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/deeptools/, dev-python/pyBigWig/, sci-biology/plinkseq/, ...
Date: Fri, 31 Mar 2017 21:05:33
Message-Id: 1490994005.4647f40e12c546cd0b18b1966acd944fc8a21641.mmokrejs@gentoo
1 commit: 4647f40e12c546cd0b18b1966acd944fc8a21641
2 Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
3 AuthorDate: Fri Mar 31 21:00:05 2017 +0000
4 Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
5 CommitDate: Fri Mar 31 21:00:05 2017 +0000
6 URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=4647f40e
7
8 Revert "sci-biology/deeptools: add a new package"
9
10 This reverts commit 81a1355ea065924e0c6426772af7c16d90432ccd.
11
12 dev-python/pyBigWig/metadata.xml | 12 ----
13 dev-python/pyBigWig/pyBigWig-0.3.4.ebuild | 16 -----
14 dev-python/pyBigWig/pyBigWig-9999.ebuild | 18 ------
15 sci-biology/deeptools/deeptools-2.5.0.ebuild | 33 ----------
16 sci-biology/deeptools/deeptools-9999.ebuild | 34 ----------
17 sci-biology/deeptools/metadata.xml | 12 ----
18 sci-biology/mira/mira-4.9.6.ebuild | 93 ----------------------------
19 sci-biology/plinkseq/plinkseq-9999.ebuild | 13 ++--
20 8 files changed, 5 insertions(+), 226 deletions(-)
21
22 diff --git a/dev-python/pyBigWig/metadata.xml b/dev-python/pyBigWig/metadata.xml
23 deleted file mode 100644
24 index f68a1b6fa..000000000
25 --- a/dev-python/pyBigWig/metadata.xml
26 +++ /dev/null
27 @@ -1,12 +0,0 @@
28 -<?xml version="1.0" encoding="UTF-8"?>
29 -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
30 -<pkgmetadata>
31 - <maintainer type="person">
32 - <email>mmokrejs@×××××××××××××××.cz</email>
33 - <name>Martin Mokrejs</name>
34 - </maintainer>
35 - <maintainer type="project">
36 - <email>sci-biology@g.o</email>
37 - <name>Gentoo Biology Project</name>
38 - </maintainer>
39 -</pkgmetadata>
40
41 diff --git a/dev-python/pyBigWig/pyBigWig-0.3.4.ebuild b/dev-python/pyBigWig/pyBigWig-0.3.4.ebuild
42 deleted file mode 100644
43 index 33664c388..000000000
44 --- a/dev-python/pyBigWig/pyBigWig-0.3.4.ebuild
45 +++ /dev/null
46 @@ -1,16 +0,0 @@
47 -# Copyright 1999-2017 Gentoo Foundation
48 -# Distributed under the terms of the GNU General Public License v2
49 -
50 -EAPI=5
51 -
52 -DESCRIPTION="Python extension written in C for quick access to and creation of bigWig files"
53 -HOMEPAGE="https://github.com/dpryan79/pyBigWig"
54 -SRC_URI="https://github.com/dpryan79/pyBigWig/archive/0.3.4.tar.gz -> ${P}.tar.gz"
55 -
56 -LICENSE="MIT"
57 -SLOT="0"
58 -KEYWORDS="~amd64 ~x86"
59 -IUSE=""
60 -
61 -DEPEND="sci-biology/libBigWig"
62 -RDEPEND="${DEPEND}"
63
64 diff --git a/dev-python/pyBigWig/pyBigWig-9999.ebuild b/dev-python/pyBigWig/pyBigWig-9999.ebuild
65 deleted file mode 100644
66 index 0e2cd40c8..000000000
67 --- a/dev-python/pyBigWig/pyBigWig-9999.ebuild
68 +++ /dev/null
69 @@ -1,18 +0,0 @@
70 -# Copyright 1999-2017 Gentoo Foundation
71 -# Distributed under the terms of the GNU General Public License v2
72 -
73 -EAPI=5
74 -
75 -inherit git-r3
76 -
77 -DESCRIPTION="Python extension written in C for quick access to and creation of bigWig files"
78 -HOMEPAGE="https://github.com/dpryan79/pyBigWig"
