From e5fab3349b68203b78b69745bbb71734fa43c515 Mon Sep 17 00:00:00 2001
From: "Andreas K. Hüttel" <dilfridge@gentoo.org>
Date: Sun, 29 Apr 2018 23:30:45 +0200
Subject: sci-biology/wgs-assembler: Revision bump using libtirpc, bug 374815

Bug: https://bugs.gentoo.org/374815
Package-Manager: Portage-2.3.31, Repoman-2.3.9
---
 .../files/wgs-assembler-7.0-libtirpc.patch         | 16 +++++
 .../wgs-assembler/wgs-assembler-7.0-r2.ebuild      | 72 ++++++++++++++++++++++
 2 files changed, 88 insertions(+)
 create mode 100644 sci-biology/wgs-assembler/files/wgs-assembler-7.0-libtirpc.patch
 create mode 100644 sci-biology/wgs-assembler/wgs-assembler-7.0-r2.ebuild

(limited to 'sci-biology')

diff --git a/sci-biology/wgs-assembler/files/wgs-assembler-7.0-libtirpc.patch b/sci-biology/wgs-assembler/files/wgs-assembler-7.0-libtirpc.patch
new file mode 100644
index 000000000000..7269b0b73c48
--- /dev/null
+++ b/sci-biology/wgs-assembler/files/wgs-assembler-7.0-libtirpc.patch
@@ -0,0 +1,16 @@
+diff -ruN wgs-7.0.orig/src/c_make.as wgs-7.0/src/c_make.as
+--- wgs-7.0.orig/src/c_make.as	2018-04-29 23:00:02.200181987 +0200
++++ wgs-7.0/src/c_make.as	2018-04-29 23:17:33.612700507 +0200
+@@ -196,6 +196,12 @@
+ CXXFLAGS        += $(ARCH_CXXFLAGS)
+ LDFLAGS         += $(ARCH_LDFLAGS)
+ 
++# libtirpc
++
++CFLAGS += -I/usr/include/tirpc
++CXXFLAGS += -I/usr/include/tirpc
++LINK_LIBS += -ltirpc
++
+ INC_IMPORT_DIRS += $(LOCAL_WORK)/src $(patsubst %, $(LOCAL_WORK)/src/%, $(strip $(SUBDIRS)))
+ INC_IMPORT_DIRS += $(ARCH_INC)
+ 
diff --git a/sci-biology/wgs-assembler/wgs-assembler-7.0-r2.ebuild b/sci-biology/wgs-assembler/wgs-assembler-7.0-r2.ebuild
new file mode 100644
index 000000000000..192dc48173e7
--- /dev/null
+++ b/sci-biology/wgs-assembler/wgs-assembler-7.0-r2.ebuild
@@ -0,0 +1,72 @@
+# Copyright 1999-2018 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=6
+
+inherit eutils toolchain-funcs
+
+DESCRIPTION="The Celera de novo whole-genome shotgun DNA sequence assembler, aka CABOG"
+HOMEPAGE="https://sourceforge.net/projects/wgs-assembler/"
+SRC_URI="mirror://sourceforge/${PN}/wgs-${PV}.tar.bz2"
+
+LICENSE="GPL-2"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+IUSE="static-libs"
+
+DEPEND="
+	net-libs/libtirpc
+	x11-libs/libXt
+	!x11-terms/terminator"
+RDEPEND="${DEPEND}
+	app-shells/tcsh
+	dev-perl/Log-Log4perl"
+
+S="${WORKDIR}/wgs-${PV}"
+
+PATCHES=(
+	"${FILESDIR}"/${P}-build.patch
+	"${FILESDIR}"/${P}-libtirpc.patch
+)
+
+src_prepare() {
+	default
+	tc-export CC CXX
+}
+
+src_configure() {
+	cd "${S}/kmer"
+	./configure.sh || die
+}
+
+src_compile() {
+	# not really an install target
+	emake -C kmer -j1 install
+	emake -C src -j1 SITE_NAME=LOCAL
+}
+
+src_install() {
+	OSTYPE=$(uname)
+	MACHTYPE=$(uname -m)
+	MACHTYPE=${MACHTYPE/x86_64/amd64}
+	MY_S="${OSTYPE}-${MACHTYPE}"
+	sed -i 's|#!/usr/local/bin/|#!/usr/bin/env |' $(find $MY_S -type f) || die
+
+	sed -i '/sub getBinDirectory ()/ a return "/usr/bin";' ${MY_S}/bin/runCA* || die
+	sed -i '/sub getBinDirectoryShellCode ()/ a return "bin=/usr/bin\n";' ${MY_S}/bin/runCA* || die
+	sed -i '1 a use lib "/usr/share/'${PN}'/lib";' $(find $MY_S -name '*.p*') || die
+
+	dobin kmer/${MY_S}/bin/*
+	insinto /usr/$(get_libdir)/${PN}
+	use static-libs && doins kmer/${MY_S}/lib/*
+
+	insinto /usr/include/${PN}
+	doins kmer/${MY_S}/include/*
+
+	insinto /usr/share/${PN}/lib
+	doins -r ${MY_S}/bin/TIGR
+	rm -rf ${MY_S}/bin/TIGR || die
+	dobin ${MY_S}/bin/*
+	use static-libs && dolib.a ${MY_S}/lib/*
+	dodoc README
+}
-- 
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