[gentoo-commits] repo/gentoo:master commit in: sci-biology/STAR/, sci-biology/STAR/files/ - gentoo-commits

From:	David Seifert <soap@g.o>
To:	gentoo-commits@l.g.o
Subject:	[gentoo-commits] repo/gentoo:master commit in: sci-biology/STAR/, sci-biology/STAR/files/
Date:	Thu, 16 Nov 2017 13:17:14
Message-Id:	`1510838205.acd76729254ed012b6898eb33fcc59ab8c2076e4.soap@gentoo`

1

commit:     acd76729254ed012b6898eb33fcc59ab8c2076e4

2

Author:     David Seifert <soap <AT> gentoo <DOT> org>

3

AuthorDate: Thu Nov 16 12:32:54 2017 +0000

4

Commit:     David Seifert <soap <AT> gentoo <DOT> org>

5

CommitDate: Thu Nov 16 13:16:45 2017 +0000

6

URL:        https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=acd76729

7

8

sci-biology/STAR: Initial addition

9

10

Closes: https://github.com/gentoo/sci/pull/814

11

Package-Manager: Portage-2.3.14, Repoman-2.3.6

12

13

 sci-biology/STAR/Manifest                          |   1 +

14

 sci-biology/STAR/STAR-2.5.3a.ebuild                |  42 +++++++

15

 .../STAR/files/STAR-2.5.3a-fix-build-system.patch  | 123 +++++++++++++++++++++

16

 sci-biology/STAR/metadata.xml                      |  19 ++++

17

 4 files changed, 185 insertions(+)

18

19

diff --git a/sci-biology/STAR/Manifest b/sci-biology/STAR/Manifest

20

new file mode 100644

21

index 00000000000..0ec6da1a3d9

22

--- /dev/null

23

+++ b/sci-biology/STAR/Manifest

24

@@ -0,0 +1 @@

25

+DIST STAR-2.5.3a.tar.gz 9857460 SHA256 2a258e77cda103aa293e528f8597f25dc760cba188d0a7bc7c9452f4698e7c04 SHA512 8bd86ad384f2c0331fd701873b02641301f4205a5ff0fceeb800d425da42c53b6c61a74500d37fee7fc13a5bff10e1fb44b9142811883b8f5cd012f51f1f9fdf WHIRLPOOL 64bb7dc68e24ecd7d198d281e98042fd1463fc96af8ab8be9cab8e1588c2d08ab7cd1435187f2e0ebe870da11ab607c8f8a981d76360c55dd76e1fb4bb304006

26

27

diff --git a/sci-biology/STAR/STAR-2.5.3a.ebuild b/sci-biology/STAR/STAR-2.5.3a.ebuild

28

new file mode 100644

29

index 00000000000..73743cbb4e5

30

--- /dev/null

31

+++ b/sci-biology/STAR/STAR-2.5.3a.ebuild

32

@@ -0,0 +1,42 @@

33

+# Copyright 1999-2017 Gentoo Foundation

34

+# Distributed under the terms of the GNU General Public License v2

35

+

36

+EAPI=6

37

+

38

+inherit toolchain-funcs

39

+

40

+DESCRIPTION="STAR aligner: align RNA-seq reads to reference genome uncompressed suffix arrays"

41

+HOMEPAGE="https://github.com/alexdobin/STAR"

42

+SRC_URI="https://github.com/alexdobin/${PN}/archive/${PV}.tar.gz -> ${P}.tar.gz"

43

+

44

+LICENSE="GPL-3"

45

+SLOT="0"

46

+KEYWORDS="~amd64"

47

+

48

+RDEPEND="sci-libs/htslib:="

49

+DEPEND="${RDEPEND}

50

+	virtual/pkgconfig"

51

+

52

+PATCHES=( "${FILESDIR}"/${PN}-2.5.3a-fix-build-system.patch )

53

+DOCS=( README.md CHANGES.md RELEASEnotes.md doc/STARmanual.pdf )

