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commit: e5fab3349b68203b78b69745bbb71734fa43c515 |
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Author: Andreas K. Hüttel <dilfridge <AT> gentoo <DOT> org> |
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AuthorDate: Sun Apr 29 21:30:45 2018 +0000 |
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Commit: Andreas Hüttel <dilfridge <AT> gentoo <DOT> org> |
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CommitDate: Sun Apr 29 21:31:06 2018 +0000 |
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URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=e5fab334 |
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|
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sci-biology/wgs-assembler: Revision bump using libtirpc, bug 374815 |
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|
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Bug: https://bugs.gentoo.org/374815 |
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Package-Manager: Portage-2.3.31, Repoman-2.3.9 |
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|
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.../files/wgs-assembler-7.0-libtirpc.patch | 16 +++++ |
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.../wgs-assembler/wgs-assembler-7.0-r2.ebuild | 72 ++++++++++++++++++++++ |
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2 files changed, 88 insertions(+) |
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|
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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 |
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new file mode 100644 |
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index 00000000000..7269b0b73c4 |
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--- /dev/null |
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+++ b/sci-biology/wgs-assembler/files/wgs-assembler-7.0-libtirpc.patch |
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@@ -0,0 +1,16 @@ |
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+diff -ruN wgs-7.0.orig/src/c_make.as wgs-7.0/src/c_make.as |
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+--- wgs-7.0.orig/src/c_make.as 2018-04-29 23:00:02.200181987 +0200 |
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++++ wgs-7.0/src/c_make.as 2018-04-29 23:17:33.612700507 +0200 |
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+@@ -196,6 +196,12 @@ |
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+ CXXFLAGS += $(ARCH_CXXFLAGS) |
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+ LDFLAGS += $(ARCH_LDFLAGS) |
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+ |
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++# libtirpc |
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++ |
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++CFLAGS += -I/usr/include/tirpc |
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++CXXFLAGS += -I/usr/include/tirpc |
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++LINK_LIBS += -ltirpc |
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++ |
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+ INC_IMPORT_DIRS += $(LOCAL_WORK)/src $(patsubst %, $(LOCAL_WORK)/src/%, $(strip $(SUBDIRS))) |
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+ INC_IMPORT_DIRS += $(ARCH_INC) |
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+ |
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|
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diff --git a/sci-biology/wgs-assembler/wgs-assembler-7.0-r2.ebuild b/sci-biology/wgs-assembler/wgs-assembler-7.0-r2.ebuild |
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new file mode 100644 |
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index 00000000000..192dc48173e |
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--- /dev/null |
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+++ b/sci-biology/wgs-assembler/wgs-assembler-7.0-r2.ebuild |
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@@ -0,0 +1,72 @@ |
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+# Copyright 1999-2018 Gentoo Foundation |
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+# Distributed under the terms of the GNU General Public License v2 |
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+ |
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+EAPI=6 |
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+ |
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+inherit eutils toolchain-funcs |
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+ |
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+DESCRIPTION="The Celera de novo whole-genome shotgun DNA sequence assembler, aka CABOG" |
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+HOMEPAGE="https://sourceforge.net/projects/wgs-assembler/" |
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+SRC_URI="mirror://sourceforge/${PN}/wgs-${PV}.tar.bz2" |
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+ |
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+LICENSE="GPL-2" |
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+SLOT="0" |
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+KEYWORDS="~amd64 ~x86" |
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+IUSE="static-libs" |
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+ |
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+DEPEND=" |
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+ net-libs/libtirpc |
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+ x11-libs/libXt |
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+ !x11-terms/terminator" |
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+RDEPEND="${DEPEND} |
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+ app-shells/tcsh |
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+ dev-perl/Log-Log4perl" |
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+ |
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+S="${WORKDIR}/wgs-${PV}" |
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+ |
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+PATCHES=( |
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+ "${FILESDIR}"/${P}-build.patch |
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+ "${FILESDIR}"/${P}-libtirpc.patch |
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+) |
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+ |
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+src_prepare() { |
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+ default |
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+ tc-export CC CXX |
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+} |
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+ |
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+src_configure() { |
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+ cd "${S}/kmer" |
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+ ./configure.sh || die |
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+} |
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+ |
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+src_compile() { |
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+ # not really an install target |
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+ emake -C kmer -j1 install |
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+ emake -C src -j1 SITE_NAME=LOCAL |
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+} |
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+ |
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+src_install() { |
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+ OSTYPE=$(uname) |
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+ MACHTYPE=$(uname -m) |
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+ MACHTYPE=${MACHTYPE/x86_64/amd64} |
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+ MY_S="${OSTYPE}-${MACHTYPE}" |
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+ sed -i 's|#!/usr/local/bin/|#!/usr/bin/env |' $(find $MY_S -type f) || die |
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+ |
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+ sed -i '/sub getBinDirectory ()/ a return "/usr/bin";' ${MY_S}/bin/runCA* || die |
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+ sed -i '/sub getBinDirectoryShellCode ()/ a return "bin=/usr/bin\n";' ${MY_S}/bin/runCA* || die |
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+ sed -i '1 a use lib "/usr/share/'${PN}'/lib";' $(find $MY_S -name '*.p*') || die |
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+ |
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+ dobin kmer/${MY_S}/bin/* |
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+ insinto /usr/$(get_libdir)/${PN} |
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+ use static-libs && doins kmer/${MY_S}/lib/* |
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+ |
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+ insinto /usr/include/${PN} |
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+ doins kmer/${MY_S}/include/* |
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+ |
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+ insinto /usr/share/${PN}/lib |
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+ doins -r ${MY_S}/bin/TIGR |
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+ rm -rf ${MY_S}/bin/TIGR || die |
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+ dobin ${MY_S}/bin/* |
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+ use static-libs && dolib.a ${MY_S}/lib/* |
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+ dodoc README |
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+} |