commit: 851ba2104e66025e2a60f260d2851d57dba3ef44 Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz> AuthorDate: Sat Apr 18 01:10:48 2015 +0000 Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz> CommitDate: Sat Apr 18 01:10:48 2015 +0000 URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=851ba210
sci-biology/wgs-assembler: version bumps; did not check if the LDFLAGS part of the v7.0 patch should be carried over; CFLAGS seems are already handled properly by current code; 8.3rc1 dies at: install: cannot stat 'Linux-amd64/bin/TIGR': No such file or directory Package-Manager: portage-2.2.18 sci-biology/wgs-assembler/ChangeLog | 13 ++++ sci-biology/wgs-assembler/metadata.xml | 5 ++ sci-biology/wgs-assembler/wgs-assembler-8.2.ebuild | 78 +++++++++++++++++++++ .../wgs-assembler/wgs-assembler-8.3_rc1.ebuild | 81 ++++++++++++++++++++++ 4 files changed, 177 insertions(+) diff --git a/sci-biology/wgs-assembler/ChangeLog b/sci-biology/wgs-assembler/ChangeLog new file mode 100644 index 0000000..6299944 --- /dev/null +++ b/sci-biology/wgs-assembler/ChangeLog @@ -0,0 +1,13 @@ +# ChangeLog for sci-biology/wgs-assembler +# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 +# $Header: $ + +*wgs-assembler-8.2 (18 Apr 2015) +*wgs-assembler-8.3_rc1 (18 Apr 2015) + + 18 Apr 2015; Martin Mokrejs <[email protected]> +metadata.xml, + +wgs-assembler-8.2.ebuild, +wgs-assembler-8.3_rc1.ebuild: + sci-biology/wgs-assembler: version bumps; did not check if the LDFLAGS part of + the v7.0 patch should be carried over; CFLAGS seems are already handled + properly by current code; 8.3rc1 dies at: install: cannot stat 'Linux- + amd64/bin/TIGR': No such file or directory diff --git a/sci-biology/wgs-assembler/metadata.xml b/sci-biology/wgs-assembler/metadata.xml new file mode 100644 index 0000000..f17a827 --- /dev/null +++ b/sci-biology/wgs-assembler/metadata.xml @@ -0,0 +1,5 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd";> +<pkgmetadata> + <herd>sci-biology</herd> +</pkgmetadata> diff --git a/sci-biology/wgs-assembler/wgs-assembler-8.2.ebuild b/sci-biology/wgs-assembler/wgs-assembler-8.2.ebuild new file mode 100644 index 0000000..831af99 --- /dev/null +++ b/sci-biology/wgs-assembler/wgs-assembler-8.2.ebuild @@ -0,0 +1,78 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Header: /var/cvsroot/gentoo-x86/sci-biology/wgs-assembler/wgs-assembler-7.0-r1.ebuild,v 1.3 2012/11/13 19:19:00 nativemad Exp $ + +EAPI=4 + +PYTHON_DEPEND=2 + +inherit eutils python toolchain-funcs + +DESCRIPTION="De novo whole-genome shotgun DNA sequence assembler also known as Celera Assembler and CABOG" +HOMEPAGE="http://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=" + x11-libs/libXt + !x11-terms/terminator" +RDEPEND="${DEPEND} + app-shells/tcsh + dev-perl/Log-Log4perl" + +S="${WORKDIR}/wgs-${PV}" + +pkg_setup() { + python_set_active_version 2 + python_pkg_setup +} + +src_prepare() { + # epatch \ + # "${FILESDIR}"/${P}-build.patch + tc-export CC CXX +} + +src_configure() { + cd "${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 + + # avoid file collision + rm -f ${D}/usr/bin/jellyfish +} diff --git a/sci-biology/wgs-assembler/wgs-assembler-8.3_rc1.ebuild b/sci-biology/wgs-assembler/wgs-assembler-8.3_rc1.ebuild new file mode 100644 index 0000000..73518ed --- /dev/null +++ b/sci-biology/wgs-assembler/wgs-assembler-8.3_rc1.ebuild @@ -0,0 +1,81 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Header: /var/cvsroot/gentoo-x86/sci-biology/wgs-assembler/wgs-assembler-7.0-r1.ebuild,v 1.3 2012/11/13 19:19:00 nativemad Exp $ + +EAPI=4 + +PYTHON_DEPEND=2 + +inherit eutils python toolchain-funcs + +MY_PV="8.3rc1" + +DESCRIPTION="De novo whole-genome shotgun DNA sequence assembler also known as Celera Assembler and CABOG" +HOMEPAGE="http://sourceforge.net/projects/wgs-assembler/"; +#SRC_URI="mirror://sourceforge/${PN}/wgs-${PV}.tar.bz2" +SRC_URI="http://sourceforge.net/projects/wgs-assembler/files/wgs-assembler/wgs-8.3/wgs-8.3rc1.tar.bz2"; + +LICENSE="GPL-2" +SLOT="0" +KEYWORDS="~amd64 ~x86" +IUSE="static-libs" + +DEPEND=" + x11-libs/libXt + !x11-terms/terminator" +RDEPEND="${DEPEND} + app-shells/tcsh + dev-perl/Log-Log4perl" + +S="${WORKDIR}/wgs-${MY_PV}" + +pkg_setup() { + python_set_active_version 2 + python_pkg_setup +} + +src_prepare() { + # epatch \ + # "${FILESDIR}"/${P}-build.patch + tc-export CC CXX +} + +src_configure() { + cd "${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 + + # avoid file collision + rm -f ${D}/usr/bin/jellyfish +}