54

+

55

+pkg_pretend() {

56

+	[[ ${MERGE_TYPE} != binary ]] && tc-check-openmp

57

+}

58

+

59

+pkg_setup() {

60

+	[[ ${MERGE_TYPE} != binary ]] && tc-check-openmp

61

+}

62

+

63

+src_configure() {

64

+	tc-export CC CXX PKG_CONFIG

65

+}

66

+

67

+src_compile() {

68

+	emake -C source STAR

69

+}

70

+

71

+src_install() {

72

+	dobin source/STAR

73

+	einstalldocs

74

+}

75

76

diff --git a/sci-biology/STAR/files/STAR-2.5.3a-fix-build-system.patch b/sci-biology/STAR/files/STAR-2.5.3a-fix-build-system.patch

77

new file mode 100644

78

index 00000000000..8e504fa429e

79

--- /dev/null

80

+++ b/sci-biology/STAR/files/STAR-2.5.3a-fix-build-system.patch

81

@@ -0,0 +1,123 @@

82

+* unbundle htslib

83

+* honour all user flags

84

+* use pkg-config for linking

85

+

86

+--- a/source/Makefile

87

++++ b/source/Makefile

88

+@@ -8,24 +8,12 @@

89

+ LDFLAGSextra ?=

90

+ CXXFLAGSextra ?=

91

+

92

+-# user may define the compiler

93

+-CXX ?= g++

94

+-

95

+ # pre-defined flags

96

+-LDFLAGS_shared := -pthread -Lhtslib -Bstatic -lhts -Bdynamic -lz -lrt

97

+-LDFLAGS_static := -static -static-libgcc -pthread -Lhtslib -lhts -lz

98

+-LDFLAGS_Mac :=-pthread -lz htslib/libhts.a

99

+-LDFLAGS_Mac_static :=-pthread -lz -static-libgcc htslib/libhts.a

100

+-LDFLAGS_gdb := $(LDFLAGS_shared)

101

+-

102

+ COMPTIMEPLACE := -D'COMPILATION_TIME_PLACE="$(shell echo `date` $(HOSTNAME):`pwd`)"'

103

+

104

+-CXXFLAGS_common := -pipe -std=c++11 -Wall -Wextra -fopenmp $(COMPTIMEPLACE)

105

+-CXXFLAGS_main := -O3 $(CXXFLAGS_common)

106

+-CXXFLAGS_gdb :=  -O0 -g $(CXXFLAGS_common)

107

+-

108

+-CFLAGS := -O3 -pipe -Wall -Wextra $(CFLAGS)

109

+-

110

++CFLAGS_common = -Wall -Wextra -pthread `$(PKG_CONFIG) --cflags htslib` `$(PKG_CONFIG) --cflags zlib`

111

++CXXFLAGS_common = $(CFLAGS_common) -std=c++11 -fopenmp $(COMPTIMEPLACE)

112

++LIBS_common = -pthread `$(PKG_CONFIG) --libs htslib` `$(PKG_CONFIG) --libs zlib` -lrt

113

+

114

+ ##########################################################################################################

115

+

116

+@@ -54,10 +42,10 @@

117

+

118

+

119

+ %.o : %.cpp

120

+-	$(CXX) -c $(CPPFLAGS) $(CXXFLAGS) $<

121

++	$(CXX) -c $(CPPFLAGS) $(CXXFLAGS) $(CXXFLAGS_common) $<

122

+

123

+ %.o : %.c

124

+-	$(CXX) -c $(CPPFLAGS) $(CFLAGS) $<

125

++	$(CXX) -c $(CPPFLAGS) $(CFLAGS) $(CFLAGS_common) $<

126

+

127

+ all: STAR

128

+

129

+@@ -84,7 +72,7 @@

130

+ ifneq ($(MAKECMDGOALS),CLEAN)

131

+ ifneq ($(MAKECMDGOALS),STARforMac)

132

+ ifneq ($(MAKECMDGOALS),STARforMacGDB)

133

+-Depend.list: $(SOURCES) parametersDefault.xxd htslib

134

++Depend.list: $(SOURCES) parametersDefault.xxd

135

+ 	echo $(SOURCES)

