1 files changed, 0 insertions, 62 deletions
diff --git a/sci-biology/SnpEff/SnpEff-4.3i.ebuild b/sci-biology/SnpEff/SnpEff-4.3i.ebuild
deleted file mode 100644
index 9921b3394..000000000
--- a/sci-biology/SnpEff/SnpEff-4.3i.ebuild
+++ /dev/null
@@ -1,62 +0,0 @@
-# Copyright 1999-2017 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-inherit java-pkg-2 java-ant-2
-
-MY_PV=${PV/./_}
-
-DESCRIPTION="SnpEff, SnpSift: Annotate SNP changes and predict effect in HGVS-compliant VCF"
-HOMEPAGE="http://snpeff.sourceforge.net"
-SRC_URI="
-	http://sourceforge.net/projects/snpeff/files/snpEff_v${MY_PV}_core.zip
-	http://snpeff.sourceforge.net/SnpSift.html -> ${P}.html"
-
-LICENSE="LGPL-3"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE=""
-
-# https://github.com/pcingola/SnpEff/blob/master/README_release.txt
-RDEPEND="
-	>=virtual/jre-1.7:*
-	dev-java/maven-bin:*
-	dev-java/antlr:*"
-DEPEND="${RDEPEND}
-	>=virtual/jdk-1.7:*
-	dev-java/ant-core"
-
-S="${WORKDIR}"
-
-#src_compile(){
-#	mvn || die
-#}
-
-src_install(){
-	cd .. || die
-	mkdir -p "${ED}"/usr/share || die
-	# but portage does not install the .* files and subdirs, grr!
-	unzip \
-		"${DISTDIR}"/snpEff_v"${MY_PV}"_core.zip -d "${ED}"/usr/share \
-		|| die "failed to unzip ${DISTDIR}/snpEff_v${MY_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.