gentoo-ebuilds/sci-biology/hmmer/hmmer-2.3.2-r6.ebuild
NHOrus 4919e107f9
sci-biology/hmmer: Add missing include into configure
There are no autotools source files, so we can't just autoreconf the problem out of existence

[sam: Revbump.]

Closes: https://bugs.gentoo.org/900551
Signed-off-by: NHOrus <jy6x2b32pie9@yahoo.com>
Closes: https://github.com/gentoo/gentoo/pull/36599
Signed-off-by: Sam James <sam@gentoo.org>
2024-05-09 02:09:05 +01:00

84 lines
1.9 KiB
Bash

# Copyright 1999-2024 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
EAPI=8
inherit flag-o-matic toolchain-funcs
DESCRIPTION="Sequence analysis using profile hidden Markov models"
HOMEPAGE="http://hmmer.org/"
SRC_URI="http://eddylab.org/software/${PN}/${PV}/${P}.tar.gz"
LICENSE="GPL-2"
SLOT="2"
KEYWORDS="~amd64 ~x86"
IUSE="cpu_flags_ppc_altivec test"
RESTRICT="!test? ( test )"
BDEPEND="test? ( dev-lang/perl )"
PATCHES=(
"${FILESDIR}/${P}-fix-perl-shebangs.patch"
"${FILESDIR}/${P}-fix-build-system-destdir.patch"
"${FILESDIR}/${P}-fix-missing-include-in-configure.patch"
)
src_configure() {
# required to expose pthread_setconcurrency(), #882279
append-cppflags -D_XOPEN_SOURCE=500
# prevent stray environmental variable
# from causing issues in the test phase
unset TMPDIR
econf \
--enable-lfs \
--enable-threads \
$(use_enable cpu_flags_ppc_altivec altivec)
}
src_compile() {
emake AR="$(tc-getAR) rcs"
}
src_install() {
default
newlib.a src/libhmmer.a libhmmer2.a
insinto /usr/include/hmmer2
doins src/*.h
dobin squid/{afetch,alistat,compalign,compstruct,revcomp,seqstat,seqsplit,sfetch,shuffle,sreformat,sindex,weight,translate}
dolib.a squid/libsquid.a
insinto /usr/include/hmmer2
doins squid/*.h
dodoc NOTES Userguide.pdf
newdoc 00README README
# rename files due to collisions with hmmer-3
# in order to make SLOTing possible
local i
# first rename man pages...
pushd "${ED}"/usr/share/man/man1/ >/dev/null || die
for i in hmm*.1; do
mv ${i%.1}{,2}.1 || die
done
popd >/dev/null || die
# ... then rename binaries
pushd "${ED}"/usr/bin/ >/dev/null || die
for i in hmm*; do
mv ${i}{,2} || die
done
popd >/dev/null || die
}
pkg_postinst() {
elog "All ${P} binaries have been renamed, in order"
elog "to avoid collisions with hmmer-3. For instance"
elog
elog " hmmalign -> hmmalign2"
elog
}