commit: 17f6c86d219f1f04c0cb2852ce1cd810169985a2
Author: Eli Schwartz <eschwartz <AT> gentoo <DOT> org>
AuthorDate: Thu Aug 22 04:14:40 2024 +0000
Commit: Eli Schwartz <eschwartz <AT> gentoo <DOT> org>
CommitDate: Thu Aug 22 04:17:11 2024 +0000
URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=17f6c86d
sci-biology/fasta: add 36.3.8i
A 2022 release, how modern. :D Ignore the part where the tag name
contains the date "2020".
It obsoletes the patch as well, which seems good. However it does NOT
fix the LTO issue.
Signed-off-by: Eli Schwartz <eschwartz <AT> gentoo.org>
sci-biology/fasta/Manifest | 1 +
sci-biology/fasta/fasta-36.3.8i.ebuild | 81 ++++++++++++++++++++++++++++++++++
2 files changed, 82 insertions(+)
diff --git a/sci-biology/fasta/Manifest b/sci-biology/fasta/Manifest
index c0bd97106d3a..8144c91b5e78 100644
--- a/sci-biology/fasta/Manifest
+++ b/sci-biology/fasta/Manifest
@@ -1 +1,2 @@
DIST fasta-36.3.8h.tar.gz 1257682 BLAKE2B
e6bd9087563150355fed6edf52a24a0b31ef0658b1e95c3df6d5b5711fc4d137ddd773fb8b3b2fa82fe3f5c310689b2f89668f5b51654eed41ed71f9ef140f99
SHA512
30d160ad083a605397c6c35d2b28f6064cd96f51f99b3664b424ec1dbbbd09772c72e89731a7257306ab58c4ad4b877e229873abd0e09407c64fae643bc04391
+DIST fasta-36.3.8i.tar.gz 1402674 BLAKE2B
5653ae18d38a8f99ac1a76235ebad7189faeaacf9a043ab81ec56036e851d45fcc47435413f81f989efc6dfbccd6e3235c9cd14a6f129719d978ffc69e5def0f
SHA512
6f34bd1a5f74362fd569d9c8e7ca7c9fcb0648ea7e861c3d0b54bbdc32ba0caad4beb2aad204122178ee6bcefd579d824412a863163050c305da0a661d55c234
diff --git a/sci-biology/fasta/fasta-36.3.8i.ebuild
b/sci-biology/fasta/fasta-36.3.8i.ebuild
new file mode 100644
index 000000000000..6363b4b56f2d
--- /dev/null
+++ b/sci-biology/fasta/fasta-36.3.8i.ebuild
@@ -0,0 +1,81 @@
+# Copyright 1999-2024 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+inherit flag-o-matic toolchain-funcs
+
+MY_PV="${PV}_14-Nov-2020"
+
+DESCRIPTION="FASTA is a DNA and Protein sequence alignment software package"
+HOMEPAGE="https://fasta.bioch.virginia.edu/fasta_www2/fasta_down.shtml";
+SRC_URI="https://github.com/wrpearson/fasta36/archive/refs/tags/v${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"
+
+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="${ALT}"
+
+ # -Werror=lto-type-mismatch
+ # https://bugs.gentoo.org/862267
+ # https://github.com/wrpearson/fasta36/issues/63
+ filter-lto
+
+ sed \
+ -e 's:-ffast-math::g' \
+ -i make/Makefile* || die
+
+ eapply_user
+}
+
+src_compile() {
+ emake -C src -f ../make/Makefile.linux${ALT} CC="${CC_ALT} ${CFLAGS}"
HFLAGS="${LDFLAGS}" 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*}
+}
