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/cd-hit/files/, sci-biology/cd-hit/
Date: Sun, 01 Jun 2014 18:20:51
Message-Id: 1401646763.4004d49530eb309e24220d3998ed32edc592f381.mmokrejs@gentoo
1 commit: 4004d49530eb309e24220d3998ed32edc592f381
2 Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
3 AuthorDate: Sun Jun 1 18:19:23 2014 +0000
4 Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
5 CommitDate: Sun Jun 1 18:19:23 2014 +0000
6 URL: http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=4004d495
7
8 sci-biology/cd-hit-4.6.1: version bump
9
10 Package-Manager: portage-2.2.7
11
12 ---
13 sci-biology/cd-hit/ChangeLog | 9 +++
14 sci-biology/cd-hit/cd-hit-4.6.1.ebuild | 44 +++++++++++
15 sci-biology/cd-hit/files/4.6.1-gentoo.patch | 118 ++++++++++++++++++++++++++++
16 sci-biology/cd-hit/metadata.xml | 23 ++++++
17 4 files changed, 194 insertions(+)
18
19 diff --git a/sci-biology/cd-hit/ChangeLog b/sci-biology/cd-hit/ChangeLog
20 new file mode 100644
21 index 0000000..2ef3e8f
22 --- /dev/null
23 +++ b/sci-biology/cd-hit/ChangeLog
24 @@ -0,0 +1,9 @@
25 +# ChangeLog for sci-biology/cd-hit
26 +# Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2
27 +# $Header: $
28 +
29 +*cd-hit-4.6.1 (01 Jun 2014)
30 +
31 + 01 Jun 2014; Martin Mokrejs <mmokrejs@×××××××××××××××.cz>
32 + +cd-hit-4.6.1.ebuild, +files/4.6.1-gentoo.patch, +metadata.xml:
33 + sci-biology/cd-hit-4.6.1: version bump
34
35 diff --git a/sci-biology/cd-hit/cd-hit-4.6.1.ebuild b/sci-biology/cd-hit/cd-hit-4.6.1.ebuild
36 new file mode 100644
37 index 0000000..1c97d86
38 --- /dev/null
39 +++ b/sci-biology/cd-hit/cd-hit-4.6.1.ebuild
40 @@ -0,0 +1,44 @@
41 +# Copyright 1999-2014 Gentoo Foundation
42 +# Distributed under the terms of the GNU General Public License v2
43 +# $Header: /var/cvsroot/gentoo-x86/sci-biology/cd-hit/cd-hit-4.6.ebuild,v 1.1 2012/06/20 18:39:24 jlec Exp $
44 +
45 +EAPI=4
46 +
47 +inherit eutils flag-o-matic toolchain-funcs
48 +
49 +RELDATE="2012-08-27"
50 +RELEASE="${PN}-v${PV}-${RELDATE}"
51 +
52 +DESCRIPTION="Clustering Database at High Identity with Tolerance"
53 +HOMEPAGE="http://weizhong-lab.ucsd.edu/cd-hit/"
54 +SRC_URI="http://cdhit.googlecode.com/files/${RELEASE}.tgz"
55 +
56 +SLOT="0"
57 +KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
58 +LICENSE="GPL-2"
59 +IUSE="doc openmp"
60 +
61 +S="${WORKDIR}"/${RELEASE}
62 +
63 +pkg_setup() {
64 + use openmp && ! tc-has-openmp && die "Please switch to an openmp compatible compiler"
65 +}
66 +
67 +src_prepare() {
68 + tc-export CXX
69 + use openmp || append-flags -DNO_OPENMP
70 + #epatch "${FILESDIR}"/${PV}-gentoo.patch
71 +}
72 +
73 +src_compile() {
74 + local myconf=
75 + use openmp && myconf="openmp=yes"
76 + emake ${myconf}
77 +}
78 +
79 +src_install() {
80 + dodir /usr/bin
81 + emake PREFIX="${ED}/usr/bin" install
82 + dodoc ChangeLog
83 + use doc && dodoc doc/*