136

+ 	/bin/rm -f ./Depend.list

137

+ 	$(CXX) $(CXXFLAGS_common) -MM $^ >> Depend.list

138

+@@ -95,57 +83,34 @@

139

+ endif

140

+ endif

141

+

142

+-htslib : htslib/libhts.a

143

+-

144

+-htslib/libhts.a :

145

+-	$(MAKE) -C htslib lib-static

146

+-

147

+ parametersDefault.xxd: parametersDefault

148

+ 	xxd -i parametersDefault > parametersDefault.xxd

149

+

150

+-STAR : CXXFLAGS := $(CXXFLAGSextra) $(CXXFLAGS_main) $(CXXFLAGS)

151

+-STAR : LDFLAGS := $(LDFLAGSextra) $(LDFLAGS_shared) $(LDFLAGS)

152

+ STAR : Depend.list parametersDefault.xxd $(OBJECTS)

153

+-	$(CXX) -o STAR $(CXXFLAGS) $(OBJECTS) $(LDFLAGS)

154

++	$(CXX) $(CXXFLAGS) $(CXXFLAGS_common) $(LDFLAGS) -o STAR $(OBJECTS) $(LIBS) $(LIBS_common)

155

+

156

+-POSIXSHARED : CXXFLAGS := $(CXXFLAGSextra) $(CXXFLAGS_main) -DPOSIX_SHARED_MEM $(CXXFLAGS)

157

+-POSIXSHARED : LDFLAGS := $(LDFLAGSextra) $(LDFLAGS_shared) $(LDFLAGS)

158

+ POSIXSHARED : Depend.list parametersDefault.xxd $(OBJECTS)

159

+-	$(CXX) -o STAR $(CXXFLAGS) $(OBJECTS) $(LDFLAGS)

160

++	$(CXX) $(CXXFLAGS) $(CXXFLAGS_common) $(LDFLAGS) -o STAR $(OBJECTS) $(LIBS) $(LIBS_common)

161

+

162

+-STARstatic : CXXFLAGS := $(CXXFLAGSextra) $(CXXFLAGS_main) $(CXXFLAGS)

163

+-STARstatic : LDFLAGS := $(LDFLAGSextra) $(LDFLAGS_static) $(LDFLAGS)

164

+ STARstatic : Depend.list parametersDefault.xxd $(OBJECTS)

165

+-	$(CXX) -o STAR $(CXXFLAGS) $(OBJECTS) $(LDFLAGS)

166

++	$(CXX) $(CXXFLAGS) $(CXXFLAGS_common) $(LDFLAGS) -o STAR $(OBJECTS) $(LIBS) $(LIBS_common)

167

+

168

+-STARlong : CXXFLAGS := $(CXXFLAGSextra) $(CXXFLAGS_main) -D'COMPILE_FOR_LONG_READS' $(CXXFLAGS)

169

+-STARlong : LDFLAGS := $(LDFLAGSextra) $(LDFLAGS_shared) $(LDFLAGS)

170

+ STARlong : Depend.list parametersDefault.xxd $(OBJECTS)

171

+-	$(CXX) -o STARlong $(CXXFLAGS) $(OBJECTS) $(LDFLAGS)

172

++	$(CXX) $(CXXFLAGS) $(CXXFLAGS_common) $(LDFLAGS) -o STARlong $(OBJECTS) $(LIBS) $(LIBS_common)

173

+

174

+-STARlongStatic : CXXFLAGS := $(CXXFLAGSextra) $(CXXFLAGS_main) -D'COMPILE_FOR_LONG_READS' $(CXXFLAGS)

175

+-STARlongStatic : LDFLAGS := $(LDFLAGSextra) $(LDFLAGS_static) $(LDFLAGS)

176

+ STARlongStatic : Depend.list parametersDefault.xxd $(OBJECTS)

177

+-	$(CXX) -o STARlong $(CXXFLAGS) $(OBJECTS) $(LDFLAGS)

