[gentoo-commits] proj/sci:master commit in: sci-biology/consed/ - gentoo-commits

From:	Martin Mokrejs <mmokrejs@×××××××××××××××.cz>
To:	gentoo-commits@l.g.o
Subject:	[gentoo-commits] proj/sci:master commit in: sci-biology/consed/
Date:	Wed, 02 Apr 2014 09:32:27
Message-Id:	`1396431037.4209a296d2ae3587c269da77976813d6f80d2b0b.mmokrejs@gentoo`

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commit:     4209a296d2ae3587c269da77976813d6f80d2b0b

2

Author:     Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>

3

AuthorDate: Wed Apr  2 09:30:37 2014 +0000

4

Commit:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>

5

CommitDate: Wed Apr  2 09:30:37 2014 +0000

6

URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=4209a296

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8

sci-biology/consed: replace hardcoded CONSED_HOME path in installed perl scripts to fix situations when user has for some reason an empty CONSED_HOME

9

10

Package-Manager: portage-2.2.7

11

12

---

13

 sci-biology/consed/ChangeLog           | 7 ++++++-

14

 sci-biology/consed/consed-20-r1.ebuild | 1 +

15

 sci-biology/consed/consed-21.ebuild    | 1 +

16

 sci-biology/consed/consed-22.ebuild    | 1 +

17

 sci-biology/consed/consed-23.ebuild    | 1 +

18

 sci-biology/consed/consed-24.ebuild    | 1 +

19

 sci-biology/consed/consed-25.ebuild    | 1 +

20

 sci-biology/consed/consed-26.ebuild    | 1 +

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 sci-biology/consed/consed-27.ebuild    | 1 +

22

 9 files changed, 14 insertions(+), 1 deletion(-)

23

24

diff --git a/sci-biology/consed/ChangeLog b/sci-biology/consed/ChangeLog

25

index 3ce8ee3..0fe8c19 100644

26

--- a/sci-biology/consed/ChangeLog

27

+++ b/sci-biology/consed/ChangeLog

28

@@ -2,6 +2,12 @@

29

 # Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2

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 # $Header: $

31

32

+  02 Apr 2014; Martin Mokrejs <mmokrejs@×××××××××××××××.cz> consed-20-r1.ebuild,

33

+  consed-21.ebuild, consed-22.ebuild, consed-23.ebuild, consed-24.ebuild,

34

+  consed-25.ebuild, consed-26.ebuild, consed-27.ebuild:

35

+  sci-biology/consed: replace hardcoded CONSED_HOME path in installed perl

36

+  scripts to fix situations when user has for some reason an empty CONSED_HOME

37

+

38

 *consed-27 (23 Mar 2014)

39

 *consed-26 (23 Mar 2014)

40

 *consed-25 (23 Mar 2014)

41

@@ -22,4 +28,3 @@

42

   renamed dependency from openmotif to motif consed-20-r1.ebuild,

43

   added some extra patches files/nLine.h.patch,

44

   files/nextPhredPipeline.cpp.patch

45

-

46

47

diff --git a/sci-biology/consed/consed-20-r1.ebuild b/sci-biology/consed/consed-20-r1.ebuild

48

index 2eb8df3..cfcb66e 100644

49

--- a/sci-biology/consed/consed-20-r1.ebuild

50

+++ b/sci-biology/consed/consed-20-r1.ebuild

51

@@ -65,6 +65,7 @@ src_install() {

52

 		solexa_example_answer selectRegions selectRegionsAnswer || die

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 	echo 'CONSED_HOME='${EPREFIX}'/usr' > "${S}/99consed"

54

 	doenvd "${S}/99consed" || die

55

+	sed -e "s#/usr/local/genome#${EPREFIX}/usr#" -i "${D}"/usr/bin/*.perl || die

56

 	dodoc README.txt *_announcement.txt || die

57

}

58

59

60

diff --git a/sci-biology/consed/consed-21.ebuild b/sci-biology/consed/consed-21.ebuild

61

index 7163d60..55ba90a 100644

62

--- a/sci-biology/consed/consed-21.ebuild

63

+++ b/sci-biology/consed/consed-21.ebuild

64

@@ -64,6 +64,7 @@ src_install() {

65

 		align454reads align454reads_answer solexa_example \

66

 		solexa_example_answer selectRegions selectRegionsAnswer || die

67

 	echo 'CONSED_HOME='${EPREFIX}'/usr' > "${S}/99consed"

