From: | "Justin Lecher (jlec)" <jlec@g.o> |
---|---|
To: | gentoo-commits@l.g.o |
Subject: | [gentoo-commits] gentoo-x86 commit in sci-biology/mafft: ChangeLog mafft-7.045.ebuild |
Date: | Thu, 06 Jun 2013 06:20:14 |
Message-Id: | 20130606062005.F16DC2171D@flycatcher.gentoo.org |
1 | jlec 13/06/06 06:20:05 |
2 | |
3 | Modified: ChangeLog |
4 | Added: mafft-7.045.ebuild |
5 | Log: |
6 | sci-biology/mafft: Version Bump |
7 | |
8 | (Portage version: 2.2.0_alpha177/cvs/Linux x86_64, signed Manifest commit with key 8009D6F070EB7916) |
9 | |
10 | Revision Changes Path |
11 | 1.15 sci-biology/mafft/ChangeLog |
12 | |
13 | file : http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-biology/mafft/ChangeLog?rev=1.15&view=markup |
14 | plain: http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-biology/mafft/ChangeLog?rev=1.15&content-type=text/plain |
15 | diff : http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-biology/mafft/ChangeLog?r1=1.14&r2=1.15 |
16 | |
17 | Index: ChangeLog |
18 | =================================================================== |
19 | RCS file: /var/cvsroot/gentoo-x86/sci-biology/mafft/ChangeLog,v |
20 | retrieving revision 1.14 |
21 | retrieving revision 1.15 |
22 | diff -u -r1.14 -r1.15 |
23 | --- ChangeLog 26 May 2013 11:12:15 -0000 1.14 |
24 | +++ ChangeLog 6 Jun 2013 06:20:05 -0000 1.15 |
25 | @@ -1,6 +1,11 @@ |
26 | # ChangeLog for sci-biology/mafft |
27 | # Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2 |
28 | -# $Header: /var/cvsroot/gentoo-x86/sci-biology/mafft/ChangeLog,v 1.14 2013/05/26 11:12:15 jlec Exp $ |
29 | +# $Header: /var/cvsroot/gentoo-x86/sci-biology/mafft/ChangeLog,v 1.15 2013/06/06 06:20:05 jlec Exp $ |
30 | + |
31 | +*mafft-7.045 (06 Jun 2013) |
32 | + |
33 | + 06 Jun 2013; Justin Lecher <jlec@g.o> +mafft-7.045.ebuild: |
34 | + Version Bump |
35 | |
36 | 26 May 2013; Justin Lecher <jlec@g.o> mafft-7.043.ebuild: |
37 | Use append-cppflags for preprocessor flags |
38 | |
39 | |
40 | |
41 | 1.1 sci-biology/mafft/mafft-7.045.ebuild |
42 | |
43 | file : http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-biology/mafft/mafft-7.045.ebuild?rev=1.1&view=markup |
44 | plain: http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-biology/mafft/mafft-7.045.ebuild?rev=1.1&content-type=text/plain |
45 | |
46 | Index: mafft-7.045.ebuild |
47 | =================================================================== |
48 | # Copyright 1999-2013 Gentoo Foundation |
49 | # Distributed under the terms of the GNU General Public License v2 |
50 | # $Header: /var/cvsroot/gentoo-x86/sci-biology/mafft/mafft-7.045.ebuild,v 1.1 2013/06/06 06:20:05 jlec Exp $ |
51 | |
52 | EAPI=5 |
53 | |
54 | inherit eutils flag-o-matic multilib toolchain-funcs |
55 | |
56 | EXTENSIONS="-without-extensions" |
57 | |
58 | DESCRIPTION="Multiple sequence alignments using a variety of algorithms" |
59 | HOMEPAGE="http://mafft.cbrc.jp/alignment/software/index.html" |
60 | SRC_URI="http://mafft.cbrc.jp/alignment/software/${P}${EXTENSIONS}-src.tgz" |
61 | |
62 | LICENSE="BSD" |
63 | SLOT="0" |
64 | KEYWORDS="~amd64 ~x86 ~x64-macos ~x86-macos" |
65 | IUSE="threads" |
66 | |
67 | S="${WORKDIR}"/${P}${EXTENSIONS} |
68 | |
69 | src_prepare() { |
70 | epatch "${FILESDIR}"/${PN}-7.037-respect.patch |
71 | use threads && append-cppflags -Denablemultithread |
72 | sed "s:GENTOOLIBDIR:$(get_libdir):g" -i core/Makefile || die |
73 | sed -i -e "s/(PREFIX)\/man/(PREFIX)\/share\/man/" "${S}"/core/Makefile || die "sed failed" |
74 | } |
75 | |
76 | src_compile() { |
77 | pushd core > /dev/null || die |
78 | emake \ |
79 | $(usex threads ENABLE_MULTITHREAD="-Denablemultithread" ENABLE_MULTITHREAD="") \ |
80 | PREFIX="${EPREFIX}"/usr \ |
81 | CC="$(tc-getCC)" \ |
82 | CFLAGS="${CFLAGS}" |
83 | popd > /dev/null || die |
84 | } |
85 | |
86 | src_test() { |
87 | export MAFFT_BINARIES="${S}"/core |
88 | cd test || die |
89 | bash ../core/mafft sample > test.fftns2 || die |
90 | bash ../core/mafft --maxiterate 100 sample > test.fftnsi || die |
91 | bash ../core/mafft --globalpair sample > test.gins1 || die |
92 | bash ../core/mafft --globalpair --maxiterate 100 sample > test.ginsi || die |
93 | bash ../core/mafft --localpair sample > test.lins1 || die |
94 | bash ../core/mafft --localpair --maxiterate 100 sample > test.linsi || die |
95 | |
96 | diff test.fftns2 sample.fftns2 || die |
97 | diff test.fftnsi sample.fftnsi || die |
98 | diff test.gins1 sample.gins1 || die |
99 | diff test.ginsi sample.ginsi || die |
100 | diff test.lins1 sample.lins1 || die |
101 | } |
102 | |
103 | src_install() { |
104 | pushd core |
105 | emake PREFIX="${ED}usr" install |
106 | popd |
107 | dodoc readme |
108 | } |