79 -EGIT_REPO_URI="https://github.com/dpryan79/pyBigWig.git"
80 -
81 -LICENSE="MIT"
82 -SLOT="0"
83 -KEYWORDS=""
84 -IUSE=""
85 -
86 -DEPEND="sci-biology/libBigWig"
87 -RDEPEND="${DEPEND}"
88
89 diff --git a/sci-biology/deeptools/deeptools-2.5.0.ebuild b/sci-biology/deeptools/deeptools-2.5.0.ebuild
90 deleted file mode 100644
91 index 6f9a41d54..000000000
92 --- a/sci-biology/deeptools/deeptools-2.5.0.ebuild
93 +++ /dev/null
94 @@ -1,33 +0,0 @@
95 -# Copyright 1999-2017 Gentoo Foundation
96 -# Distributed under the terms of the GNU General Public License v2
97 -
98 -EAPI=5
99 -
100 -PYTHON_COMPAT=( python2_7 python3_5 )
101 -
102 -inherit distutils-r1
103 -
104 -[ "$PV" == "9999" ] && inherit git-2
105 -
106 -DESCRIPTION="Extract reads from BAM files, normalize, draw figures, convert BAM to bigWig"
107 -HOMEPAGE="https://github.com/fidelram/deepTools"
108 -if [ "$PV" == "9999" ]; then
109 - EGIT_REPO_URI="https://github.com/fidelram/deepTools"
110 - KEYWORDS=""
111 -else
112 - SRC_URI="https://github.com/fidelram/deepTools/archive/2.5.0.tar.gz -> ${P}.tar.gz"
113 - KEYWORDS="~amd64"
114 -fi
115 -
116 -LICENSE="GPL-3"
117 -SLOT="0"
118 -IUSE=""
119 -
120 -DEPEND=">=dev-python/numpy-1.8.0
121 - >=sci-libs/scipy-0.17.0
122 - >=dev-python/py2bit-0.1.0
123 - >=dev-python/pyBigWig-0.2.1
124 - >=sci-biology/pysam-0.8
125 - >=dev-python/matplotlib-1.4.0"
126 -RDEPEND="${DEPEND}"
127 -
128
129 diff --git a/sci-biology/deeptools/deeptools-9999.ebuild b/sci-biology/deeptools/deeptools-9999.ebuild
130 deleted file mode 100644
131 index 4d6d2fa77..000000000
132 --- a/sci-biology/deeptools/deeptools-9999.ebuild
133 +++ /dev/null
134 @@ -1,34 +0,0 @@
135 -# Copyright 1999-2017 Gentoo Foundation
136 -# Distributed under the terms of the GNU General Public License v2
137 -# $Id$
138 -
139 -EAPI=5
140 -
141 -PYTHON_COMPAT=( python2_7 python3_5 )
142 -
143 -inherit distutils-r1
144 -
145 -[ "$PV" == "9999" ] && inherit git-2
146 -
147 -DESCRIPTION="Extract reads from BAM files, normalize, draw figures, convert BAM to bigWig"
148 -HOMEPAGE="https://github.com/fidelram/deepTools"
149 -if [ "$PV" == "9999" ]; then
150 - EGIT_REPO_URI="https://github.com/fidelram/deepTools"
151 - KEYWORDS=""
152 -else
153 - SRC_URI="https://github.com/fidelram/deepTools/archive/2.5.0.tar.gz -> ${P}.tar.gz"
154 - KEYWORDS="~amd64"
155 -fi
156 -
157 -LICENSE="GPL-3"
158 -SLOT="0"
159 -IUSE=""
160 -
161 -DEPEND=">=dev-python/numpy-1.8.0
162 - >=sci-libs/scipy-0.17.0
163 - >=dev-python/py2bit-0.1.0
164 - >=dev-python/pyBigWig-0.2.1
165 - >=sci-biology/pysam-0.8
166 - >=dev-python/matplotlib-1.4.0"
167 -RDEPEND="${DEPEND}"
168 -
169
170 diff --git a/sci-biology/deeptools/metadata.xml b/sci-biology/deeptools/metadata.xml
171 deleted file mode 100644
172 index f68a1b6fa..000000000
173 --- a/sci-biology/deeptools/metadata.xml
174 +++ /dev/null
175 @@ -1,12 +0,0 @@
176 -<?xml version="1.0" encoding="UTF-8"?>
177 -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
178 -<pkgmetadata>
179 - <maintainer type="person">
180 - <email>mmokrejs@×××××××××××××××.cz</email>
