commit: e5fab3349b68203b78b69745bbb71734fa43c515 Author: Andreas K. Hüttel <dilfridge <AT> gentoo <DOT> org> AuthorDate: Sun Apr 29 21:30:45 2018 +0000 Commit: Andreas Hüttel <dilfridge <AT> gentoo <DOT> org> CommitDate: Sun Apr 29 21:31:06 2018 +0000 URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=e5fab334
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(+) 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 +}
