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, 55 insertions, 0 deletions

diff --git a/sci-biology/shrimp/shrimp-2.0.1.ebuild b/sci-biology/shrimp/shrimp-2.0.1.ebuild
new file mode 100644
index 00000000000..771432f0bad
--- /dev/null
+++ b/sci-biology/shrimp/shrimp-2.0.1.ebuild
@@ -0,0 +1,55 @@
+# Copyright 1999-2013 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=4
+
+inherit flag-o-matic toolchain-funcs
+
+MY_PV=${PV//./_}
+
+DESCRIPTION="SHort Read Mapping Package"
+HOMEPAGE="http://compbio.cs.toronto.edu/shrimp/"
+SRC_URI="http://compbio.cs.toronto.edu/shrimp/releases/SHRiMP_${MY_PV}.src.tar.gz"
+
+LICENSE="shrimp"
+SLOT="0"
+KEYWORDS="amd64 x86"
+IUSE="custom-cflags"
+
+# file collision on /usr/bin/utils #453044
+DEPEND="
+	!sci-biology/emboss
+	!sci-mathematics/cado-nfs"
+RDEPEND="${DEPEND}"
+
+S=${WORKDIR}/SHRiMP_${MY_PV}
+
+pkg_setup() {
+	if [[ ${CC} == *gcc* ]] &&	! tc-has-openmp; then
+		elog "Please set CC to an OPENMP capable compiler (e.g. gcc[openmp] or icc"
+		die "C compiler lacks OPENMP support"
+	fi
+}
+
+src_prepare() {
+	sed -e '1 a #include <stdint.h>' -i common/dag_glue.cpp || die
+	# respect LDFLAGS wrt 331823
+	sed -i -e "s/LDFLAGS/LIBS/" -e "s/\$(LD)/& \$(LDFLAGS)/" \
+		-e 's/-static//' Makefile || die
+}
+
+src_compile() {
+	append-flags -fopenmp
+	use custom-cflags || append-flags -O3 # per instructions in BUILDING
+	tc-export CXX
+	emake CXXFLAGS="${CXXFLAGS}" LDFLAGS="${LDFLAGS}"
+}
+
+src_install() {
+	rm bin/README
+	dobin bin/*
+	insinto /usr/share/${PN}
+	doins -r utils
+	dodoc HISTORY README TODO SPLITTING_AND_MERGING
+}