68

+	sed -e "s#/usr/local/genome#${EPREFIX}/usr#" -i "${D}"/usr/bin/*.perl || die

69

 	doenvd "${S}/99consed" || die

70

 	dodoc README.txt *_announcement.txt || die

71

}

72

73

diff --git a/sci-biology/consed/consed-22.ebuild b/sci-biology/consed/consed-22.ebuild

74

index 7163d60..d0a26e8 100644

75

--- a/sci-biology/consed/consed-22.ebuild

76

+++ b/sci-biology/consed/consed-22.ebuild

77

@@ -65,6 +65,7 @@ src_install() {

78

 		solexa_example_answer selectRegions selectRegionsAnswer || die

79

 	echo 'CONSED_HOME='${EPREFIX}'/usr' > "${S}/99consed"

80

 	doenvd "${S}/99consed" || die

81

+	sed -e "s#/usr/local/genome#${EPREFIX}/usr#" -i "${D}"/usr/bin/*.perl || die

82

 	dodoc README.txt *_announcement.txt || die

83

}

84

85

86

diff --git a/sci-biology/consed/consed-23.ebuild b/sci-biology/consed/consed-23.ebuild

87

index 7163d60..d0a26e8 100644

88

--- a/sci-biology/consed/consed-23.ebuild

89

+++ b/sci-biology/consed/consed-23.ebuild

90

@@ -65,6 +65,7 @@ src_install() {

91

 		solexa_example_answer selectRegions selectRegionsAnswer || die

92

 	echo 'CONSED_HOME='${EPREFIX}'/usr' > "${S}/99consed"

93

 	doenvd "${S}/99consed" || die

94

+	sed -e "s#/usr/local/genome#${EPREFIX}/usr#" -i "${D}"/usr/bin/*.perl || die

95

 	dodoc README.txt *_announcement.txt || die

96

}

97

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99

diff --git a/sci-biology/consed/consed-24.ebuild b/sci-biology/consed/consed-24.ebuild

100

index 7163d60..d0a26e8 100644

101

--- a/sci-biology/consed/consed-24.ebuild

102

+++ b/sci-biology/consed/consed-24.ebuild

103

@@ -65,6 +65,7 @@ src_install() {

104

 		solexa_example_answer selectRegions selectRegionsAnswer || die

105

 	echo 'CONSED_HOME='${EPREFIX}'/usr' > "${S}/99consed"

106

 	doenvd "${S}/99consed" || die

107

+	sed -e "s#/usr/local/genome#${EPREFIX}/usr#" -i "${D}"/usr/bin/*.perl || die

108

 	dodoc README.txt *_announcement.txt || die

109

}

110

111

112

diff --git a/sci-biology/consed/consed-25.ebuild b/sci-biology/consed/consed-25.ebuild

113

index 7163d60..d0a26e8 100644

114

--- a/sci-biology/consed/consed-25.ebuild

115

+++ b/sci-biology/consed/consed-25.ebuild

116

@@ -65,6 +65,7 @@ src_install() {

117

 		solexa_example_answer selectRegions selectRegionsAnswer || die

118

 	echo 'CONSED_HOME='${EPREFIX}'/usr' > "${S}/99consed"

119

 	doenvd "${S}/99consed" || die

120

+	sed -e "s#/usr/local/genome#${EPREFIX}/usr#" -i "${D}"/usr/bin/*.perl || die

121

 	dodoc README.txt *_announcement.txt || die

122

}

123

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125

diff --git a/sci-biology/consed/consed-26.ebuild b/sci-biology/consed/consed-26.ebuild

126

index 7163d60..d0a26e8 100644

127

--- a/sci-biology/consed/consed-26.ebuild

128

+++ b/sci-biology/consed/consed-26.ebuild

129

@@ -65,6 +65,7 @@ src_install() {

130

 		solexa_example_answer selectRegions selectRegionsAnswer || die

131

 	echo 'CONSED_HOME='${EPREFIX}'/usr' > "${S}/99consed"

132

 	doenvd "${S}/99consed" || die

133

+	sed -e "s#/usr/local/genome#${EPREFIX}/usr#" -i "${D}"/usr/bin/*.perl || die

134

 	dodoc README.txt *_announcement.txt || die

135

}

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138

diff --git a/sci-biology/consed/consed-27.ebuild b/sci-biology/consed/consed-27.ebuild

139

index 7163d60..d0a26e8 100644

140

--- a/sci-biology/consed/consed-27.ebuild

141

+++ b/sci-biology/consed/consed-27.ebuild

142

@@ -65,6 +65,7 @@ src_install() {

143

 		solexa_example_answer selectRegions selectRegionsAnswer || die

144

 	echo 'CONSED_HOME='${EPREFIX}'/usr' > "${S}/99consed"

