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commit: 4004d49530eb309e24220d3998ed32edc592f381 |
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Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz> |
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AuthorDate: Sun Jun 1 18:19:23 2014 +0000 |
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Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz> |
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CommitDate: Sun Jun 1 18:19:23 2014 +0000 |
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URL: http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=4004d495 |
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|
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sci-biology/cd-hit-4.6.1: version bump |
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|
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Package-Manager: portage-2.2.7 |
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|
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--- |
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sci-biology/cd-hit/ChangeLog | 9 +++ |
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sci-biology/cd-hit/cd-hit-4.6.1.ebuild | 44 +++++++++++ |
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sci-biology/cd-hit/files/4.6.1-gentoo.patch | 118 ++++++++++++++++++++++++++++ |
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sci-biology/cd-hit/metadata.xml | 23 ++++++ |
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4 files changed, 194 insertions(+) |
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|
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diff --git a/sci-biology/cd-hit/ChangeLog b/sci-biology/cd-hit/ChangeLog |
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new file mode 100644 |
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index 0000000..2ef3e8f |
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--- /dev/null |
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+++ b/sci-biology/cd-hit/ChangeLog |
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@@ -0,0 +1,9 @@ |
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+# ChangeLog for sci-biology/cd-hit |
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+# Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2 |
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+# $Header: $ |
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+ |
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+*cd-hit-4.6.1 (01 Jun 2014) |
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+ |
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+ 01 Jun 2014; Martin Mokrejs <mmokrejs@×××××××××××××××.cz> |
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+ +cd-hit-4.6.1.ebuild, +files/4.6.1-gentoo.patch, +metadata.xml: |
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+ sci-biology/cd-hit-4.6.1: version bump |
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|
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diff --git a/sci-biology/cd-hit/cd-hit-4.6.1.ebuild b/sci-biology/cd-hit/cd-hit-4.6.1.ebuild |
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new file mode 100644 |
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index 0000000..1c97d86 |
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--- /dev/null |
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+++ b/sci-biology/cd-hit/cd-hit-4.6.1.ebuild |
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@@ -0,0 +1,44 @@ |
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+# Copyright 1999-2014 Gentoo Foundation |
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+# Distributed under the terms of the GNU General Public License v2 |
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+# $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 $ |
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+ |
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+EAPI=4 |
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+ |
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+inherit eutils flag-o-matic toolchain-funcs |
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+ |
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+RELDATE="2012-08-27" |
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+RELEASE="${PN}-v${PV}-${RELDATE}" |
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+ |
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+DESCRIPTION="Clustering Database at High Identity with Tolerance" |
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+HOMEPAGE="http://weizhong-lab.ucsd.edu/cd-hit/" |
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+SRC_URI="http://cdhit.googlecode.com/files/${RELEASE}.tgz" |
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+ |
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+SLOT="0" |
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+KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" |
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+LICENSE="GPL-2" |
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+IUSE="doc openmp" |
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+ |
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+S="${WORKDIR}"/${RELEASE} |
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+ |
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+pkg_setup() { |
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+ use openmp && ! tc-has-openmp && die "Please switch to an openmp compatible compiler" |
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+} |
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+ |
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+src_prepare() { |
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+ tc-export CXX |
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+ use openmp || append-flags -DNO_OPENMP |
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+ #epatch "${FILESDIR}"/${PV}-gentoo.patch |
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+} |
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+ |
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+src_compile() { |
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+ local myconf= |
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+ use openmp && myconf="openmp=yes" |
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+ emake ${myconf} |
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+} |
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+ |
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+src_install() { |
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+ dodir /usr/bin |
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+ emake PREFIX="${ED}/usr/bin" install |
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+ dodoc ChangeLog |