178

++	$(CXX) $(CXXFLAGS) $(CXXFLAGS_common) $(LDFLAGS) -o STARlong $(OBJECTS) $(LIBS) $(LIBS_common)

179

+

180

+-gdb : CXXFLAGS := $(CXXFLAGSextra) $(CXXFLAGS_gdb) $(CXXFLAGS)

181

+-gdb : LDFLAGS := $(LDFLAGSextra) $(LDFLAGS_gdb) $(LDFLAGS)

182

+ gdb : Depend.list parametersDefault.xxd $(OBJECTS)

183

+-	$(CXX) -o STAR $(CXXFLAGS) $(OBJECTS) $(LDFLAGS)

184

++	$(CXX) $(CXXFLAGS) $(CXXFLAGS_common) $(LDFLAGS) -o STAR $(OBJECTS) $(LIBS) $(LIBS_common)

185

+

186

+-gdb-long : CXXFLAGS := $(CXXFLAGSextra) $(CXXFLAGS_gdb) -D'COMPILE_FOR_LONG_READS' $(CXXFLAGS)

187

+-gdb-long : LDFLAGS := $(LDFLAGSextra) $(LDFLAGS_gdb) $(LDFLAGS)

188

+ gdb-long : Depend.list parametersDefault.xxd $(OBJECTS)

189

+-	$(CXX) -o STARlong $(CXXFLAGS) $(OBJECTS) $(LDFLAGS)

190

++	$(CXX) $(CXXFLAGS) $(CXXFLAGS_common) $(LDFLAGS) -o STARlong $(OBJECTS) $(LIBS) $(LIBS_common)

191

+

192

+-STARforMacStatic : CXXFLAGS := $(CXXFLAGSextra) $(CXXFLAGS_main) -D'COMPILE_FOR_MAC' $(CXXFLAGS)

193

+-STARforMacStatic : LDFLAGS := $(LDFLAGSextra) $(LDFLAGS_Mac_static) $(LDFLAGS)

194

+ STARforMacStatic : Depend.list parametersDefault.xxd $(OBJECTS)

195

+-	$(CXX) -o STAR $(CXXFLAGS) $(OBJECTS) $(LDFLAGS)

196

++	$(CXX) $(CXXFLAGS) $(CXXFLAGS_common) $(LDFLAGS) -o STAR $(OBJECTS) $(LIBS) $(LIBS_common)

197

+

198

+-STARlongForMacStatic : CXXFLAGS := -D'COMPILE_FOR_LONG_READS' $(CXXFLAGSextra) $(CXXFLAGS_main) -D'COMPILE_FOR_MAC' $(CXXFLAGS)

199

+-STARlongForMacStatic : LDFLAGS := $(LDFLAGSextra) $(LDFLAGS_Mac_static) $(LDFLAGS)

200

+ STARlongForMacStatic : Depend.list parametersDefault.xxd $(OBJECTS)

201

+-	$(CXX) -o STARlong $(CXXFLAGS) $(OBJECTS) $(LDFLAGS)

202

++	$(CXX) $(CXXFLAGS) $(CXXFLAGS_common) $(LDFLAGS) -o STARlong $(OBJECTS) $(LIBS) $(LIBS_common)

