proj/gentoo: Initial commit

This commit represents a new era for Gentoo:
Storing the gentoo-x86 tree in Git, as converted from CVS.

This commit is the start of the NEW history.
Any historical data is intended to be grafted onto this point.

Creation process:
1. Take final CVS checkout snapshot
2. Remove ALL ChangeLog* files
3. Transform all Manifests to thin
4. Remove empty Manifests
5. Convert all stale $Header$/$Id$ CVS keywords to non-expanded Git $Id$
5.1. Do not touch files with -kb/-ko keyword flags.

Signed-off-by: Robin H. Johnson <robbat2@gentoo.org>
X-Thanks: Alec Warner <antarus@gentoo.org> - did the GSoC 2006 migration tests
X-Thanks: Robin H. Johnson <robbat2@gentoo.org> - infra guy, herding this project
X-Thanks: Nguyen Thai Ngoc Duy <pclouds@gentoo.org> - Former Gentoo developer, wrote Git features for the migration
X-Thanks: Brian Harring <ferringb@gentoo.org> - wrote much python to improve cvs2svn
X-Thanks: Rich Freeman <rich0@gentoo.org> - validation scripts
X-Thanks: Patrick Lauer <patrick@gentoo.org> - Gentoo dev, running new 2014 work in migration
X-Thanks: Michał Górny <mgorny@gentoo.org> - scripts, QA, nagging
X-Thanks: All of other Gentoo developers - many ideas and lots of paint on the bikeshed

1 files changed, 61 insertions, 0 deletions

diff --git a/sci-biology/glimmer/glimmer-3.02-r3.ebuild b/sci-biology/glimmer/glimmer-3.02-r3.ebuild
new file mode 100644
index 000000000000..acc0eb98e18b
--- /dev/null
+++ b/sci-biology/glimmer/glimmer-3.02-r3.ebuild
@@ -0,0 +1,61 @@
+# Copyright 1999-2015 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI="5"
+
+inherit eutils toolchain-funcs
+
+MY_PV=${PV//./}
+
+DESCRIPTION="An HMM-based microbial gene finding system from TIGR"
+HOMEPAGE="http://www.cbcb.umd.edu/software/glimmer/"
+SRC_URI="http://www.cbcb.umd.edu/software/${PN}/${PN}${MY_PV}.tar.gz"
+
+LICENSE="Artistic"
+SLOT="0"
+IUSE=""
+KEYWORDS="amd64 x86"
+
+DEPEND=""
+RDEPEND="app-shells/tcsh"
+
+S="${WORKDIR}/${PN}${PV}"
+
+PATCHES=(
+	"${FILESDIR}"/${P}-glibc210.patch
+	"${FILESDIR}"/${P}-jobserver-fix.patch
+	"${FILESDIR}"/${P}-ldflags.patch
+	"${FILESDIR}"/${PN}-3.02b-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) $(TGT) || exit 1/' src/c_make.gen || die
+	# GCC 4.3 include fix
+	sed -i 's/include  <string>/include  <string.h>/' src/Common/delcher.hh || die
+	epatch "${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
+}