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-rw-r--r--sci-biology/BBmap/BBmap-38.87.ebuild4
-rw-r--r--sci-biology/MeV/MeV-4.8.1.ebuild6
-rw-r--r--sci-biology/SnpEff/Manifest1
-rw-r--r--sci-biology/SnpEff/SnpEff-4.3t.ebuild9
-rw-r--r--sci-biology/fastqc/fastqc-0.11.9.ebuild16
-rw-r--r--sci-biology/genomeview-bin/genomeview-bin-2450.ebuild2
-rw-r--r--sci-biology/imagej/imagej-1.54i-r1.ebuild9
-rw-r--r--sci-biology/imagej/imagej-9999.ebuild8
-rw-r--r--sci-biology/jtreeview-bin/jtreeview-bin-1.2.0.ebuild2
-rw-r--r--sci-biology/trimmomatic/trimmomatic-0.39.ebuild19
-rw-r--r--sci-chemistry/jligand/jligand-1.0.40.ebuild2
11 files changed, 51 insertions, 27 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}_${MY_PV}"
-
src_install() {
dodoc -r documentation/*
rm -r documentation
diff --git a/sci-biology/SnpEff/Manifest b/sci-biology/SnpEff/Manifest
index 183a71158..c6ab841fc 100644
--- a/sci-biology/SnpEff/Manifest
+++ b/sci-biology/SnpEff/Manifest
@@ -1,2 +1 @@
-DIST SnpEff-4.3t.html 10041 BLAKE2B fe3f9b3cf2198af8690bd1f7fdda0a718c354f69343280d29b3021aa00a426653079aec738f8e0d0be0856d789526678481c8a255f0d77463e7e7dc2b4aec7a5 SHA512 fba76ce6e9414a610e2ee4247c6fa34601d0b2925cce1c35ffa7fc865ad80684c28e2a23c0f551cf5ee47057f847c5e2ebfaca18d5c47f41722951b192b1fbfb
DIST snpEff_v4_3t_core.zip 69708122 BLAKE2B c64c68c9923951f086df447b93adf55e5555e545c59e30a2ce2fdef7e9690cf5219aaab112a6dce23ce6ea72d80772f686a7eb5f000d11b28503f792e0df09a7 SHA512 dfb48c2ae6b9b6dc07b02d44ae0b6ee09d235f1abce8e4df9e9bafbe8e9cd00f914f6e83dee7e67fcd7db0369e00c9dbb8f39575a956ddf3c611298d9c8e062f
diff --git a/sci-biology/SnpEff/SnpEff-4.3t.ebuild b/sci-biology/SnpEff/SnpEff-4.3t.ebuild
index 843c00356..aa6ce5247 100644
--- a/sci-biology/SnpEff/SnpEff-4.3t.ebuild
+++ b/sci-biology/SnpEff/SnpEff-4.3t.ebuild
@@ -3,14 +3,15 @@
EAPI=7
-inherit java-pkg-2 java-ant-2
+inherit java-pkg-2
DESCRIPTION="SnpEff, SnpSift: Annotate SNP changes and predict effect in HGVS-compliant VCF"
HOMEPAGE="https://pcingola.github.io/SnpEff/"
SRC_URI="
https://downloads.sourceforge.net/project/snpeff/snpEff_v${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"