203

+

204

+

205

206

diff --git a/sci-biology/STAR/metadata.xml b/sci-biology/STAR/metadata.xml

207

new file mode 100644

208

index 00000000000..22727da1cad

209

--- /dev/null

210

+++ b/sci-biology/STAR/metadata.xml

211

@@ -0,0 +1,19 @@

212

+<?xml version="1.0" encoding="UTF-8"?>

213

+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">

214

+<pkgmetadata>

215

+	<maintainer type="person">

216

+		<email>mmokrejs@×××××××××××××××.cz</email>

217

+		<name>Martin Mokrejs</name>

218

+	</maintainer>

219

+	<maintainer type="project">

220

+		<email>proxy-maint@g.o</email>

221

+		<name>Proxy Maintainers</name>

222

+	</maintainer>

223

+	<maintainer type="project">

224

+		<email>sci-biology@g.o</email>

225

+		<name>Gentoo Biology Project</name>

226

+	</maintainer>

227

+	<upstream>

228

+		<remote-id type="github">alexdobin/STAR</remote-id>

229

+	</upstream>

230

+</pkgmetadata>

1	commit: acd76729254ed012b6898eb33fcc59ab8c2076e4
2	Author: David Seifert <soap <AT> gentoo <DOT> org>
3	AuthorDate: Thu Nov 16 12:32:54 2017 +0000
4	Commit: David Seifert <soap <AT> gentoo <DOT> org>
5	CommitDate: Thu Nov 16 13:16:45 2017 +0000
6	URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=acd76729
7
8	sci-biology/STAR: Initial addition
9
10	Closes: https://github.com/gentoo/sci/pull/814
11	Package-Manager: Portage-2.3.14, Repoman-2.3.6
12
13	sci-biology/STAR/Manifest \| 1 +
14	sci-biology/STAR/STAR-2.5.3a.ebuild \| 42 +++++++
15	.../STAR/files/STAR-2.5.3a-fix-build-system.patch \| 123 +++++++++++++++++++++
16	sci-biology/STAR/metadata.xml \| 19 ++++
17	4 files changed, 185 insertions(+)
18
19	diff --git a/sci-biology/STAR/Manifest b/sci-biology/STAR/Manifest
20	new file mode 100644
21	index 00000000000..0ec6da1a3d9
22	--- /dev/null
23	+++ b/sci-biology/STAR/Manifest
24	@@ -0,0 +1 @@
25	+DIST STAR-2.5.3a.tar.gz 9857460 SHA256 2a258e77cda103aa293e528f8597f25dc760cba188d0a7bc7c9452f4698e7c04 SHA512 8bd86ad384f2c0331fd701873b02641301f4205a5ff0fceeb800d425da42c53b6c61a74500d37fee7fc13a5bff10e1fb44b9142811883b8f5cd012f51f1f9fdf WHIRLPOOL 64bb7dc68e24ecd7d198d281e98042fd1463fc96af8ab8be9cab8e1588c2d08ab7cd1435187f2e0ebe870da11ab607c8f8a981d76360c55dd76e1fb4bb304006
26
27	diff --git a/sci-biology/STAR/STAR-2.5.3a.ebuild b/sci-biology/STAR/STAR-2.5.3a.ebuild
28	new file mode 100644
29	index 00000000000..73743cbb4e5
30	--- /dev/null
31	+++ b/sci-biology/STAR/STAR-2.5.3a.ebuild
32	@@ -0,0 +1,42 @@
33	+# Copyright 1999-2017 Gentoo Foundation
34	+# Distributed under the terms of the GNU General Public License v2
35	+
36	+EAPI=6
37	+
38	+inherit toolchain-funcs
39	+