145

 	doenvd "${S}/99consed" || die

146

+	sed -e "s#/usr/local/genome#${EPREFIX}/usr#" -i "${D}"/usr/bin/*.perl || die

147

 	dodoc README.txt *_announcement.txt || die

148

}

1	commit: 4209a296d2ae3587c269da77976813d6f80d2b0b
2	Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
3	AuthorDate: Wed Apr 2 09:30:37 2014 +0000
4	Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
5	CommitDate: Wed Apr 2 09:30:37 2014 +0000
6	URL: http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=4209a296
7
8	sci-biology/consed: replace hardcoded CONSED_HOME path in installed perl scripts to fix situations when user has for some reason an empty CONSED_HOME
9
10	Package-Manager: portage-2.2.7
11
12	---
13	sci-biology/consed/ChangeLog \| 7 ++++++-
14	sci-biology/consed/consed-20-r1.ebuild \| 1 +
15	sci-biology/consed/consed-21.ebuild \| 1 +
16	sci-biology/consed/consed-22.ebuild \| 1 +
17	sci-biology/consed/consed-23.ebuild \| 1 +
18	sci-biology/consed/consed-24.ebuild \| 1 +
19	sci-biology/consed/consed-25.ebuild \| 1 +
20	sci-biology/consed/consed-26.ebuild \| 1 +
21	sci-biology/consed/consed-27.ebuild \| 1 +
22	9 files changed, 14 insertions(+), 1 deletion(-)
23
24	diff --git a/sci-biology/consed/ChangeLog b/sci-biology/consed/ChangeLog
25	index 3ce8ee3..0fe8c19 100644
26	--- a/sci-biology/consed/ChangeLog
27	+++ b/sci-biology/consed/ChangeLog
28	@@ -2,6 +2,12 @@
29	# Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2
30	# $Header: $
31
32	+ 02 Apr 2014; Martin Mokrejs <mmokrejs@×××××××××××××××.cz> consed-20-r1.ebuild,
33	+ consed-21.ebuild, consed-22.ebuild, consed-23.ebuild, consed-24.ebuild,
34	+ consed-25.ebuild, consed-26.ebuild, consed-27.ebuild:
35	+ sci-biology/consed: replace hardcoded CONSED_HOME path in installed perl
36	+ scripts to fix situations when user has for some reason an empty CONSED_HOME
37	+
38	*consed-27 (23 Mar 2014)
39	*consed-26 (23 Mar 2014)
40	*consed-25 (23 Mar 2014)
41	@@ -22,4 +28,3 @@
42	renamed dependency from openmotif to motif consed-20-r1.ebuild,
43	added some extra patches files/nLine.h.patch,
44	files/nextPhredPipeline.cpp.patch
45	-
46
47	diff --git a/sci-biology/consed/consed-20-r1.ebuild b/sci-biology/consed/consed-20-r1.ebuild
48	index 2eb8df3..cfcb66e 100644
49	--- a/sci-biology/consed/consed-20-r1.ebuild
50	+++ b/sci-biology/consed/consed-20-r1.ebuild
51	@@ -65,6 +65,7 @@ src_install() {
52	solexa_example_answer selectRegions selectRegionsAnswer \|\| die
53	echo 'CONSED_HOME='${EPREFIX}'/usr' > "${S}/99consed"
54	doenvd "${S}/99consed" \|\| die
55	+ sed -e "s#/usr/local/genome#${EPREFIX}/usr#" -i "${D}"/usr/bin/*.perl \|\| die
56	dodoc README.txt *_announcement.txt \|\| die
57	}
58
59
60	diff --git a/sci-biology/consed/consed-21.ebuild b/sci-biology/consed/consed-21.ebuild
61	index 7163d60..55ba90a 100644
62	--- a/sci-biology/consed/consed-21.ebuild
63	+++ b/sci-biology/consed/consed-21.ebuild
64	@@ -64,6 +64,7 @@ src_install() {
65	align454reads align454reads_answer solexa_example \
66	solexa_example_answer selectRegions selectRegionsAnswer \|\| die
67	echo 'CONSED_HOME='${EPREFIX}'/usr' > "${S}/99consed"
68	+ sed -e "s#/usr/local/genome#${EPREFIX}/usr#" -i "${D}"/usr/bin/*.perl \|\| die
69	doenvd "${S}/99consed" \|\| die
70	dodoc README.txt *_announcement.txt \|\| die
71	}
72
73	diff --git a/sci-biology/consed/consed-22.ebuild b/sci-biology/consed/consed-22.ebuild
