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, 79 insertions, 0 deletions

diff --git a/sci-biology/fasta/fasta-36.3.5e.ebuild b/sci-biology/fasta/fasta-36.3.5e.ebuild
new file mode 100644
index 000000000000..a9466820c4e8
--- /dev/null
+++ b/sci-biology/fasta/fasta-36.3.5e.ebuild
@@ -0,0 +1,79 @@
+# Copyright 1999-2015 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=5
+
+inherit eutils flag-o-matic toolchain-funcs
+
+DESCRIPTION="FASTA is a DNA and Protein sequence alignment software package"
+HOMEPAGE="http://fasta.bioch.virginia.edu/fasta_www2/fasta_down.shtml"
+SRC_URI="http://faculty.virginia.edu/wrpearson/${PN}/${PN}36/${P}.tar.gz"
+
+LICENSE="fasta"
+SLOT="0"
+KEYWORDS="~amd64 ~ppc ~x86 ~amd64-linux ~x86-linux ~x64-macos ~x86-macos"
+IUSE="debug cpu_flags_x86_sse2 test"
+
+DEPEND="test? ( app-shells/tcsh )"
+RDEPEND=""
+
+src_prepare() {
+	CC_ALT=
+	CFLAGS_ALT=
+	ALT=
+
+	use debug && append-flags -DDEBUG
+
+	if [[ $(tc-getCC) == *icc* ]]; then
+		CC_ALT=icc
+		ALT="${ALT}_icc"
+	else
+		CC_ALT=$(tc-getCC)
+		use x86 && ALT="32"
+		use amd64 && ALT="64"
+	fi
+
+	if use cpu_flags_x86_sse2 ; then
+		ALT="${ALT}_sse2"
+		append-flags -msse2
+		[[ $(tc-getCC) == *icc* ]] || append-flags -ffast-math
+	fi
+
+	export CC_ALT="${CC_ALT}"
+	export ALT="${ALT}"
+
+	epatch "${FILESDIR}"/${P}-ldflags.patch
+
+	sed \
+		-e 's:-ffast-math::g' \
+		-i make/Makefile* || die
+
+}
+
+src_compile() {
+	cd src || die
+	emake -f ../make/Makefile.linux${ALT} CC="${CC_ALT} ${CFLAGS}" HFLAGS="${LDFLAGS} -o" all
+}
+
+src_test() {
+	cd test || die
+	FASTLIBS="../conf" bash test.sh || die
+}
+
+src_install() {
+	local bin
+	dobin bin/*
+
+	pushd bin > /dev/null || die
+	for bin in *36; do
+		dosym ${bin} /usr/bin/${bin%36} || die
+	done
+	popd
+
+	insinto /usr/share/${PN}
+	doins -r conf/* data seq
+
+	doman doc/{prss3.1,fasta36.1,fasts3.1,fastf3.1,ps_lav.1,map_db.1}
+	dodoc  FASTA_LIST README doc/{README.versions,readme*,fasta*,changes*}
+}