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 |
} |