[gentoo-commits] proj/sci:master commit in: sci-biology/mothur/, sci-biology/mothur/files/

[Martin Mokrejs]

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 <mmokrejs@×××××××××××××××.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}
+}