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+ use doc && dodoc doc/* |
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+} |
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|
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diff --git a/sci-biology/cd-hit/files/4.6.1-gentoo.patch b/sci-biology/cd-hit/files/4.6.1-gentoo.patch |
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new file mode 100644 |
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index 0000000..d9db28c |
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--- /dev/null |
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+++ b/sci-biology/cd-hit/files/4.6.1-gentoo.patch |
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@@ -0,0 +1,118 @@ |
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+--- Makefile.ori 2014-06-01 20:12:44.000000000 +0200 |
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++++ Makefile 2014-06-01 20:16:34.000000000 +0200 |
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+@@ -1,16 +1,13 @@ |
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+- |
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+-CC = g++ -Wall -ggdb |
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+-CC = g++ -pg |
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+-CC = g++ |
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++CXX ?= g++ |
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+ |
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+ # without OpenMP |
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+-CCFLAGS = -DNO_OPENMP |
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++#CXXFLAGS = -DNO_OPENMP |
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+ |
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+ # with OpenMP |
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+ # in command line: |
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+ # make openmp=yes |
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+ ifeq ($(openmp),yes) |
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+-CCFLAGS = -fopenmp |
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++CXXFLAGS += -fopenmp |
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+ endif |
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+ |
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+ # support debugging |
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+@@ -18,17 +15,17 @@ |
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+ # make debug=yes |
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+ # make openmp=yes debug=yes |
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+ ifeq ($(debug),yes) |
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+-CCFLAGS += -ggdb |
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++CXXFLAGS += |
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+ else |
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+-CCFLAGS += -O2 |
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++CXXFLAGS += |
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+ endif |
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+ |
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+ ifdef MAX_SEQ |
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+-CCFLAGS += -DMAX_SEQ=$(MAX_SEQ) |
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++CXXFLAGS += -DMAX_SEQ=$(MAX_SEQ) |
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+ endif |
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+ |
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+ #LDFLAGS = -static -o |
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+-LDFLAGS += -o |
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++#LDFLAGS += -o |
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+ |
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+ PROGS = cd-hit cd-hit-est cd-hit-2d cd-hit-est-2d cd-hit-div cd-hit-454 |
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+ |
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+@@ -36,7 +33,7 @@ |
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+ CCFLAGS := $(CPPFLAGS) $(CCFLAGS) $(CXXFLAGS) |
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+ |
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+ .c++.o: |
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+- $(CC) $(CCFLAGS) -c $< |
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++ $(CXX) $(CXXFLAGS) -c $< |
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+ |
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+ all: $(PROGS) |
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+ |
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+@@ -46,49 +43,49 @@ |
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+ # programs |
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+ |
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+ cd-hit: cdhit-common.o cdhit-utility.o cdhit.o |
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+- $(CC) $(CCFLAGS) cdhit.o cdhit-common.o cdhit-utility.o $(LDFLAGS) cd-hit |
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++ $(CXX) $(CXXFLAGS) $(LDFLAGS) cdhit.o cdhit-common.o cdhit-utility.o -o cd-hit |
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+ |
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+ cd-hit-2d: cdhit-common.o cdhit-utility.o cdhit-2d.o |
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+- $(CC) $(CCFLAGS) cdhit-2d.o cdhit-common.o cdhit-utility.o $(LDFLAGS) cd-hit-2d |
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++ $(CXX) $(CXXFLAGS) $(LDFLAGS) cdhit-2d.o cdhit-common.o cdhit-utility.o -o cd-hit-2d |
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+ |
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+ cd-hit-est: cdhit-common.o cdhit-utility.o cdhit-est.o |
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+- $(CC) $(CCFLAGS) cdhit-est.o cdhit-common.o cdhit-utility.o $(LDFLAGS) cd-hit-est |
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++ $(CXX) $(CXXFLAGS) $(LDFLAGS) cdhit-est.o cdhit-common.o cdhit-utility.o -o cd-hit-est |
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+ |
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+ cd-hit-est-2d: cdhit-common.o cdhit-utility.o cdhit-est-2d.o |
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+- $(CC) $(CCFLAGS) cdhit-est-2d.o cdhit-common.o cdhit-utility.o $(LDFLAGS) cd-hit-est-2d |
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++ $(CXX) $(CXXFLAGS) $(LDFLAGS) cdhit-est-2d.o cdhit-common.o cdhit-utility.o -o cd-hit-est-2d |
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+ |
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+ cd-hit-div: cdhit-common.o cdhit-utility.o cdhit-div.o |
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+- $(CC) $(CCFLAGS) cdhit-div.o cdhit-common.o cdhit-utility.o $(LDFLAGS) cd-hit-div |