40	+DESCRIPTION="STAR aligner: align RNA-seq reads to reference genome uncompressed suffix arrays"
41	+HOMEPAGE="https://github.com/alexdobin/STAR"
42	+SRC_URI="https://github.com/alexdobin/${PN}/archive/${PV}.tar.gz -> ${P}.tar.gz"
43	+
44	+LICENSE="GPL-3"
45	+SLOT="0"
46	+KEYWORDS="~amd64"
47	+
48	+RDEPEND="sci-libs/htslib:="
49	+DEPEND="${RDEPEND}
50	+ virtual/pkgconfig"
51	+
52	+PATCHES=( "${FILESDIR}"/${PN}-2.5.3a-fix-build-system.patch )
53	+DOCS=( README.md CHANGES.md RELEASEnotes.md doc/STARmanual.pdf )
54	+
55	+pkg_pretend() {
56	+ [[ ${MERGE_TYPE} != binary ]] && tc-check-openmp
57	+}
58	+
59	+pkg_setup() {
60	+ [[ ${MERGE_TYPE} != binary ]] && tc-check-openmp
61	+}
62	+
63	+src_configure() {
64	+ tc-export CC CXX PKG_CONFIG
65	+}
66	+
67	+src_compile() {
68	+ emake -C source STAR
69	+}
70	+
71	+src_install() {
72	+ dobin source/STAR
73	+ einstalldocs
74	+}
75
76	diff --git a/sci-biology/STAR/files/STAR-2.5.3a-fix-build-system.patch b/sci-biology/STAR/files/STAR-2.5.3a-fix-build-system.patch
77	new file mode 100644
78	index 00000000000..8e504fa429e
79	--- /dev/null
80	+++ b/sci-biology/STAR/files/STAR-2.5.3a-fix-build-system.patch
81	@@ -0,0 +1,123 @@
82	+* unbundle htslib
83	+* honour all user flags
84	+* use pkg-config for linking
85	+
86	+--- a/source/Makefile
87	++++ b/source/Makefile
88	+@@ -8,24 +8,12 @@
89	+ LDFLAGSextra ?=
90	+ CXXFLAGSextra ?=
91	+
92	+-# user may define the compiler
93	+-CXX ?= g++
94	+-
95	+ # pre-defined flags
96	+-LDFLAGS_shared := -pthread -Lhtslib -Bstatic -lhts -Bdynamic -lz -lrt
97	+-LDFLAGS_static := -static -static-libgcc -pthread -Lhtslib -lhts -lz
98	+-LDFLAGS_Mac :=-pthread -lz htslib/libhts.a
99	+-LDFLAGS_Mac_static :=-pthread -lz -static-libgcc htslib/libhts.a
100	+-LDFLAGS_gdb := $(LDFLAGS_shared)
101	+-
102	+ COMPTIMEPLACE := -D'COMPILATION_TIME_PLACE="$(shell echo `date` $(HOSTNAME):`pwd`)"'
103	+
104	+-CXXFLAGS_common := -pipe -std=c++11 -Wall -Wextra -fopenmp $(COMPTIMEPLACE)
105	+-CXXFLAGS_main := -O3 $(CXXFLAGS_common)
106	+-CXXFLAGS_gdb := -O0 -g $(CXXFLAGS_common)
107	+-
108	+-CFLAGS := -O3 -pipe -Wall -Wextra $(CFLAGS)
109	+-
110	++CFLAGS_common = -Wall -Wextra -pthread `$(PKG_CONFIG) --cflags htslib` `$(PKG_CONFIG) --cflags zlib`
111	++CXXFLAGS_common = $(CFLAGS_common) -std=c++11 -fopenmp $(COMPTIMEPLACE)
112	++LIBS_common = -pthread `$(PKG_CONFIG) --libs htslib` `$(PKG_CONFIG) --libs zlib` -lrt
113	+
114	+ ##########################################################################################################
115	+
116	+@@ -54,10 +42,10 @@
117	+
118	+
119	+ %.o : %.cpp
120	+- $(CXX) -c $(CPPFLAGS) $(CXXFLAGS) $<
121	++ $(CXX) -c $(CPPFLAGS) $(CXXFLAGS) $(CXXFLAGS_common) $<
