From 4f2d7949f03e1c198bc888f2d05f421d35c57e21 Mon Sep 17 00:00:00 2001
From: V3n3RiX <venerix@redcorelinux.org>
Date: Mon, 9 Oct 2017 18:53:29 +0100
Subject: reinit the tree, so we can have metadata

---
 sci-biology/glimmer/glimmer-3.02b.ebuild | 67 ++++++++++++++++++++++++++++++++
 1 file changed, 67 insertions(+)
 create mode 100644 sci-biology/glimmer/glimmer-3.02b.ebuild

(limited to 'sci-biology/glimmer/glimmer-3.02b.ebuild')

diff --git a/sci-biology/glimmer/glimmer-3.02b.ebuild b/sci-biology/glimmer/glimmer-3.02b.ebuild
new file mode 100644
index 000000000000..9653024a1de2
--- /dev/null
+++ b/sci-biology/glimmer/glimmer-3.02b.ebuild
@@ -0,0 +1,67 @@
+# Copyright 1999-2015 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI="5"
+
+inherit eutils toolchain-funcs
+
+MY_PV=${PV//./}
+
+DESCRIPTION="An HMM-based microbial gene finding system from TIGR"
+HOMEPAGE="http://ccb.jhu.edu/software/glimmer"
+SRC_URI="http://ccb.jhu.edu/software/${PN}/${PN}${MY_PV}.tar.gz"
+
+LICENSE="Artistic"
+SLOT="0"
+IUSE=""
+KEYWORDS="~amd64 ~x86"
+
+DEPEND=""
+RDEPEND="app-shells/tcsh
+	sci-biology/elph"
+
+#S="${WORKDIR}/${PN}${PV}"
+S="${WORKDIR}/${PN}3.02"
+
+PATCHES=(
+	"${FILESDIR}"/${P}-jobserver-fix.patch
+	"${FILESDIR}"/${P}-ldflags.patch
+	"${FILESDIR}"/${P}-rename_extract.patch
+)
+
+src_prepare() {
+	sed -i -e 's|\(set awkpath =\).*|\1 /usr/share/'${PN}'/scripts|' \
+		-e 's|\(set glimmerpath =\).*|\1 /usr/bin|' scripts/* || die "failed to rewrite paths"
+	# Fix Makefile to die on failure
+	sed -i 's/$(MAKE) $(TGT)/$(MAKE) $(TGT) || exit 1/' src/c_make.gen || die
+	# GCC 4.3 include fix
+	sed -i 's/include  <string>/include  <string.h>/' src/Common/delcher.hh || die
+	#
+	sed -i "s+/fs/szgenefinding/Glimmer3/bin+%${D}/bin/glimmer3+" scripts/g3-* || die
+	sed -i "s+/fs/szgenefinding/Glimmer3/scripts+%${D}/share/glimmer/scripts+" scripts/g3-* || die
+	sed -i "s+/nfshomes/adelcher/bin/elph+%${D}/bin/elph+" scripts/g3-* || die
+	sed -i "s/@ if/if/" src/c_make.gen || die
+	# avoid file collision on /usr/bin/extract #247394
+	epatch "${PATCHES[@]}"
+}
+
+src_compile() {
+	emake \
+		-C src \
+		CC=$(tc-getCC) \
+		CXX=$(tc-getCXX) \
+		AR=$(tc-getAR) \
+		CXXFLAGS="${CXXFLAGS}" \
+		CFLAGS="${CFLAGS}" \
+		LDFLAGS="${LDFLAGS}"
+}
+
+src_install() {
+	rm bin/test || die
+	dobin bin/*
+
+	insinto /usr/share/${PN}
+	doins -r scripts
+
+	dodoc glim302notes.pdf
+}
-- 
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