle-jdk-bin-1.7 while ibm-jdk-bin-1.6 works
+src_prepare() {
+	sed -i -E 's/source="[0-9\.]+"//g' build.xml || die
+	sed -i -E 's/target="[0-9\.]+"//g' build.xml || die
+	default
+}
 
-EANT_BUILD_TARGET="dist"
+src_compile() {
+	eant dist \
+		-Dant.build.javac.source="$(java-pkg_get-source)" \
+		-Dant.build.javac.target="$(java-pkg_get-target)"
+}
 
 src_install() {
 	java-pkg_newjar "dist/jar/${P}.jar" "${PN}.jar"