Diff hmmer-2.3.2-r4 with a hmmer-3.1_beta2

/usr/portage/sci-biology/hmmer/hmmer-3.1_beta2.ebuild 2019-12-11 02:41:00.000000000 +0300
3 3

  
4 4
EAPI=6
5 5

  
6
MY_PV="${PV/_beta/b}"
7

  
6 8
DESCRIPTION="Sequence analysis using profile hidden Markov models"
7
LICENSE="GPL-2"
8 9
HOMEPAGE="http://hmmer.org/"
9
SRC_URI="http://eddylab.org/software/${PN}/${PV}/${P}.tar.gz"
10
SRC_URI="http://eddylab.org/software/${PN}3/${MY_PV}/hmmer-${MY_PV}.tar.gz"
10 11

  
11
SLOT="2"
12
IUSE="altivec test threads"
12
LICENSE="GPL-3"
13
SLOT="0"
14
IUSE="altivec cpu_flags_x86_sse gsl mpi test +threads"
13 15
RESTRICT="!test? ( test )"
14
KEYWORDS="~amd64 ~x86"
16
KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux ~ppc-macos"
15 17

  
16
DEPEND="test? ( dev-lang/perl )"
17
RDEPEND=""
18
RDEPEND="
19
	mpi? ( virtual/mpi )
20
	gsl? ( sci-libs/gsl:= )"
21
DEPEND="${RDEPEND}
22
	test? ( dev-lang/perl )"
18 23

  
24
S="${WORKDIR}/${PN}-${MY_PV}"
19 25
PATCHES=(
20
	"${FILESDIR}/${P}-fix-perl-shebangs.patch"
21
	"${FILESDIR}/${P}-fix-build-system-destdir.patch"
26
	"${FILESDIR}/${PN}-3.1_beta2-fix-perl-shebangs.patch"
27
	"${FILESDIR}/${PN}-3.1_beta2-fix-header-install-path.patch"
22 28
)
23 29

  
24 30
src_configure() {
25
	# prevent stray environmental variable
26
	# from causing issues in the test phase
27
	unset TMPDIR
31
	# make build verbose, bug 429308
32
	export V=1
28 33

  
29 34
	econf \
30
		--enable-lfs \
31
		$(use_enable altivec) \
32
		$(use_enable threads)
35
		--disable-pic \
36
		$(use_enable altivec vmx) \
37
		$(use_enable cpu_flags_x86_sse sse) \
38
		$(use_enable mpi) \
39
		$(use_enable threads) \
40
		$(use_with gsl)
33 41
}
34 42

  
35 43
src_install() {
36 44
	default
45
	dodoc Userguide.pdf
37 46

  
38
	newlib.a src/libhmmer.a libhmmer2.a
39
	insinto /usr/include/hmmer2
40
	doins src/*.h
41

  
42
	dobin squid/{afetch,alistat,compalign,compstruct,revcomp,seqstat,seqsplit,sfetch,shuffle,sreformat,sindex,weight,translate}
43
	dolib.a squid/libsquid.a
44
	insinto /usr/include/hmmer2
45
	doins squid/*.h
46

  
47
	dodoc NOTES Userguide.pdf
48
	newdoc 00README README
49

  
50
	# rename files due to collisions with hmmer-3
51
	# in order to make SLOTing possible
52
	local i
53

  
54
	# first rename man pages...
55
	pushd "${ED%/}"/usr/share/man/man1/ >/dev/null || die
56
	for i in hmm*.1; do
57
		mv ${i%.1}{,2}.1 || die
58
	done
59
	popd >/dev/null || die
60

  
61
	# ... then rename binaries
62
	pushd "${ED%/}"/usr/bin/ >/dev/null || die
63
	for i in hmm*; do
64
		mv ${i}{,2} || die
65
	done
66
	popd >/dev/null || die
67
}
68

  
69
pkg_postinst() {
70
	elog "All ${P} binaries have been renamed, in order"
71
	elog "to avoid collisions with hmmer-3. For instance"
72
	elog
73
	elog "    hmmalign -> hmmalign2"
74
	elog
47
	insinto /usr/share/${PN}
48
	doins -r tutorial
75 49
}
Thank you!