commit: 4301eeb9419fd475d20e7c46d5fe4ea0bcbda847 Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz> AuthorDate: Mon Nov 30 23:50:30 2015 +0000 Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz> CommitDate: Mon Nov 30 23:50:30 2015 +0000 URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=4301eeb9
sci-biology/mothur: version bump; update makefile patch, the other patch from 1.27 series seems not necessary anymore; added few more IUSE values but the makefile could ideally respect them before forcing boost and zlib libraries into LIBS Package-Manager: portage-2.2.18 sci-biology/mothur/ChangeLog | 12 +++++ .../mothur/files/mothur-1.36.1-makefile.patch | 61 ++++++++++++++++++++++ sci-biology/mothur/metadata.xml | 5 ++ sci-biology/mothur/mothur-1.36.1.ebuild | 46 ++++++++++++++++ 4 files changed, 124 insertions(+) diff --git a/sci-biology/mothur/ChangeLog b/sci-biology/mothur/ChangeLog new file mode 100644 index 0000000..7e1aa76 --- /dev/null +++ b/sci-biology/mothur/ChangeLog @@ -0,0 +1,12 @@ +# ChangeLog for sci-biology/mothur +# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 +# $Id$ + +*mothur-1.36.1 (30 Nov 2015) + + 30 Nov 2015; Martin Mokrejs <mmokr...@fold.natur.cuni.cz> + +files/mothur-1.36.1-makefile.patch, +metadata.xml, +mothur-1.36.1.ebuild: + sci-biology/mothur: version bump; update makefile patch, the other patch from + 1.27 series seems not necessary anymore; added few more IUSE values but the + makefile could ideally respect them before forcing boost and zlib libraries + into LIBS diff --git a/sci-biology/mothur/files/mothur-1.36.1-makefile.patch b/sci-biology/mothur/files/mothur-1.36.1-makefile.patch new file mode 100644 index 0000000..08e0b7b --- /dev/null +++ b/sci-biology/mothur/files/mothur-1.36.1-makefile.patch @@ -0,0 +1,61 @@ +--- mothur-1.36.1/makefile.ori 2015-11-30 18:38:40.511576683 +0100 ++++ mothur-1.36.1/makefile 2015-11-30 18:41:24.261579412 +0100 +@@ -9,7 +9,7 @@ + # + + USEMPI ?= no +-64BIT_VERSION ?= yes ++64BIT_VERSION ?= no + USEREADLINE ?= yes + USECOMPRESSION ?= no + USEBOOST ?= yes +@@ -18,7 +18,7 @@ + VERSION = "\"1.36.1\"" + + # Optimize to level 3: +-CXXFLAGS += -O3 ++# CXXFLAGS += -O3 + + + ifeq ($(strip $(64BIT_VERSION)),yes) +@@ -58,7 +58,7 @@ + + + ifeq ($(strip $(USEMPI)),yes) +- CXX = mpic++ ++# CXX = mpic++ + CXXFLAGS += -DUSE_MPI + endif + +@@ -106,10 +106,8 @@ + OBJECTS+=$(patsubst %.cpp,%.o,$(wildcard *.cpp)) + OBJECTS+=$(patsubst %.c,%.o,$(wildcard *.c)) + +-mothur : $(OBJECTS) uchime ++mothur : $(OBJECTS) + $(CXX) $(LDFLAGS) $(TARGET_ARCH) -o $@ $(OBJECTS) $(LIBS) +- strip mothur +- + + uchime: + cd source/uchime_src && ./mk && mv uchime ../../ && cd .. +--- mothur-1.36.1/makefile.ori 2015-11-30 18:46:41.411584697 +0100 ++++ mothur-1.36.1/makefile 2015-11-30 19:15:18.531613315 +0100 +@@ -64,14 +64,12 @@ + + #The boost libraries allow you to read gz files. + ifeq ($(strip $(USEBOOST)),yes) +- BOOST_INCLUDE_DIR="/usr/local/include" +- BOOST_LIBRARY_DIR="/usr/local/lib" ++ BOOST_INCLUDE_DIR="/usr/include" ++ BOOST_LIBRARY_DIR="/usr/lib" + + CXXFLAGS += -DUSE_BOOST + +- LIBS += \ +- ${BOOST_LIBRARY_DIR}/libboost_iostreams.a \ +- ${BOOST_LIBRARY_DIR}/zlib.a ++ LIBS += -lboost_iostreams -lz + + #if linux or windows then ${BOOST_LIBRARY_DIR}/libz.a + endif diff --git a/sci-biology/mothur/metadata.xml b/sci-biology/mothur/metadata.xml new file mode 100644 index 0000000..f17a827 --- /dev/null +++ b/sci-biology/mothur/metadata.xml @@ -0,0 +1,5 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <herd>sci-biology</herd> +</pkgmetadata> diff --git a/sci-biology/mothur/mothur-1.36.1.ebuild b/sci-biology/mothur/mothur-1.36.1.ebuild new file mode 100644 index 0000000..c82f7fc --- /dev/null +++ b/sci-biology/mothur/mothur-1.36.1.ebuild @@ -0,0 +1,46 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=5 + +inherit eutils flag-o-matic fortran-2 toolchain-funcs + +DESCRIPTION="A suite of algorithms for ecological bioinformatics" +HOMEPAGE="http://www.mothur.org/" +SRC_URI="https://github.com/mothur/mothur/archive/v${PV}.tar.gz -> ${P}.tar.gz" + +LICENSE="GPL-3" +SLOT="0" +IUSE="mpi readline zlib" +KEYWORDS="~amd64 ~x86" + +CDEPEND="dev-libs/boost" +RDEPEND=" + sci-biology/uchime + mpi? ( virtual/mpi )" +DEPEND="${RDEPEND} + app-arch/unzip" + +pkg_setup() { + fortran-2_pkg_setup + use mpi && export CXX=mpicxx || export CXX=$(tc-getCXX) + use amd64 && append-cppflags -DBIT_VERSION + use readline && export USEREADLINE=yes || export USEREADLINE=no + # use boost && export USEBOOST=yes || export USEBOOST=no + use zlib && export USECOMPRESSION=yes || export USECOMPRESSION=no +} + +src_prepare() { + epatch \ + "${FILESDIR}"/${P}-makefile.patch \ +# "${FILESDIR}"/${PN}-1.27.0-overflows.patch +} + +src_compile() { + emake USEMPI=$(usex mpi) USEREADLINE=$(usex readline) USEBOOST=$(usex boost) USECOMPRESSION=$(usex zlib) +} + +src_install() { + dobin ${PN} +}