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authorAndreas K. Hüttel <dilfridge@gentoo.org>2018-04-29 23:30:45 +0200
committerAndreas K. Hüttel <dilfridge@gentoo.org>2018-04-29 23:31:06 +0200
commite5fab3349b68203b78b69745bbb71734fa43c515 (patch)
tree888cbfe19ad48a33f957fba61ecafbeb4d57ced8 /sci-biology
parentapp-editors/kile: Drop old snapshot (diff)
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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
Diffstat (limited to 'sci-biology')
-rw-r--r--sci-biology/wgs-assembler/files/wgs-assembler-7.0-libtirpc.patch16
-rw-r--r--sci-biology/wgs-assembler/wgs-assembler-7.0-r2.ebuild72
2 files changed, 88 insertions, 0 deletions
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 00000000000..7269b0b73c4
--- /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 += $(ARCH_INC)
+
diff --git a/sci-biology/wgs-assembler/wgs-assembler-7.0-r2.ebuild b/sci-biology/wgs-assembler/wgs-assembler-7.0-r2.ebuild
new file mode 100644
index 00000000000..192dc48173e
--- /dev/null
+++ b/sci-biology/wgs-assembler/wgs-assembler-7.0-r2.ebuild
@@ -0,0 +1,72 @@
+# Copyright 1999-2018 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=6
+
+inherit eutils toolchain-funcs
+
+DESCRIPTION="The Celera de novo whole-genome shotgun DNA sequence assembler, aka CABOG"
+HOMEPAGE="https://sourceforge.net/projects/wgs-assembler/"
+SRC_URI="mirror://sourceforge/${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
+}