84 +}
85
86 diff --git a/sci-biology/cd-hit/files/4.6.1-gentoo.patch b/sci-biology/cd-hit/files/4.6.1-gentoo.patch
87 new file mode 100644
88 index 0000000..d9db28c
89 --- /dev/null
90 +++ b/sci-biology/cd-hit/files/4.6.1-gentoo.patch
91 @@ -0,0 +1,118 @@
92 +--- Makefile.ori 2014-06-01 20:12:44.000000000 +0200
93 ++++ Makefile 2014-06-01 20:16:34.000000000 +0200
94 +@@ -1,16 +1,13 @@
95 +-
96 +-CC = g++ -Wall -ggdb
97 +-CC = g++ -pg
98 +-CC = g++
99 ++CXX ?= g++
100 +
101 + # without OpenMP
102 +-CCFLAGS = -DNO_OPENMP
103 ++#CXXFLAGS = -DNO_OPENMP
104 +
105 + # with OpenMP
106 + # in command line:
107 + # make openmp=yes
108 + ifeq ($(openmp),yes)
109 +-CCFLAGS = -fopenmp
110 ++CXXFLAGS += -fopenmp
111 + endif
112 +
113 + # support debugging
114 +@@ -18,17 +15,17 @@
115 + # make debug=yes
116 + # make openmp=yes debug=yes
117 + ifeq ($(debug),yes)
118 +-CCFLAGS += -ggdb
119 ++CXXFLAGS +=
120 + else
121 +-CCFLAGS += -O2
122 ++CXXFLAGS +=
123 + endif
124 +
125 + ifdef MAX_SEQ
126 +-CCFLAGS += -DMAX_SEQ=$(MAX_SEQ)
127 ++CXXFLAGS += -DMAX_SEQ=$(MAX_SEQ)
128 + endif
129 +
130 + #LDFLAGS = -static -o
131 +-LDFLAGS += -o
132 ++#LDFLAGS += -o
133 +
134 + PROGS = cd-hit cd-hit-est cd-hit-2d cd-hit-est-2d cd-hit-div cd-hit-454
135 +
136 +@@ -36,7 +33,7 @@
137 + CCFLAGS := $(CPPFLAGS) $(CCFLAGS) $(CXXFLAGS)
138 +
139 + .c++.o:
140 +- $(CC) $(CCFLAGS) -c $<
141 ++ $(CXX) $(CXXFLAGS) -c $<
142 +
143 + all: $(PROGS)
144 +
145 +@@ -46,49 +43,49 @@
146 + # programs
147 +
148 + cd-hit: cdhit-common.o cdhit-utility.o cdhit.o
149 +- $(CC) $(CCFLAGS) cdhit.o cdhit-common.o cdhit-utility.o $(LDFLAGS) cd-hit
150 ++ $(CXX) $(CXXFLAGS) $(LDFLAGS) cdhit.o cdhit-common.o cdhit-utility.o -o cd-hit
151 +
152 + cd-hit-2d: cdhit-common.o cdhit-utility.o cdhit-2d.o
153 +- $(CC) $(CCFLAGS) cdhit-2d.o cdhit-common.o cdhit-utility.o $(LDFLAGS) cd-hit-2d
154 ++ $(CXX) $(CXXFLAGS) $(LDFLAGS) cdhit-2d.o cdhit-common.o cdhit-utility.o -o cd-hit-2d
155 +
156 + cd-hit-est: cdhit-common.o cdhit-utility.o cdhit-est.o
157 +- $(CC) $(CCFLAGS) cdhit-est.o cdhit-common.o cdhit-utility.o $(LDFLAGS) cd-hit-est
158 ++ $(CXX) $(CXXFLAGS) $(LDFLAGS) cdhit-est.o cdhit-common.o cdhit-utility.o -o cd-hit-est
159 +
160 + cd-hit-est-2d: cdhit-common.o cdhit-utility.o cdhit-est-2d.o
161 +- $(CC) $(CCFLAGS) cdhit-est-2d.o cdhit-common.o cdhit-utility.o $(LDFLAGS) cd-hit-est-2d
162 ++ $(CXX) $(CXXFLAGS) $(LDFLAGS) cdhit-est-2d.o cdhit-common.o cdhit-utility.o -o cd-hit-est-2d
163 +
164 + cd-hit-div: cdhit-common.o cdhit-utility.o cdhit-div.o
165 +- $(CC) $(CCFLAGS) cdhit-div.o cdhit-common.o cdhit-utility.o $(LDFLAGS) cd-hit-div
166 ++ $(CXX) $(CXXFLAGS) $(LDFLAGS) cdhit-div.o cdhit-common.o cdhit-utility.o -o cd-hit-div
167 +
168 + cd-hit-454: cdhit-common.o cdhit-utility.o cdhit-454.o
169 +- $(CC) $(CCFLAGS) cdhit-454.o cdhit-common.o cdhit-utility.o $(LDFLAGS) cd-hit-454