181 - <name>Martin Mokrejs</name>
182 - </maintainer>
183 - <maintainer type="project">
184 - <email>sci-biology@g.o</email>
185 - <name>Gentoo Biology Project</name>
186 - </maintainer>
187 -</pkgmetadata>
188
189 diff --git a/sci-biology/mira/mira-4.9.6.ebuild b/sci-biology/mira/mira-4.9.6.ebuild
190 deleted file mode 100644
191 index 22ddea015..000000000
192 --- a/sci-biology/mira/mira-4.9.6.ebuild
193 +++ /dev/null
194 @@ -1,93 +0,0 @@
195 -# Copyright 1999-2015 Gentoo Foundation
196 -# Distributed under the terms of the GNU General Public License v2
197 -# $Id$
198 -
199 -EAPI=5
200 -
201 -MIRA_3RDPARTY_PV="06-07-2012"
202 -MY_PV="${PV/_}" # convert from mira-4.0_rc2 (Gentoo ebuild filename derived) to mira-4.0rc2 (upstream fromat)
203 -
204 -inherit autotools eutils multilib
205 -
206 -DESCRIPTION="Whole Genome Shotgun and EST Sequence Assembler for Sanger, 454 and Solexa / Illumina"
207 -HOMEPAGE="http://www.chevreux.org/projects_mira.html"
208 -SRC_URI="
209 - http://sourceforge.net/projects/mira-assembler/files/MIRA/development/"${PN}"-"${MY_PV}".tar.bz2
210 - mirror://sourceforge/mira-assembler/mira_3rdparty_${MIRA_3RDPARTY_PV}.tar.bz2"
211 -# http://sourceforge.net/projects/mira-assembler/files/MIRA/stable/"${PN}"-"${MY_PV}".tar.bz2
212 -# http://sourceforge.net/projects/mira-assembler/files/MIRA/development/${P}.tar.bz2
213 -# mirror://sourceforge/mira-assembler/mira_3rdparty_${MIRA_3RDPARTY_PV}.tar.bz2"
214 -
215 -S="${WORKDIR}"/"${PN}"-"${MY_PV}"
216 -
217 -SLOT="0"
218 -LICENSE="GPL-2"
219 -KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux ~x86-macos"
220 -IUSE="doc"
221 -
222 -CDEPEND="
223 - dev-libs/boost
224 - dev-util/google-perftools"
225 -DEPEND="${CDEPEND}
226 - app-editors/vim-core
227 - dev-libs/expat"
228 -RDEPEND="${CDEPEND}"
229 -
230 -#DOCS=( AUTHORS GETTING_STARTED NEWS README HELP_WANTED
231 -# THANKS doc/3rdparty/scaffolding_MIRA_BAMBUS.pdf )
232 -DOCS=( AUTHORS GETTING_STARTED NEWS README HELP_WANTED THANKS )
233 -
234 -# mira 4.9.x requires C++14 standard compliant compiler, so >=gcc-4.9.1
235 -src_prepare() {
236 - find -name 'configure*' -or -name 'Makefile*' | xargs sed -i 's/flex++/flex -+/' || die
237 - epatch \
238 - "${FILESDIR}"/${PN}-3.4.0.2-boost-1.50.patch \
239 - "${FILESDIR}"/${P}-cout.patch \
240 - "${FILESDIR}"/${P}-DESTDIR.patch
241 -
242 - sed \
243 - -e "s:-O[23]::g" \
244 - -e "s:-funroll-loops::g" \
245 - -i configure.ac || die
246 -
247 - eautoreconf
248 -}
249 -
250 -src_configure() {
251 - econf \
252 - --with-boost="${EPREFIX}/usr/$(get_libdir)" \
253 - --with-boost-libdir="${EPREFIX}/usr/$(get_libdir)" \
254 - --with-boost-thread=boost_thread-mt
255 -}
256 -
257 -#src_compile() {
258 -# base_src_compile
259 -# # TODO: resolve docbook incompatibility for building docs
260 -# if use doc; then emake -C doc clean docs || die; fi
261 -#}
262 -
263 -src_install() {
264 - default
265 - dodoc ${DOCS[@]}
266 -
267 - dobin "${WORKDIR}"/3rdparty/{sff_extract,qual2ball,*.pl}
268 - dodoc "${WORKDIR}"/3rdparty/{README.txt,midi_screen.fasta}
269 -
270 - # if sci-biology/staden is installed, ideally use configprotect?
