From 1a4dc5be8fd24487de1306cf68af5a7d507edb01 Mon Sep 17 00:00:00 2001
From: Martin Mokrejš <mmokrejs@fold.natur.cuni.cz>
Date: Wed, 10 Feb 2016 14:28:39 +0100
Subject: sci-biology/SnpEff: version bump

Package-Manager: portage-2.2.26
---
 sci-biology/SnpEff/Manifest           |  2 ++
 sci-biology/SnpEff/SnpEff-4.1e.ebuild | 56 +++++++++++++++++++++++++++++++++++
 sci-biology/SnpEff/metadata.xml       |  9 ++++++
 3 files changed, 67 insertions(+)
 create mode 100644 sci-biology/SnpEff/Manifest
 create mode 100644 sci-biology/SnpEff/SnpEff-4.1e.ebuild
 create mode 100644 sci-biology/SnpEff/metadata.xml

diff --git a/sci-biology/SnpEff/Manifest b/sci-biology/SnpEff/Manifest
new file mode 100644
index 000000000..f170dd6b4
--- /dev/null
+++ b/sci-biology/SnpEff/Manifest
@@ -0,0 +1,2 @@
+DIST SnpEff-4.1e.html 101225 SHA256 c0292d24c1c793e1e71f8c17c9e8fb1d05980f8f10b729ba24eaebea9f735eba SHA512 d1a83381cdc0d8ccc2d561654114785a18dd68ed195a1e9bd1d7ce48a419a6457c9c2274803ef6579418cef4b85d504bd6efdcbb5242b08e486f44208270ed47 WHIRLPOOL d91ce987b8492eb461144e5f8d2b870f3435775cda513ccaba2700c3a717a04501580263f75a7aee26662b73a5e0110c4d282970bb90c965850487471035435d
+DIST snpEff_v4_1e_core.zip 48391193 SHA256 728573ab7d1cb00660a095d48bcea5a4a9459cdffc83806aa1667f03e2ff0272 SHA512 84dd8de4716de6168da074806618294aaf8002c418cac384123a0d315a7c0bd1345c5c878b9ac775d566533b7d172b1bfc45fcbf9899fb6b4b6b4fb1b29a7c50 WHIRLPOOL 955d457a7d537cdc83bfc5b6b0f696335269364a844ac1da091421e4d997a3e7a6c539ae2848d270fe175aa7bf0feac57b62da3f1fcec1105f4267c81b4d3fc6
diff --git a/sci-biology/SnpEff/SnpEff-4.1e.ebuild b/sci-biology/SnpEff/SnpEff-4.1e.ebuild
new file mode 100644
index 000000000..5e9434a4c
--- /dev/null
+++ b/sci-biology/SnpEff/SnpEff-4.1e.ebuild
@@ -0,0 +1,56 @@
+# Copyright 1999-2016 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: $
+
+EAPI=5
+
+inherit java-pkg-2 java-ant-2
+
+[ "$PV" == "9999" ] && inherit git-2
+
+DESCRIPTION="Annotate SNP changes and predict their effect"
+HOMEPAGE="http://snpeff.sourceforge.net"
+
+if [ "$PV" == "9999" ]; then
+	EGIT_REPO_URI="https://github.com/pcingola/SnpEff.git"
+	#EGIT_BRANCH="v4.1B"
+	KEYWORDS=""
+else
+	SRC_URI="http://sourceforge.net/projects/snpeff/files/snpEff_v4_1e_core.zip
+			http://snpeff.sourceforge.net/SnpSift.html -> ${P}.html"
+	KEYWORDS="~amd64"
+	S="${WORKDIR}"
+fi
+
+LICENSE="LGPL-3"
+SLOT="0"
+IUSE=""
+
+# https://github.com/pcingola/SnpEff/blob/master/README_release.txt
+DEPEND=">=virtual/jre-1.7:*
+	dev-java/maven-bin:*
+	dev-java/antlr:*"
+RDEPEND="${DEPEND}
+	>=virtual/jdk-1.7:*"
+
+#src_compile(){
+#	mvn || die
+#}
+
+src_install(){
+	cd .. || die
+	mkdir -p "${D}"/usr/share
+	# but portage does not install the .* files and subdirs, grr!
+	unzip "${DISTDIR}"/snpEff_v4_1e_core.zip -d "${D}"/usr/share || die "failed to unzip ${DISTDIR}/snpEff_v4_1e_core.zip"
+	sed -e 's#$HOME/tools/picard/#/usr/share/picard/lib/#' -i "${D}"/usr/share/snpEff/scripts/annotate_demo_GATK.sh || die
+	sed -e 's#$HOME/tools/gatk/#/usr/share/gatk/lib/#' -i "${D}"/usr/share/snpEff/scripts/annotate_demo_GATK.sh || die
+	sed -e 's#$HOME/snpEff/#/usr/share/snpEff/#' -i "${D}"/usr/share/snpEff/scripts/annotate_demo_GATK.sh || die
+	sed -e 's#$HOME/snpEff/snpEff.config#/usr/share/snpEff/snpEff.config#' -i "${D}"/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.
diff --git a/sci-biology/SnpEff/metadata.xml b/sci-biology/SnpEff/metadata.xml
new file mode 100644
index 000000000..2bc893037
--- /dev/null
+++ b/sci-biology/SnpEff/metadata.xml
@@ -0,0 +1,9 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+  <herd>sci-biology</herd>
+  <maintainer>
+    <email>mmokrejs@fold.natur.cuni.cz</email>
+    <name>Martin Mokrejs</name>
+  </maintainer>
+</pkgmetadata>
-- 
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