Gentoo Archives: gentoo-commits

From: Martin Mokrejs <mmokrejs@×××××××××××××××.cz>
To: gentoo-commits@l.g.o
Subject: [gentoo-commits] proj/sci:master commit in: sci-biology/bowtie/files/, sci-biology/bowtie/
Date: Tue, 19 Feb 2019 11:21:14
Message-Id: 1550575251.85794dc2e25580c628e007d4a528ffc2e24d4239.mmokrejs@gentoo
1 commit: 85794dc2e25580c628e007d4a528ffc2e24d4239
2 Author: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
3 AuthorDate: Tue Feb 19 11:20:51 2019 +0000
4 Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
5 CommitDate: Tue Feb 19 11:20:51 2019 +0000
6 URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=85794dc2
7
8 sci-biology/bowtie: working 1.2.2 snapshot
9
10 This ebuild keeps the bundled SeqAn-1.1 sources (a library of
11 headers) and does not insist on system-wide installed
12 SeqAn-1.4 (for which too many patches are needed and I am unable
13 to evaluate/apply them all).
14
15 Package-Manager: Portage-2.3.61, Repoman-2.3.12
16 Signed-off-by: Martin Mokrejs <mmokrejs <AT> fold.natur.cuni.cz>
17
18 .../bowtie/bowtie-1.2.2_beta20190219.ebuild | 81 ++++++++++++++++++++++
19 sci-biology/bowtie/bowtie-9999.ebuild | 81 ++++++++++++++++++++++
20 .../files/bowtie-1.2.2-fix-isa-return-type.patch | 22 ++++++
21 3 files changed, 184 insertions(+)
22
23 diff --git a/sci-biology/bowtie/bowtie-1.2.2_beta20190219.ebuild b/sci-biology/bowtie/bowtie-1.2.2_beta20190219.ebuild
24 new file mode 100644
25 index 000000000..fcf0b4516
26 --- /dev/null
27 +++ b/sci-biology/bowtie/bowtie-1.2.2_beta20190219.ebuild
28 @@ -0,0 +1,81 @@
29 +# Copyright 1999-2019 Gentoo Authors
30 +# Distributed under the terms of the GNU General Public License v2
31 +
32 +EAPI=6
33 +
34 +inherit flag-o-matic toolchain-funcs git-r3
35 +
36 +DESCRIPTION="Popular short read aligner for Next-generation sequencing data"
37 +HOMEPAGE="http://bowtie-bio.sourceforge.net/"
38 +EGIT_REPO_URI="https://github.com/BenLangmead/bowtie.git"
39 +EGIT_BRANCH="bug_fixes"
40 +COMMIT="f253e204f5ba4565d14ae1b300ea6cb10dfe4660"
41 +
42 +LICENSE="Artistic"
43 +SLOT="1"
44 +KEYWORDS="~amd64 ~x86"
45 +
46 +IUSE="examples +tbb"
47 +
48 +RDEPEND="tbb? ( dev-cpp/tbb )"
49 +DEPEND="${RDEPEND}
50 + app-arch/unzip"
51 +# sci-biology/seqan:1.4"
52 +
53 +DOCS=( AUTHORS NEWS TUTORIAL doc/README )
54 +HTML_DOCS=( doc/{manual.html,style.css} )
55 +
56 +PATCHES=( "${FILESDIR}/bowtie-1.2.2-fix-isa-return-type.patch" )
57 +# not needed
58 +# "${FILESDIR}/${P}-fix-Intel-compilation.patch", obsoleted by https://github.com/BenLangmead/bowtie/commit/d8b661fb36c129cb9899fcd3689b3618036f8c7b
59 +#
60 +# still to be considered
61 +#PATCHES=(
62 +# "${FILESDIR}/${P}-_ContextLss-1.1-1.4.patch"
63 +# "${FILESDIR}/${P}-unbundle-seqan.patch"
64 +# "${FILESDIR}/${P}-fix-setBegin-call.patch"
65 +# "${FILESDIR}/${P}-seqan-popcount.patch"
66 +# "${FILESDIR}/${P}-seqan-rename-ChunkPool.patch"
67 +# "${FILESDIR}/${P}-seqan-rename-fill-to-resize.patch"
68 +# "${FILESDIR}/${P}-spelling.patch"
69 +# "${FILESDIR}/${P}-tbb-tinythread-missing.patch"
70 +#)
71 +
72 +src_prepare() {
73 + default
74 +
75 + # remove bundled library of headers, use system seqan 1.4
76 + # rm -rf SeqAn-1.1/ third_party/ || die
77 +
78 + # innocuous non-security flags, prevent log pollution
79 + append-cxxflags \
80 + -Wno-unused-local-typedefs \
81 + -Wno-unused-but-set-variable \
82 + -Wno-unused-variable
83 +}
84 +
85 +src_compile() {
86 + emake \
87 + CC="$(tc-getCC)" \
88 + CPP="$(tc-getCXX)" \
89 + CFLAGS="" \
90 + CXXFLAGS="" \
91 + EXTRA_FLAGS="${LDFLAGS}" \
92 + RELEASE_FLAGS="${CXXFLAGS}" \
93 + WITH_TBB="$(usex tbb 1 0)"
94 +}
95 +
96 +src_install() {
97 + dobin ${PN} ${PN}-*
98 +
99 + exeinto /usr/libexec/${PN}
100 + doexe scripts/*
101 +
102 + newman MANUAL ${PN}.1
103 + einstalldocs
104 +
105 + if use examples; then
106 + insinto /usr/share/${PN}
