Gentoo Archives: gentoo-commits

From: "Justin Lecher (jlec)" <jlec@g.o>
To: gentoo-commits@l.g.o
Subject: [gentoo-commits] gentoo-x86 commit in sci-biology/samtools: samtools-0.1.12a-r1.ebuild ChangeLog samtools-0.1.16.ebuild samtools-0.1.12.ebuild
Date: Sat, 30 Apr 2011 11:13:00
Message-Id: 20110430111250.2582420054@flycatcher.gentoo.org
1 jlec 11/04/30 11:12:50
2
3 Modified: samtools-0.1.12a-r1.ebuild ChangeLog
4 samtools-0.1.12.ebuild
5 Added: samtools-0.1.16.ebuild
6 Log:
7 Version BUmp, #365265
8
9 (Portage version: 2.2.0_alpha30/cvs/Linux x86_64)
10
11 Revision Changes Path
12 1.2 sci-biology/samtools/samtools-0.1.12a-r1.ebuild
13
14 file : http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-biology/samtools/samtools-0.1.12a-r1.ebuild?rev=1.2&view=markup
15 plain: http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-biology/samtools/samtools-0.1.12a-r1.ebuild?rev=1.2&content-type=text/plain
16 diff : http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-biology/samtools/samtools-0.1.12a-r1.ebuild?r1=1.1&r2=1.2
17
18 Index: samtools-0.1.12a-r1.ebuild
19 ===================================================================
20 RCS file: /var/cvsroot/gentoo-x86/sci-biology/samtools/samtools-0.1.12a-r1.ebuild,v
21 retrieving revision 1.1
22 retrieving revision 1.2
23 diff -u -r1.1 -r1.2
24 --- samtools-0.1.12a-r1.ebuild 14 Mar 2011 09:37:27 -0000 1.1
25 +++ samtools-0.1.12a-r1.ebuild 30 Apr 2011 11:12:49 -0000 1.2
26 @@ -1,6 +1,6 @@
27 # Copyright 1999-2011 Gentoo Foundation
28 # Distributed under the terms of the GNU General Public License v2
29 -# $Header: /var/cvsroot/gentoo-x86/sci-biology/samtools/samtools-0.1.12a-r1.ebuild,v 1.1 2011/03/14 09:37:27 xarthisius Exp $
30 +# $Header: /var/cvsroot/gentoo-x86/sci-biology/samtools/samtools-0.1.12a-r1.ebuild,v 1.2 2011/04/30 11:12:49 jlec Exp $
31
32 EAPI="2"
33
34 @@ -33,7 +33,7 @@
35 dobin $(find misc -type f -executable) || die
36 dolib.so libbam.so.1 || die
37 insinto /usr/include/bam
38 - doins bam.h bgzf.h faidx.h kaln.h khash.h kprobaln.h kseq.h ksort.h sam.h|| die
39 + doins bam.h bgzf.h faidx.h kaln.h khash.h kprobaln.h kseq.h ksort.h sam.h || die
40 insinto /usr/share/${PN}
41 doins -r examples || die
42 doman ${PN}.1 || die
43
44
45
46 1.6 sci-biology/samtools/ChangeLog
47
48 file : http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-biology/samtools/ChangeLog?rev=1.6&view=markup
49 plain: http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-biology/samtools/ChangeLog?rev=1.6&content-type=text/plain
50 diff : http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-biology/samtools/ChangeLog?r1=1.5&r2=1.6
51
52 Index: ChangeLog
53 ===================================================================
54 RCS file: /var/cvsroot/gentoo-x86/sci-biology/samtools/ChangeLog,v
55 retrieving revision 1.5
56 retrieving revision 1.6
57 diff -u -r1.5 -r1.6
58 --- ChangeLog 14 Mar 2011 09:37:27 -0000 1.5
59 +++ ChangeLog 30 Apr 2011 11:12:49 -0000 1.6
60 @@ -1,6 +1,12 @@
61 # ChangeLog for sci-biology/samtools
62 # Copyright 1999-2011 Gentoo Foundation; Distributed under the GPL v2
63 -# $Header: /var/cvsroot/gentoo-x86/sci-biology/samtools/ChangeLog,v 1.5 2011/03/14 09:37:27 xarthisius Exp $
64 +# $Header: /var/cvsroot/gentoo-x86/sci-biology/samtools/ChangeLog,v 1.6 2011/04/30 11:12:49 jlec Exp $
65 +
66 +*samtools-0.1.16 (30 Apr 2011)
67 +
68 + 30 Apr 2011; Justin Lecher <jlec@g.o> samtools-0.1.12.ebuild,
69 + samtools-0.1.12a-r1.ebuild, +samtools-0.1.16.ebuild:
70 + Version BUmp, #365265
