1 files changed, 55 insertions, 0 deletions
diff --git a/sci-biology/SnpEff/SnpEff-4.3t.ebuild b/sci-biology/SnpEff/SnpEff-4.3t.ebuild
new file mode 100644
index 000000000..843c00356
--- /dev/null
+++ b/sci-biology/SnpEff/SnpEff-4.3t.ebuild
@@ -0,0 +1,55 @@
+# 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
+
+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 -> ${P}.html"
+
+LICENSE="LGPL-3"
+SLOT="0"
+KEYWORDS="~amd64"
+
+RDEPEND="
+	>=virtual/jre-1.7:*
+	dev-java/maven-bin:*
+	dev-java/antlr:*"
+DEPEND="${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
+	# but portage does not install the .* files and subdirs, grr!
+	unzip \
+		"${DISTDIR}"/snpEff_v"${PV//./_}"_core.zip -d "${ED}"/usr/share \
+		|| die "failed to unzip ${DISTDIR}/snpEff_v${PV//./_}_core.zip"
+	sed \
+		-e "s#$HOME/tools/picard/#${ED}/usr/share/picard/lib/#" \
+		-i "${ED}"/usr/share/snpEff/scripts/annotate_demo_GATK.sh || die
+	sed \
+		-e "s#$HOME/tools/gatk/#${ED}/usr/share/gatk/lib/#" \
+		-i "${ED}"/usr/share/snpEff/scripts/annotate_demo_GATK.sh || die
+	sed \
+		-e "s#$HOME/snpEff/#${ED}/usr/share/snpEff/#" \
+		-i "${ED}"/usr/share/snpEff/scripts/annotate_demo_GATK.sh || die
+	sed \
+	-e "s#$HOME/snpEff/snpEff.config#${ED}/usr/share/snpEff/snpEff.config#" \
+	-i "${ED}"/usr/share/snpEff/scripts/annotate_demo_GATK.sh || die
+}
+
+# now fetch the version-specific databases from http://sourceforge.net/projects/snpeff/files/databases/v4_1/
+# it also automagically fetches them but into /tmp/ unlike $CWD
+#
+# java -Xmx4g path/to/snpEff/snpEff.jar -c path/to/snpEff/snpEff.config GRCh37.75 path/to/snps.vcf
+#
+# It is best to just unpack the tarball locally and not use portage at all.