sci-biology/fasta: fix broken README symlink

Closes: https://bugs.gentoo.org/835634
Signed-off-by: David Seifert <soap@gentoo.org>

1 files changed, 81 insertions, 0 deletions

diff --git a/sci-biology/fasta/fasta-36.3.8h-r1.ebuild b/sci-biology/fasta/fasta-36.3.8h-r1.ebuild
new file mode 100644
index 000000000000..1c396edf4586
--- /dev/null
+++ b/sci-biology/fasta/fasta-36.3.8h-r1.ebuild
@@ -0,0 +1,81 @@
+# Copyright 1999-2022 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+inherit flag-o-matic toolchain-funcs
+
+MY_PV="${PV}_04-May-2020"
+
+DESCRIPTION="FASTA is a DNA and Protein sequence alignment software package"
+HOMEPAGE="https://fasta.bioch.virginia.edu/fasta_www2/fasta_down.shtml"
+SRC_URI="https://github.com/wrpearson/fasta36/archive/refs/tags/v${MY_PV}.tar.gz -> ${P}.tar.gz"
+S="${WORKDIR}/${PN}36-${MY_PV}"
+
+LICENSE="fasta"
+SLOT="0"
+KEYWORDS="~amd64 ~ppc ~x86 ~amd64-linux ~x86-linux ~x64-macos"
+IUSE="debug cpu_flags_x86_sse2 test"
+RESTRICT="!test? ( test )"
+
+BDEPEND="test? ( app-shells/tcsh )"
+
+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="${ALT}"
+
+	eapply "${FILESDIR}"/${P}-ldflags.patch
+
+	sed \
+		-e 's:-ffast-math::g' \
+		-i make/Makefile* || die
+
+	eapply_user
+}
+
+src_compile() {
+	emake -C src -f ../make/Makefile.linux${ALT} CC="${CC_ALT} ${CFLAGS}" HFLAGS="${LDFLAGS} -o" all
+}
+
+src_test() {
+	cd test || die
+	FASTLIBS="../conf" bash test.sh || die
+}
+
+src_install() {
+	dobin bin/*
+
+	pushd bin >/dev/null || die
+		local i
+		for i in *36; do
+			dosym ${i} /usr/bin/${i%36}
+		done
+	popd >/dev/null || die
+
+	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*,readme*,fasta*,changes*}
+}