diff --git a/profiles/package.mask b/profiles/package.mask index 03b10f53a2a..c184ca27b94 100644 --- a/profiles/package.mask +++ b/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 diff --git a/sci-biology/BBmap/BBmap-38.87.ebuild b/sci-biology/BBmap/BBmap-38.87.ebuild index 7e196a47d41..c9ade12fed0 100644 --- a/sci-biology/BBmap/BBmap-38.87.ebuild +++ b/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(){ diff --git a/sci-biology/MeV/MeV-4.8.1.ebuild b/sci-biology/MeV/MeV-4.8.1.ebuild index eb605976e58..44d7a56f50e 100644 --- a/sci-biology/MeV/MeV-4.8.1.ebuild +++ b/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}_${MY_PV}" - src_install() { dodoc -r documentation/* rm -r documentation diff --git a/sci-biology/SnpEff/Manifest b/sci-biology/SnpEff/Manifest index 183a711588a..c6ab841fc73 100644 --- a/sci-biology/SnpEff/Manifest +++ b/sci-biology/SnpEff/Manifest @@ -1,2 +1 @@ -DIST SnpEff-4.3t.html 10041 BLAKE2B fe3f9b3cf2198af8690bd1f7fdda0a718c354f69343280d29b3021aa00a426653079aec738f8e0d0be0856d789526678481c8a255f0d77463e7e7dc2b4aec7a5 SHA512 fba76ce6e9414a610e2ee4247c6fa34601d0b2925cce1c35ffa7fc865ad80684c28e2a23c0f551cf5ee47057f847c5e2ebfaca18d5c47f41722951b192b1fbfb DIST snpEff_v4_3t_core.zip 69708122 BLAKE2B c64c68c9923951f086df447b93adf55e5555e545c59e30a2ce2fdef7e9690cf5219aaab112a6dce23ce6ea72d80772f686a7eb5f000d11b28503f792e0df09a7 SHA512 dfb48c2ae6b9b6dc07b02d44ae0b6ee09d235f1abce8e4df9e9bafbe8e9cd00f914f6e83dee7e67fcd7db0369e00c9dbb8f39575a956ddf3c611298d9c8e062f diff --git a/sci-biology/SnpEff/SnpEff-4.3t.ebuild b/sci-biology/SnpEff/SnpEff-4.3t.ebuild index 843c0035664..aa6ce524792 100644 --- a/sci-biology/SnpEff/SnpEff-4.3t.ebuild +++ b/sci-biology/SnpEff/SnpEff-4.3t.ebuild @@ -3,14 +3,15 @@ EAPI=7 -inherit java-pkg-2 java-ant-2 +inherit java-pkg-2 DESCRIPTION="SnpEff, SnpSift: Annotate SNP changes and predict effect in HGVS-compliant VCF" HOMEPAGE="https://pcingola.github.io/SnpEff/" SRC_URI=" https://downloads.sourceforge.net/project/snpeff/snpEff_v${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 "${ED}"/usr/share || die diff --git a/sci-biology/fastqc/fastqc-0.11.9.ebuild b/sci-biology/fastqc/fastqc-0.11.9.ebuild index be2d3b3408c..5d42f295a36 100644 --- a/sci-biology/fastqc/fastqc-0.11.9.ebuild +++ b/sci-biology/fastqc/fastqc-0.11.9.ebuild @@ -3,7 +3,7 @@ EAPI=8 -inherit desktop java-pkg-2 java-ant-2 xdg +inherit desktop java-pkg-2 xdg DESCRIPTION="Quality control FASTA/FASTQ sequence files" HOMEPAGE="https://www.bioinformatics.babraham.ac.uk/projects/fastqc/" @@ -24,7 +24,19 @@ DEPEND=" " BDEPEND="media-gfx/imagemagick" -EANT_BUILD_TARGET="build" +src_prepare() { + sed -i -E 's/<property name="source" value="[0-9.]+" \/>//g' build.xml || die + sed -i -E 's/<property name="target" value="[0-9.]+" \/>//g' build.xml || die + sed -i 's/source="${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}" diff --git a/sci-biology/genomeview-bin/genomeview-bin-2450.ebuild b/sci-biology/genomeview-bin/genomeview-bin-2450.ebuild index 9d4480272ea..3244e79b59f 100644 --- a/sci-biology/genomeview-bin/genomeview-bin-2450.ebuild +++ b/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" diff --git a/sci-biology/imagej/imagej-1.54i-r1.ebuild b/sci-biology/imagej/imagej-1.54i-r1.ebuild index f95167bcdf5..92449b3685e 100644 --- a/sci-biology/imagej/imagej-1.54i-r1.ebuild +++ b/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 @@ -65,6 +65,9 @@ src_prepare() { if ! use debug ; then sed -i 's: debug="on">: debug="off">:' "${S}"/build.xml || die fi + sed -i -E 's/source="[0-9.]+"//g' build.xml || die + sed -i -E 's/target="[0-9.]