gentoo resync : 30.04.2018

4 files changed, 90 insertions, 0 deletions

diff --git a/sci-biology/Manifest.gz b/sci-biology/Manifest.gz
index c155261853fa..a405ff2dcf3f 100644
--- a/sci-biology/Manifest.gz
+++ b/sci-biology/Manifest.gz
diff --git a/sci-biology/wgs-assembler/Manifest b/sci-biology/wgs-assembler/Manifest
index 48ee07cb0de4..e41a36839647 100644
--- a/sci-biology/wgs-assembler/Manifest
+++ b/sci-biology/wgs-assembler/Manifest
@@ -1,4 +1,6 @@
 AUX wgs-assembler-7.0-build.patch 10279 BLAKE2B 9fd4a113d4ea3b07570c39e32892b535a0ed7d0e958602ca891c75fa3aa73a44d205fe43580e43d98cdafa1d431c12f68d5fe55e52aca82e451d5aae3ea2c551 SHA512 77e432319cb279d188ab74edda822f6b4dda127f1e5f1d75febb6fe0533b66d5bfd066781f1ff5d4d0d8f832c491d31ec470653b9c36b29d8280b5786783c5b9
+AUX wgs-assembler-7.0-libtirpc.patch 516 BLAKE2B 1ee7876f767e559a008d86b8f6ccdbf70763646b782ea23d2bc9f74edab84ff633270ff15d0cd5b888674c5ee0d0bdcd3b73a48bf040f06f2a56bf4e366125cf SHA512 b2a29b2dc0578d4e8544dce258327a34ac4a5ca6bea3e901bee06d89618e9cba7f569fd54da6148372826d053829bc991db7c4cfd5a8564dd81545566698c947
 DIST wgs-7.0.tar.bz2 1952253 BLAKE2B 2dbff6ffb9f4310d3d1301405e74476b7b7bbed4359c1701b5100d9597db46cc9956ccbe467bb37f8976d176ab9f92bfabcd5d1210b1e10675cff9a87ff379b9 SHA512 e5ef1d4533e3dd17d13c6aca9631f5300768a258f8241f3f7f90de3785bf7a340b6896febe335682c282434c9983bc4a02fe2128a5b0e7ec415dd65e0fe400ba
 EBUILD wgs-assembler-7.0-r1.ebuild 1597 BLAKE2B 046fee583f335d5554069c0b9d489af94fa78d98b9d41cfbee518ff124e06c0f603afb6494c50bb6958f6f92c63957e6fefc6357eb358a950a71db8396753c07 SHA512 d874b917c4b86cfb56681473c4c99ec38bd9a681b7e0832a0e9240f2a1c20a754be30316ca4b64f579cbd8c3bb50cad18e874664f5e51e41194e6941088bcb86
+EBUILD wgs-assembler-7.0-r2.ebuild 1664 BLAKE2B 4b26527866626c7661f4ef449d9099e79be13ccf81b6fbdd3e4da5ddbb623404e4ce9fdf6e40feecab68165a7fb509a7225c1ae8b4dfe7c70a488de24b856b03 SHA512 fff6a237bb346551d078571e3bd4128bae3a536f7ef9a99fe23de234727edb6c90c88b2f25eec58121746f41a9b091984010ca9e9f8e74d21d572f8bc22bf835
 MISC metadata.xml 354 BLAKE2B eaf844f74ea3b2a51cba2f00ebc0a3cc895312e04a995000e93426fa0e2f9d8601edb2011ff6c837f85b3a5755b819dc7ce517d3787c2e7bd37e097e144fb156 SHA512 b46f437eb224dbc7d7cec21941565ab48055f1d7b787fae7e66b135a8abeff0ea55dc191643d1e5f6212012001d98e4b7e8a7a655c9a66c9f3124bf7e700e193
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
+}