71
72 *samtools-0.1.12a-r1 (14 Mar 2011)
73
74
75
76
77 1.4 sci-biology/samtools/samtools-0.1.12.ebuild
78
79 file : http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-biology/samtools/samtools-0.1.12.ebuild?rev=1.4&view=markup
80 plain: http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-biology/samtools/samtools-0.1.12.ebuild?rev=1.4&content-type=text/plain
81 diff : http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-biology/samtools/samtools-0.1.12.ebuild?r1=1.3&r2=1.4
82
83 Index: samtools-0.1.12.ebuild
84 ===================================================================
85 RCS file: /var/cvsroot/gentoo-x86/sci-biology/samtools/samtools-0.1.12.ebuild,v
86 retrieving revision 1.3
87 retrieving revision 1.4
88 diff -u -r1.3 -r1.4
89 --- samtools-0.1.12.ebuild 17 Feb 2011 09:05:13 -0000 1.3
90 +++ samtools-0.1.12.ebuild 30 Apr 2011 11:12:50 -0000 1.4
91 @@ -1,13 +1,13 @@
92 # Copyright 1999-2011 Gentoo Foundation
93 # Distributed under the terms of the GNU General Public License v2
94 -# $Header: /var/cvsroot/gentoo-x86/sci-biology/samtools/samtools-0.1.12.ebuild,v 1.3 2011/02/17 09:05:13 tomka Exp $
95 +# $Header: /var/cvsroot/gentoo-x86/sci-biology/samtools/samtools-0.1.12.ebuild,v 1.4 2011/04/30 11:12:50 jlec Exp $
96
97 EAPI="2"
98
99 MY_P="${P}a"
100
101 DESCRIPTION="Utilities for SAM (Sequence Alignment/Map), a format for large nucleotide sequence alignments"
102 -HOMEPAGE="http://${PN}.sourceforge.net/"
103 +HOMEPAGE="http://samtools.sourceforge.net/"
104 SRC_URI="mirror://sourceforge/${PN}/${MY_P}.tar.bz2"
105
106 LICENSE="MIT"
107 @@ -15,9 +15,6 @@
108 IUSE=""
109 KEYWORDS="amd64 x86"
110
111 -DEPEND=""
112 -RDEPEND=""
113 -
114 S="${WORKDIR}/${MY_P}"
115
116 src_prepare() {
117
118
119
120 1.1 sci-biology/samtools/samtools-0.1.16.ebuild
121
122 file : http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-biology/samtools/samtools-0.1.16.ebuild?rev=1.1&view=markup
123 plain: http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-biology/samtools/samtools-0.1.16.ebuild?rev=1.1&content-type=text/plain
124
125 Index: samtools-0.1.16.ebuild
126 ===================================================================
127 # Copyright 1999-2011 Gentoo Foundation
128 # Distributed under the terms of the GNU General Public License v2
129 # $Header: /var/cvsroot/gentoo-x86/sci-biology/samtools/samtools-0.1.16.ebuild,v 1.1 2011/04/30 11:12:50 jlec Exp $
130
131 EAPI="2"
132
133 inherit toolchain-funcs
134
135 DESCRIPTION="Utilities for SAM (Sequence Alignment/Map), a format for large nucleotide sequence alignments"
136 HOMEPAGE="http://samtools.sourceforge.net/"
137 SRC_URI="mirror://sourceforge/${PN}/${P}.tar.bz2"
138
139 LICENSE="MIT"
140 SLOT="0"
141 IUSE=""
142 KEYWORDS="~amd64 ~x86 ~x64-macos"
143
144 src_prepare() {
145 sed -e '/^CFLAGS=/d' \
146 -e "s/\$(CC) \$(CFLAGS)/& \$(LDFLAGS)/g" \
147 -e "s/-shared/& \$(LDFLAGS)/" \
148 -i "${S}"/{Makefile,misc/Makefile} || die #358563
149 sed -i 's~/software/bin/python~/usr/bin/env python~' "${S}"/misc/varfilter.py || die
150 }
151
152 src_compile() {
153 emake CC="$(tc-getCC)" dylib || die
154 emake CC="$(tc-getCC)" || die
155 }
156
157 src_install() {
158 dobin samtools || die
159 dobin $(find misc -type f -executable) || die
160 dolib.so libbam.so.1 || die
161 insinto /usr/include/bam
162 doins bam.h bgzf.h faidx.h kaln.h khash.h kprobaln.h kseq.h ksort.h sam.h || die
163 insinto /usr/share/${PN}
164 doins -r examples || die
165 doman ${PN}.1 || die
166 dodoc AUTHORS ChangeLog NEWS
167 }