170 ++ $(CXX) $(CXXFLAGS) $(LDFLAGS) cdhit-454.o cdhit-common.o cdhit-utility.o -o cd-hit-454
171 +
172 + # objects
173 + cdhit-common.o: cdhit-common.c++ cdhit-common.h
174 +- $(CC) $(CCFLAGS) cdhit-common.c++ -c
175 ++ $(CXX) $(CXXFLAGS) cdhit-common.c++ -c
176 +
177 + cdhit-utility.o: cdhit-utility.c++ cdhit-utility.h
178 +- $(CC) $(CCFLAGS) cdhit-utility.c++ -c
179 ++ $(CXX) $(CXXFLAGS) cdhit-utility.c++ -c
180 +
181 + cdhit.o: cdhit.c++ cdhit-utility.h
182 +- $(CC) $(CCFLAGS) cdhit.c++ -c
183 ++ $(CXX) $(CXXFLAGS) cdhit.c++ -c
184 +
185 + cdhit-2d.o: cdhit-2d.c++ cdhit-utility.h
186 +- $(CC) $(CCFLAGS) cdhit-2d.c++ -c
187 ++ $(CXX) $(CXXFLAGS) cdhit-2d.c++ -c
188 +
189 + cdhit-est.o: cdhit-est.c++ cdhit-utility.h
190 +- $(CC) $(CCFLAGS) cdhit-est.c++ -c
191 ++ $(CXX) $(CXXFLAGS) cdhit-est.c++ -c
192 +
193 + cdhit-est-2d.o: cdhit-est-2d.c++ cdhit-utility.h
194 +- $(CC) $(CCFLAGS) cdhit-est-2d.c++ -c
195 ++ $(CXX) $(CXXFLAGS) cdhit-est-2d.c++ -c
196 +
197 + cdhit-div.o: cdhit-div.c++ cdhit-common.h
198 +- $(CC) $(CCFLAGS) cdhit-div.c++ -c
199 ++ $(CXX) $(CXXFLAGS) cdhit-div.c++ -c
200 +
201 + cdhit-454.o: cdhit-454.c++ cdhit-common.h
202 +- $(CC) $(CCFLAGS) cdhit-454.c++ -c
203 ++ $(CXX) $(CXXFLAGS) cdhit-454.c++ -c
204 +
205 +-PREFIX ?= /usr/local/bin
206 ++PREFIX ?= $(DESTDIR)/usr/bin
207 +
208 + install:
209 + for prog in $(PROGS); do \
210
211 diff --git a/sci-biology/cd-hit/metadata.xml b/sci-biology/cd-hit/metadata.xml
212 new file mode 100644
213 index 0000000..bd5607a
214 --- /dev/null
215 +++ b/sci-biology/cd-hit/metadata.xml
216 @@ -0,0 +1,23 @@
217 +<?xml version="1.0" encoding="UTF-8"?>
218 +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
219 +<pkgmetadata>
220 + <herd>sci-biology</herd>
221 + <longdescription>
222 +CD-HIT is a very widely used program for clustering and comparing large sets
223 +of protein or nucleotide sequences. CD-HIT is very fast and can handle
224 +extremely large databases. CD-HIT helps to significantly reduce the
225 +computational and manual efforts in many sequence analysis tasks and aids in
226 +understanding the data structure and correct the bias within a dataset.
227 +The CD-HIT package has CD-HIT, CD-HIT-2D, CD-HIT-EST, CD-HIT-EST-2D,
228 +CD-HIT-454, CD-HIT-PARA, PSI-CD-HIT and over a dozen scripts. CD-HIT
229 +(CD-HIT-EST) clusters similar proteins (DNAs) into clusters that meet a
230 +user-defined similarity threshold. CD-HIT-2D (CD-HIT-EST-2D) compares 2
231 +datasets and identifies the sequences in db2 that are similar to db1 above
232 +a threshold. CD-HIT-454 is a program to identify natural and artificial
233 +duplicates from pyrosequencing reads. The usage of other programs and
234 +scripts can be found in CD-HIT user's guide.
235 +</longdescription>
236 + <upstream>
237 + <remote-id type="google-code">cdhit</remote-id>
238 + </upstream>
239 +</pkgmetadata>