107 + doins -r genomes indexes
108 + fi
109 +}
110
111 diff --git a/sci-biology/bowtie/bowtie-9999.ebuild b/sci-biology/bowtie/bowtie-9999.ebuild
112 new file mode 100644
113 index 000000000..d54d0a544
114 --- /dev/null
115 +++ b/sci-biology/bowtie/bowtie-9999.ebuild
116 @@ -0,0 +1,81 @@
117 +# Copyright 1999-2019 Gentoo Authors
118 +# Distributed under the terms of the GNU General Public License v2
119 +
120 +EAPI=6
121 +
122 +inherit flag-o-matic toolchain-funcs git-r3
123 +
124 +DESCRIPTION="Popular short read aligner for Next-generation sequencing data"
125 +HOMEPAGE="http://bowtie-bio.sourceforge.net/"
126 +EGIT_REPO_URI="https://github.com/BenLangmead/bowtie.git"
127 +EGIT_BRANCH="bug_fixes"
128 +
129 +LICENSE="Artistic"
130 +SLOT="1"
131 +KEYWORDS=""
132 +
133 +IUSE="examples +tbb"
134 +
135 +RDEPEND="tbb? ( dev-cpp/tbb )"
136 +DEPEND="${RDEPEND}
137 + sci-biology/seqan:1.4
138 + app-arch/unzip"
139 +
140 +DOCS=( AUTHORS NEWS TUTORIAL doc/README )
141 +HTML_DOCS=( doc/{manual.html,style.css} )
142 +
143 +PATCHES=( "${FILESDIR}/bowtie-9999-fix-isa-return-type.patch" )
144 +# not needed
145 +# "${FILESDIR}/${P}-fix-Intel-compilation.patch", obsoleted by https://github.com/BenLangmead/bowtie/commit/d8b661fb36c129cb9899fcd3689b3618036f8c7b
146 +#PATCHES=(
147 +# "${FILESDIR}/${P}-_ContextLss-1.1-1.4.patch"
148 +# "${FILESDIR}/${P}-fix-Intel-compilation.patch"
149 +# "${FILESDIR}/${P}-unbundle-seqan.patch"
150 +#)
151 +# other patches to be still considered
152 +# "${FILESDIR}/${P}-fix-setBegin-call.patch"
153 +# "${FILESDIR}/${P}-seqan-popcount.patch"
154 +# "${FILESDIR}/${P}-seqan-rename-ChunkPool.patch"
155 +# "${FILESDIR}/${P}-seqan-rename-fill-to-resize.patch"
156 +# "${FILESDIR}/${P}-spelling.patch"
157 +# "${FILESDIR}/${P}-tbb-tinythread-missing.patch"
158 +#)
159 +
160 +src_prepare() {
161 + default
162 +
163 + # remove bundled libraries, use system seqan 1.4
164 + # rm -rf SeqAn-1.1/ third_party/ || die
165 +
166 + # innocuous non-security flags, prevent log pollution
167 + append-cxxflags \
168 + -Wno-unused-local-typedefs \
169 + -Wno-unused-but-set-variable \
170 + -Wno-unused-variable
171 +}
172 +
173 +src_compile() {
174 + emake \
175 + CC="$(tc-getCC)" \
176 + CPP="$(tc-getCXX)" \
177 + CFLAGS="" \
178 + CXXFLAGS="" \
179 + EXTRA_FLAGS="${LDFLAGS}" \
180 + RELEASE_FLAGS="${CXXFLAGS}" \
181 + WITH_TBB="$(usex tbb 1 0)"
182 +}
183 +
184 +src_install() {
185 + dobin ${PN} ${PN}-*
186 +
187 + exeinto /usr/libexec/${PN}
188 + doexe scripts/*
189 +
190 + newman MANUAL ${PN}.1
191 + einstalldocs
192 +
193 + if use examples; then
194 + insinto /usr/share/${PN}
195 + doins -r genomes indexes
196 + fi
197 +}
198
199 diff --git a/sci-biology/bowtie/files/bowtie-1.2.2-fix-isa-return-type.patch b/sci-biology/bowtie/files/bowtie-1.2.2-fix-isa-return-type.patch
200 new file mode 100644
201 index 000000000..de19e42a8
202 --- /dev/null
203 +++ b/sci-biology/bowtie/files/bowtie-1.2.2-fix-isa-return-type.patch
204 @@ -0,0 +1,22 @@
205 +From 58c6ac97b1938909881877ef83167f5eff0e8ab1 Mon Sep 17 00:00:00 2001
206 +From: Rone Charles <rone_charles@××××××××.com>
207 +Date: Tue, 4 Sep 2018 21:06:39 -0400
208 +Subject: [PATCH] Fix isa return type
209 +
210 +---
211 + ebwt.h | 2 +-
212 + 1 file changed, 1 insertion(+), 1 deletion(-)
213 +
214 +diff --git a/ebwt.h b/ebwt.h
215 +index fe6300cc..8f886b8d 100644
216 +--- a/ebwt.h
217 ++++ b/ebwt.h
218 +@@ -862,7 +862,7 @@ class Ebwt {
219 + TIndexOffU* ftab() const { return _ftab; }
220 + TIndexOffU* eftab() const { return _eftab; }
221 + TIndexOffU* offs() const { return _offs; }
222 +- uint32_t* isa() const { return _isa; } /* check */
223 ++ TIndexOffU* isa() const { return _isa; } /* check */
224 + TIndexOffU* plen() const { return _plen; }
225 + TIndexOffU* rstarts() const { return _rstarts; }
226 + uint8_t* ebwt() const { return _ebwt; }