74	index 7163d60..d0a26e8 100644
75	--- a/sci-biology/consed/consed-22.ebuild
76	+++ b/sci-biology/consed/consed-22.ebuild
77	@@ -65,6 +65,7 @@ src_install() {
78	solexa_example_answer selectRegions selectRegionsAnswer \|\| die
79	echo 'CONSED_HOME='${EPREFIX}'/usr' > "${S}/99consed"
80	doenvd "${S}/99consed" \|\| die
81	+ sed -e "s#/usr/local/genome#${EPREFIX}/usr#" -i "${D}"/usr/bin/*.perl \|\| die
82	dodoc README.txt *_announcement.txt \|\| die
83	}
84
85
86	diff --git a/sci-biology/consed/consed-23.ebuild b/sci-biology/consed/consed-23.ebuild
87	index 7163d60..d0a26e8 100644
88	--- a/sci-biology/consed/consed-23.ebuild
89	+++ b/sci-biology/consed/consed-23.ebuild
90	@@ -65,6 +65,7 @@ src_install() {
91	solexa_example_answer selectRegions selectRegionsAnswer \|\| die
92	echo 'CONSED_HOME='${EPREFIX}'/usr' > "${S}/99consed"
93	doenvd "${S}/99consed" \|\| die
94	+ sed -e "s#/usr/local/genome#${EPREFIX}/usr#" -i "${D}"/usr/bin/*.perl \|\| die
95	dodoc README.txt *_announcement.txt \|\| die
96	}
97
98
99	diff --git a/sci-biology/consed/consed-24.ebuild b/sci-biology/consed/consed-24.ebuild
100	index 7163d60..d0a26e8 100644
101	--- a/sci-biology/consed/consed-24.ebuild
102	+++ b/sci-biology/consed/consed-24.ebuild
103	@@ -65,6 +65,7 @@ src_install() {
104	solexa_example_answer selectRegions selectRegionsAnswer \|\| die
105	echo 'CONSED_HOME='${EPREFIX}'/usr' > "${S}/99consed"
106	doenvd "${S}/99consed" \|\| die
107	+ sed -e "s#/usr/local/genome#${EPREFIX}/usr#" -i "${D}"/usr/bin/*.perl \|\| die
108	dodoc README.txt *_announcement.txt \|\| die
109	}
110
111
112	diff --git a/sci-biology/consed/consed-25.ebuild b/sci-biology/consed/consed-25.ebuild
113	index 7163d60..d0a26e8 100644
114	--- a/sci-biology/consed/consed-25.ebuild
115	+++ b/sci-biology/consed/consed-25.ebuild
116	@@ -65,6 +65,7 @@ src_install() {
117	solexa_example_answer selectRegions selectRegionsAnswer \|\| die
118	echo 'CONSED_HOME='${EPREFIX}'/usr' > "${S}/99consed"
119	doenvd "${S}/99consed" \|\| die
120	+ sed -e "s#/usr/local/genome#${EPREFIX}/usr#" -i "${D}"/usr/bin/*.perl \|\| die
121	dodoc README.txt *_announcement.txt \|\| die
122	}
123
124
125	diff --git a/sci-biology/consed/consed-26.ebuild b/sci-biology/consed/consed-26.ebuild
126	index 7163d60..d0a26e8 100644
127	--- a/sci-biology/consed/consed-26.ebuild
128	+++ b/sci-biology/consed/consed-26.ebuild
129	@@ -65,6 +65,7 @@ src_install() {
130	solexa_example_answer selectRegions selectRegionsAnswer \|\| die
131	echo 'CONSED_HOME='${EPREFIX}'/usr' > "${S}/99consed"
132	doenvd "${S}/99consed" \|\| die
133	+ sed -e "s#/usr/local/genome#${EPREFIX}/usr#" -i "${D}"/usr/bin/*.perl \|\| die
134	dodoc README.txt *_announcement.txt \|\| die
135	}
136
137
138	diff --git a/sci-biology/consed/consed-27.ebuild b/sci-biology/consed/consed-27.ebuild
139	index 7163d60..d0a26e8 100644
140	--- a/sci-biology/consed/consed-27.ebuild
141	+++ b/sci-biology/consed/consed-27.ebuild
142	@@ -65,6 +65,7 @@ src_install() {
143	solexa_example_answer selectRegions selectRegionsAnswer \|\| die
144	echo 'CONSED_HOME='${EPREFIX}'/usr' > "${S}/99consed"
145	doenvd "${S}/99consed" \|\| die
146	+ sed -e "s#/usr/local/genome#${EPREFIX}/usr#" -i "${D}"/usr/bin/*.perl \|\| die
147	dodoc README.txt *_announcement.txt \|\| die
148	}

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