122	+
123	+ %.o : %.c
124	+- $(CXX) -c $(CPPFLAGS) $(CFLAGS) $<
125	++ $(CXX) -c $(CPPFLAGS) $(CFLAGS) $(CFLAGS_common) $<
126	+
127	+ all: STAR
128	+
129	+@@ -84,7 +72,7 @@
130	+ ifneq ($(MAKECMDGOALS),CLEAN)
131	+ ifneq ($(MAKECMDGOALS),STARforMac)
132	+ ifneq ($(MAKECMDGOALS),STARforMacGDB)
133	+-Depend.list: $(SOURCES) parametersDefault.xxd htslib
134	++Depend.list: $(SOURCES) parametersDefault.xxd
135	+ echo $(SOURCES)
136	+ /bin/rm -f ./Depend.list
137	+ $(CXX) $(CXXFLAGS_common) -MM $^ >> Depend.list
138	+@@ -95,57 +83,34 @@
139	+ endif
140	+ endif
141	+
142	+-htslib : htslib/libhts.a
143	+-
144	+-htslib/libhts.a :
145	+- $(MAKE) -C htslib lib-static
146	+-
147	+ parametersDefault.xxd: parametersDefault
148	+ xxd -i parametersDefault > parametersDefault.xxd
149	+
150	+-STAR : CXXFLAGS := $(CXXFLAGSextra) $(CXXFLAGS_main) $(CXXFLAGS)
151	+-STAR : LDFLAGS := $(LDFLAGSextra) $(LDFLAGS_shared) $(LDFLAGS)
152	+ STAR : Depend.list parametersDefault.xxd $(OBJECTS)
153	+- $(CXX) -o STAR $(CXXFLAGS) $(OBJECTS) $(LDFLAGS)
154	++ $(CXX) $(CXXFLAGS) $(CXXFLAGS_common) $(LDFLAGS) -o STAR $(OBJECTS) $(LIBS) $(LIBS_common)
155	+
156	+-POSIXSHARED : CXXFLAGS := $(CXXFLAGSextra) $(CXXFLAGS_main) -DPOSIX_SHARED_MEM $(CXXFLAGS)
157	+-POSIXSHARED : LDFLAGS := $(LDFLAGSextra) $(LDFLAGS_shared) $(LDFLAGS)
158	+ POSIXSHARED : Depend.list parametersDefault.xxd $(OBJECTS)
159	+- $(CXX) -o STAR $(CXXFLAGS) $(OBJECTS) $(LDFLAGS)
160	++ $(CXX) $(CXXFLAGS) $(CXXFLAGS_common) $(LDFLAGS) -o STAR $(OBJECTS) $(LIBS) $(LIBS_common)
161	+
162	+-STARstatic : CXXFLAGS := $(CXXFLAGSextra) $(CXXFLAGS_main) $(CXXFLAGS)
163	+-STARstatic : LDFLAGS := $(LDFLAGSextra) $(LDFLAGS_static) $(LDFLAGS)
164	+ STARstatic : Depend.list parametersDefault.xxd $(OBJECTS)
165	+- $(CXX) -o STAR $(CXXFLAGS) $(OBJECTS) $(LDFLAGS)
166	++ $(CXX) $(CXXFLAGS) $(CXXFLAGS_common) $(LDFLAGS) -o STAR $(OBJECTS) $(LIBS) $(LIBS_common)
167	+
168	+-STARlong : CXXFLAGS := $(CXXFLAGSextra) $(CXXFLAGS_main) -D'COMPILE_FOR_LONG_READS' $(CXXFLAGS)
169	+-STARlong : LDFLAGS := $(LDFLAGSextra) $(LDFLAGS_shared) $(LDFLAGS)
170	+ STARlong : Depend.list parametersDefault.xxd $(OBJECTS)
171	+- $(CXX) -o STARlong $(CXXFLAGS) $(OBJECTS) $(LDFLAGS)
172	++ $(CXX) $(CXXFLAGS) $(CXXFLAGS_common) $(LDFLAGS) -o STARlong $(OBJECTS) $(LIBS) $(LIBS_common)
173	+
174	+-STARlongStatic : CXXFLAGS := $(CXXFLAGSextra) $(CXXFLAGS_main) -D'COMPILE_FOR_LONG_READS' $(CXXFLAGS)
175	+-STARlongStatic : LDFLAGS := $(LDFLAGSextra) $(LDFLAGS_static) $(LDFLAGS)
176	+ STARlongStatic : Depend.list parametersDefault.xxd $(OBJECTS)
177	+- $(CXX) -o STARlong $(CXXFLAGS) $(OBJECTS) $(LDFLAGS)
