commit: b9e1397d441af5d9ea9e076f61719eadbabff069 Author: Alexander Puck Neuwirth <alexander <AT> neuwirth-informatik <DOT> de> AuthorDate: Thu Nov 7 14:24:35 2024 +0000 Commit: Alexander Puck Neuwirth <alexander <AT> neuwirth-informatik <DOT> de> CommitDate: Sat Nov 9 07:53:00 2024 +0000 URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=b9e1397d
sci-*/*: remove dead java-ant-2 eclass See: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=f28ab51fad9acb876a8fef5dd56f656afcd2776c Signed-off-by: Alexander Puck Neuwirth <alexander <AT> neuwirth-informatik.de> sci-biology/BBmap/BBmap-38.87.ebuild | 4 ++-- sci-biology/MeV/MeV-4.8.1.ebuild | 6 ++---- sci-biology/SnpEff/SnpEff-4.3t.ebuild | 9 ++++----- sci-biology/fastqc/fastqc-0.11.9.ebuild | 16 ++++++++++++++-- sci-biology/genomeview-bin/genomeview-bin-2450.ebuild | 2 +- sci-biology/imagej/imagej-1.54i-r1.ebuild | 9 +++++++-- sci-biology/imagej/imagej-9999.ebuild | 8 ++++++-- sci-biology/jtreeview-bin/jtreeview-bin-1.2.0.ebuild | 2 +- sci-biology/trimmomatic/trimmomatic-0.39.ebuild | 19 +++++++++++++------ sci-chemistry/jligand/jligand-1.0.40.ebuild | 2 +- 10 files changed, 51 insertions(+), 26 deletions(-) diff --git a/sci-biology/BBmap/BBmap-38.87.ebuild b/sci-biology/BBmap/BBmap-38.87.ebuild index 7e196a47d..c9ade12fe 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 eb605976e..44d7a56f5 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}_${MY_PV}" - src_install() { dodoc -r documentation/* rm -r documentation diff --git a/sci-biology/SnpEff/SnpEff-4.3t.ebuild b/sci-biology/SnpEff/SnpEff-4.3t.ebuild index 843c00356..aa6ce5247 100644 --- a/sci-biology/SnpEff/SnpEff-4.3t.ebuild +++ b/sci-biology/SnpEff/SnpEff-4.3t.ebuild @@ -3,14 +3,15 @@ EAPI=7 -inherit java-pkg-2 java-ant-2 +inherit java-pkg-2 DESCRIPTION="SnpEff, SnpSift: Annotate SNP changes and predict effect in HGVS-compliant VCF" HOMEPAGE="https://pcingola.github.io/SnpEff/"; SRC_URI=" https://downloads.sourceforge.net/project/snpeff/snpEff_v${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 "${ED}"/usr/share || die diff --git a/sci-biology/fastqc/fastqc-0.11.9.ebuild b/sci-biology/fastqc/fastqc-0.11.9.ebuild index be2d3b340..5d42f295a 100644 --- a/sci-biology/fastqc/fastqc-0.11.9.ebuild +++ b/sci-biology/fastqc/fastqc-0.11.9.ebuild @@ -3,7 +3,7 @@ EAPI=8 -inherit desktop java-pkg-2 java-ant-2 xdg +inherit desktop java-pkg-2 xdg DESCRIPTION="Quality control FASTA/FASTQ sequence files" HOMEPAGE="https://www.bioinformatics.babraham.ac.uk/projects/fastqc/"; @@ -24,7 +24,19 @@ DEPEND=" " BDEPEND="media-gfx/imagemagick" -EANT_BUILD_TARGET="build" +src_prepare() { + sed -i -E 's/<property name="source" value="[0-9.]+" \/>//g' build.xml || die + sed -i -E 's/<property name="target" value="[0-9.]+" \/>//g' build.xml || die + sed -i 's/source="${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 9d4480272..3244e79b5 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 f95167bcd..92449b368 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 f95167bcd..40f04311b 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 63ec84d2f..d386ca896 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="${WORKDIR}"/TreeView-1.1.6r4-bin diff --git a/sci-biology/trimmomatic/trimmomatic-0.39.ebuild b/sci-biology/trimmomatic/trimmomatic-0.39.ebuild index 3b491b390..f48e98b3b 100644 --- a/sci-biology/trimmomatic/trimmomatic-0.39.ebuild +++ b/sci-biology/trimmomatic/trimmomatic-0.39.ebuild @@ -3,7 +3,7 @@ EAPI=7 -inherit java-pkg-2 java-ant-2 +inherit java-pkg-2 DESCRIPTION="Illumina adapter trimming tool" HOMEPAGE="http://www.usadellab.org/cms/?page=trimmomatic"; @@ -17,14 +17,21 @@ LICENSE="GPL-3" SLOT="0" KEYWORDS="~amd64" -DEPEND=">=virtual/jdk-1.6:* - dev-java/ant-core +DEPEND=">=virtual/jdk-1.7:* app-arch/unzip" -RDEPEND=">=virtual/jre-1.6:*" +RDEPEND=">=virtual/jre-1.7:*" -# somehow fails to build with oracle-jdk-bin-1.7 while ibm-jdk-bin-1.6 works +src_prepare() { + sed -i -E 's/source="[0-9\.]+"//g' build.xml || die + sed -i -E 's/target="[0-9\.]+"//g' build.xml || die + default +} -EANT_BUILD_TARGET="dist" +src_compile() { + eant dist \ + -Dant.build.javac.source="$(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/jligand-1.0.40.ebuild b/sci-chemistry/jligand/jligand-1.0.40.ebuild index 879964bbf..d81a7c2b4 100644 --- a/sci-chemistry/jligand/jligand-1.0.40.ebuild +++ b/sci-chemistry/jligand/jligand-1.0.40.ebuild @@ -3,7 +3,7 @@ EAPI=7 -inherit java-pkg-2 java-ant-2 +inherit java-pkg-2 MY_PN="JLigand"