+"//g' build.xml || die + default } @@ -72,7 +75,9 @@ src_compile() { local antflags="build" use doc && antflags="${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]*) diff --git a/sci-biology/imagej/imagej-9999.ebuild b/sci-biology/imagej/imagej-9999.ebuild index f95167bcdf5..40f04311b64 100644 --- a/sci-biology/imagej/imagej-9999.ebuild +++ b/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 @@ -65,6 +65,8 @@ src_prepare() { if ! use debug ; then sed -i 's: debug="on">: debug="off">:' "${S}"/build.xml || die fi + sed -i -E 's/source="[0-9.]+"//g' build.xml || die + sed -i -E 's/target="[0-9.]+"//g' build.xml || die default } @@ -72,7 +74,9 @@ src_compile() { local antflags="build" use doc && antflags="${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]*) diff --git a/sci-biology/jtreeview-bin/jtreeview-bin-1.2.0.ebuild b/sci-biology/jtreeview-bin/jtreeview-bin-1.2.0.ebuild index 63ec84d2f82..d386ca896d9 100644 --- a/sci-biology/jtreeview-bin/jtreeview-bin-1.2.0.ebuild +++ b/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="${WORKDIR}"/TreeView-1.1.6r4-bin diff --git a/sci-biology/trimmomatic/trimmomatic-0.39.ebuild b/sci-biology/trimmomatic/trimmomatic-0.39.ebuild index 3b491b3900e..f48e98b3b54 100644 --- a/sci-biology/trimmomatic/trimmomatic-0.39.ebuild +++ b/sci-biology/trimmomatic/trimmomatic-0.39.ebuild @@ -3,7 +3,7 @@ EAPI=7 -inherit java-pkg-2 java-ant-2 +inherit java-pkg-2 DESCRIPTION="Illumina adapter trimming tool" HOMEPAGE="http://www.usadellab.org/cms/?page=trimmomatic" @@ -17,14 +17,21 @@ LICENSE="GPL-3" SLOT="0" KEYWORDS="~amd64" -DEPEND=">=virtual/jdk-1.6:* - dev-java/ant-core +DEPEND=">=virtual/jdk-1.7:* app-arch/unzip" -RDEPEND=">=virtual/jre-1.6:*" +RDEPEND=">=virtual/jre-1.7:*" -# somehow fails to build with oracle-jdk-bin-1.7 while ibm-jdk-bin-1.6 works +src_prepare() { + sed -i -E 's/source="[0-9\.]+"//g' build.xml || die + sed -i -E 's/target="[0-9\.]+"//g' build.xml || die + default +} -EANT_BUILD_TARGET="dist" +src_compile() { + eant dist \ + -Dant.build.javac.source="$(java-pkg_get-source)" \ + -Dant.build.javac.target="$(java-pkg_get-target)" +} src_install() { java-pkg_newjar "dist/jar/${P}.jar" "${PN}.jar" diff --git a/sci-chemistry/jligand/Manifest b/sci-chemistry/jligand/Manifest deleted file mode 100644 index cbd60dfb1b7..00000000000 --- a/sci-chemistry/jligand/Manifest +++ /dev/null @@ -1 +0,0 @@ -DIST JLigand.1.0.40.tar.gz 69101 BLAKE2B 8c1b2c029abd19b04e7ef29774657fb84f63afa98b04afc8bb300b41a50397b5071d974b2f7e674ada9a21b27a3bb01ac410b57f0e3bb44276e54c8af1fbaa40 SHA512 9600e8a18c015e56f8bb9fc272fbdfe77963be0ceb2ea15b0b037452c58c65ac1acc129e54f5cf5531a27f72843cc1368a78a5f4bd6bc8c7e752b8999cc6dbae diff --git a/sci-chemistry/jligand/jligand-1.0.40.ebuild b/sci-chemistry/jligand/jligand-1.0.40.ebuild deleted file mode 100644 index 879964bbf7f..00000000000 --- a/sci-chemistry/jligand/jligand-1.0.40.ebuild +++ /dev/null @@ -1,32 +0,0 @@ -# Copyright 1999-2021 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=7 - -inherit java-pkg-2 java-ant-2 - -MY_PN="JLigand" - -DESCRIPTION="Java interface which allows links descriptions to be created" -HOMEPAGE="http://www.ysbl.york.ac.uk/mxstat/JLigand/" -SRC_URI="http://www.ysbl.york.ac.uk/mxstat/${MY_PN}/${MY_PN}.${PV}.tar.gz" - -LICENSE="ccp4" -SLOT="0" -KEYWORDS="~amd64" - -RDEPEND=">=virtual/jre-1.5" -DEPEND=">=virtual/jdk-1.5" - -S="${WORKDIR}/${MY_PN}.${PV}" - -src_compile() { - sed 's:makefile::g' -i Makefile || die - default -} - -src_install() { - java-pkg_newjar JLigand.jar "${PN}.jar" - java-pkg_dolauncher JLigand \ - --jar "${PN}.jar" -} diff --git a/sci-chemistry/jligand/metadata.xml b/sci-chemistry/jligand/metadata.xml deleted file mode 100644 index da36ecbfcd6..00000000000 --- a/sci-chemistry/jligand/metadata.xml +++ /dev/null @@ -1,8 +0,0 @@ -<?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> -<pkgmetadata> - <maintainer type="project"> - <email>sci-chemistry@gentoo.org</email> - <name>Gentoo Chemistry Project</name> - </maintainer> -</pkgmetadata>