271 - if [ -e "${ED}"/usr/share/staden/etc/GTAGDB ]; then
272 - if [ `grep -c HAF "${ED}"/usr/share/staden/etc/GTAGDB` -eq 0 ]; then
273 - cat "${ED}"/usr/share/staden/etc/GTAGDB "${S}"/src/support/GTAGDB > "${WORKDIR}"/GTAGDB || die
274 - insinto /usr/share/staden/etc/
275 - doins "${WORKDIR}"/GTAGDB
276 - fi
277 - fi
278 - if [ -e "/etc/consedrc/" ]; then
279 - insinto /etc/consedrc
280 - doins "${S}"/src/support/consedtaglib.txt
281 - fi
282 -}
283 -
284 -pkg_postinst() {
285 - einfo "Documentation is no longer built, you can find it at:"
286 - einfo "http://mira-assembler.sourceforge.net/docs/DefinitiveGuideToMIRA.html"
287 -}
288
289 diff --git a/sci-biology/plinkseq/plinkseq-9999.ebuild b/sci-biology/plinkseq/plinkseq-9999.ebuild
290 index cffdaff97..461e62f84 100644
291 --- a/sci-biology/plinkseq/plinkseq-9999.ebuild
292 +++ b/sci-biology/plinkseq/plinkseq-9999.ebuild
293 @@ -20,6 +20,7 @@ IUSE=""
294
295 DEPEND="sys-libs/zlib
296 dev-libs/protobuf
297 + www-servers/mongoose
298 !sci-biology/fsl" # file collision on /usr/bin/mm
299 RDEPEND="${DEPEND}"
300
301 @@ -28,9 +29,7 @@ src_prepare(){
302 sed -e "s/= -static/=/g" -i config_defs.Makefile || die
303 rm -rf sources/ext/protobuf-* || die
304 rm sources/ext/protobuf sources/ext/sources/include/google || die
305 - # we cannot zap calls to bundled mongoose because www-servers/mongoose does not build a library at all
306 - # rm -rf sources/mongoose || die
307 - # sed -e "s@$(MONGOOSE_LIB_DIR) @@;s@$(MONGOOSE_INC) @@;s@$(MONGOOSE_LIB_BASE_DIR) @@" - Makefile || die
308 + rm -rf sources/mongoose || die
309 sed -e 's@^all:.*@all: # skipping compilation of bundled dev-libs/protobuf@' -i sources/ext/Makefile || die
310 find . -name \*.proto | while read f; do \
311 d=`dirname $f`; \
312 @@ -45,13 +44,11 @@ src_prepare(){
313 sed -e 's/google::protobuf::internal::kEmptyString/google::protobuf::internal::GetEmptyStringAlreadyInited()/g' -i sources/plinkseq/sources/lib/matrix.pb.cpp || die
314 sed -e 's/google::protobuf::internal::kEmptyString/google::protobuf::internal::GetEmptyStringAlreadyInited()/g' -i sources/plinkseq/sources/lib/variant.pb.cpp || die
315 local myinc=`pkg-config protobuf --variable=includedir`
316 - sed -e 's@$(PROTOBUF_LIB_BASE_DIR)/$(INC_DIR)/@'"${myinc}@" -i Makefile || die
317 + sed -e "s@\$(PROTOBUF_LIB_BASE_DIR)/\$(INC_DIR)/@$myinc@" -i Makefile || die
318 local mylib=`pkg-config protobuf --variable=libdir`
319 - sed -e 's@$(PROTOBUF_LIB_BASE_DIR)/$(BLD_LIB_DIR)/@'"-L${mylib} @" -i Makefile || die # note the trailing space as it get prepended to PROTOBUF_LIBS
320 - # anyway $(PROTOBUF_LIB_FULL_PATH) is a necessary build target, just drop it
321 - sed -e 's@^PROTOBUF_LIB_FULL_PATH =.*/@PROTOBUF_LIB_FULL_PATH =@' -i Makefile || die
322 + sed -e "s@$(PROTOBUF_LIB_BASE_DIR)/$(BLD_LIB_DIR)/@$mylib@" -i Makefile || die
323 local mylibs=`pkg-config protobuf --libs`
324 - sed -e "s@libprotobuf.a@ ${mylibs}@ " -i Makefile || die
325 + sed -e "s@libprotobuf.a@$mylibs@" -i Makefile || die
326 }
327
328 src_install(){