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++ $(CXX) $(CXXFLAGS) $(LDFLAGS) cdhit-div.o cdhit-common.o cdhit-utility.o -o cd-hit-div |
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+ |
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+ cd-hit-454: cdhit-common.o cdhit-utility.o cdhit-454.o |
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+- $(CC) $(CCFLAGS) cdhit-454.o cdhit-common.o cdhit-utility.o $(LDFLAGS) cd-hit-454 |
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++ $(CXX) $(CXXFLAGS) $(LDFLAGS) cdhit-454.o cdhit-common.o cdhit-utility.o -o cd-hit-454 |
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+ |
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+ # objects |
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+ cdhit-common.o: cdhit-common.c++ cdhit-common.h |
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+- $(CC) $(CCFLAGS) cdhit-common.c++ -c |
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++ $(CXX) $(CXXFLAGS) cdhit-common.c++ -c |
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+ |
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+ cdhit-utility.o: cdhit-utility.c++ cdhit-utility.h |
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+- $(CC) $(CCFLAGS) cdhit-utility.c++ -c |
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++ $(CXX) $(CXXFLAGS) cdhit-utility.c++ -c |
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+ |
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+ cdhit.o: cdhit.c++ cdhit-utility.h |
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+- $(CC) $(CCFLAGS) cdhit.c++ -c |
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++ $(CXX) $(CXXFLAGS) cdhit.c++ -c |
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+ |
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+ cdhit-2d.o: cdhit-2d.c++ cdhit-utility.h |
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+- $(CC) $(CCFLAGS) cdhit-2d.c++ -c |
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++ $(CXX) $(CXXFLAGS) cdhit-2d.c++ -c |
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+ |
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+ cdhit-est.o: cdhit-est.c++ cdhit-utility.h |
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+- $(CC) $(CCFLAGS) cdhit-est.c++ -c |
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++ $(CXX) $(CXXFLAGS) cdhit-est.c++ -c |
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+ |
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+ cdhit-est-2d.o: cdhit-est-2d.c++ cdhit-utility.h |
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+- $(CC) $(CCFLAGS) cdhit-est-2d.c++ -c |
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++ $(CXX) $(CXXFLAGS) cdhit-est-2d.c++ -c |
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+ |
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+ cdhit-div.o: cdhit-div.c++ cdhit-common.h |
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+- $(CC) $(CCFLAGS) cdhit-div.c++ -c |
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++ $(CXX) $(CXXFLAGS) cdhit-div.c++ -c |
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+ |
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+ cdhit-454.o: cdhit-454.c++ cdhit-common.h |
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+- $(CC) $(CCFLAGS) cdhit-454.c++ -c |
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++ $(CXX) $(CXXFLAGS) cdhit-454.c++ -c |
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+ |
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+-PREFIX ?= /usr/local/bin |
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++PREFIX ?= $(DESTDIR)/usr/bin |
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+ |
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+ install: |
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+ for prog in $(PROGS); do \ |
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|
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diff --git a/sci-biology/cd-hit/metadata.xml b/sci-biology/cd-hit/metadata.xml |
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new file mode 100644 |
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index 0000000..bd5607a |
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--- /dev/null |
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+++ b/sci-biology/cd-hit/metadata.xml |
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@@ -0,0 +1,23 @@ |
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+<?xml version="1.0" encoding="UTF-8"?> |
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+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> |
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+<pkgmetadata> |
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+ <herd>sci-biology</herd> |
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+ <longdescription> |
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+CD-HIT is a very widely used program for clustering and comparing large sets |
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+of protein or nucleotide sequences. CD-HIT is very fast and can handle |
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+extremely large databases. CD-HIT helps to significantly reduce the |
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+computational and manual efforts in many sequence analysis tasks and aids in |
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+understanding the data structure and correct the bias within a dataset. |
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+The CD-HIT package has CD-HIT, CD-HIT-2D, CD-HIT-EST, CD-HIT-EST-2D, |
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+CD-HIT-454, CD-HIT-PARA, PSI-CD-HIT and over a dozen scripts. CD-HIT |
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+(CD-HIT-EST) clusters similar proteins (DNAs) into clusters that meet a |
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+user-defined similarity threshold. CD-HIT-2D (CD-HIT-EST-2D) compares 2 |
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+datasets and identifies the sequences in db2 that are similar to db1 above |
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+a threshold. CD-HIT-454 is a program to identify natural and artificial |
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+duplicates from pyrosequencing reads. The usage of other programs and |
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+scripts can be found in CD-HIT user's guide. |
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+</longdescription> |
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+ <upstream> |
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+ <remote-id type="google-code">cdhit</remote-id> |
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+ </upstream> |
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+</pkgmetadata> |