178	++ $(CXX) $(CXXFLAGS) $(CXXFLAGS_common) $(LDFLAGS) -o STARlong $(OBJECTS) $(LIBS) $(LIBS_common)
179	+
180	+-gdb : CXXFLAGS := $(CXXFLAGSextra) $(CXXFLAGS_gdb) $(CXXFLAGS)
181	+-gdb : LDFLAGS := $(LDFLAGSextra) $(LDFLAGS_gdb) $(LDFLAGS)
182	+ gdb : Depend.list parametersDefault.xxd $(OBJECTS)
183	+- $(CXX) -o STAR $(CXXFLAGS) $(OBJECTS) $(LDFLAGS)
184	++ $(CXX) $(CXXFLAGS) $(CXXFLAGS_common) $(LDFLAGS) -o STAR $(OBJECTS) $(LIBS) $(LIBS_common)
185	+
186	+-gdb-long : CXXFLAGS := $(CXXFLAGSextra) $(CXXFLAGS_gdb) -D'COMPILE_FOR_LONG_READS' $(CXXFLAGS)
187	+-gdb-long : LDFLAGS := $(LDFLAGSextra) $(LDFLAGS_gdb) $(LDFLAGS)
188	+ gdb-long : Depend.list parametersDefault.xxd $(OBJECTS)
189	+- $(CXX) -o STARlong $(CXXFLAGS) $(OBJECTS) $(LDFLAGS)
190	++ $(CXX) $(CXXFLAGS) $(CXXFLAGS_common) $(LDFLAGS) -o STARlong $(OBJECTS) $(LIBS) $(LIBS_common)
191	+
192	+-STARforMacStatic : CXXFLAGS := $(CXXFLAGSextra) $(CXXFLAGS_main) -D'COMPILE_FOR_MAC' $(CXXFLAGS)
193	+-STARforMacStatic : LDFLAGS := $(LDFLAGSextra) $(LDFLAGS_Mac_static) $(LDFLAGS)
194	+ STARforMacStatic : Depend.list parametersDefault.xxd $(OBJECTS)
195	+- $(CXX) -o STAR $(CXXFLAGS) $(OBJECTS) $(LDFLAGS)
196	++ $(CXX) $(CXXFLAGS) $(CXXFLAGS_common) $(LDFLAGS) -o STAR $(OBJECTS) $(LIBS) $(LIBS_common)
197	+
198	+-STARlongForMacStatic : CXXFLAGS := -D'COMPILE_FOR_LONG_READS' $(CXXFLAGSextra) $(CXXFLAGS_main) -D'COMPILE_FOR_MAC' $(CXXFLAGS)
199	+-STARlongForMacStatic : LDFLAGS := $(LDFLAGSextra) $(LDFLAGS_Mac_static) $(LDFLAGS)
200	+ STARlongForMacStatic : Depend.list parametersDefault.xxd $(OBJECTS)
201	+- $(CXX) -o STARlong $(CXXFLAGS) $(OBJECTS) $(LDFLAGS)
202	++ $(CXX) $(CXXFLAGS) $(CXXFLAGS_common) $(LDFLAGS) -o STARlong $(OBJECTS) $(LIBS) $(LIBS_common)
203	+
204	+
205
206	diff --git a/sci-biology/STAR/metadata.xml b/sci-biology/STAR/metadata.xml
207	new file mode 100644
208	index 00000000000..22727da1cad
209	--- /dev/null
210	+++ b/sci-biology/STAR/metadata.xml
211	@@ -0,0 +1,19 @@
212	+<?xml version="1.0" encoding="UTF-8"?>
213	+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
214	+<pkgmetadata>
215	+ <maintainer type="person">
216	+ <email>mmokrejs@×××××××××××××××.cz</email>
217	+ <name>Martin Mokrejs</name>
218	+ </maintainer>
219	+ <maintainer type="project">
220	+ <email>proxy-maint@g.o</email>
221	+ <name>Proxy Maintainers</name>
222	+ </maintainer>
223	+ <maintainer type="project">
224	+ <email>sci-biology@g.o</email>
225	+ <name>Gentoo Biology Project</name>
226	+ </maintainer>
227	+ <upstream>
228	+ <remote-id type="github">alexdobin/STAR</remote-id>
229	+ </upstream>
230	+</pkgmetadata>

Gentoo Archives: gentoo-commits