commit: 529d9a71cf4c1b3ae1dc6e437923544e2cc84741 Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz> AuthorDate: Tue Mar 31 20:26:02 2015 +0000 Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz> CommitDate: Tue Mar 31 20:26:02 2015 +0000 URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=529d9a71
sci-biology/bambus: fix installation process and use current perl-module files from amos package instead Package-Manager: portage-2.2.18 sci-biology/bambus/ChangeLog | 7 +++++ sci-biology/bambus/bambus-2.33.ebuild | 57 ++++++++++++++++++++--------------- 2 files changed, 39 insertions(+), 25 deletions(-) diff --git a/sci-biology/bambus/ChangeLog b/sci-biology/bambus/ChangeLog new file mode 100644 index 0000000..9140d87 --- /dev/null +++ b/sci-biology/bambus/ChangeLog @@ -0,0 +1,7 @@ +# ChangeLog for sci-biology/bambus +# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 +# $Header: $ + + 31 Mar 2015; Martin Mokrejs <[email protected]> bambus-2.33.ebuild: + sci-biology/bambus: fix installation process and use current perl-module files + from amos package instead diff --git a/sci-biology/bambus/bambus-2.33.ebuild b/sci-biology/bambus/bambus-2.33.ebuild index 2c05ad1..71ecb4b 100644 --- a/sci-biology/bambus/bambus-2.33.ebuild +++ b/sci-biology/bambus/bambus-2.33.ebuild @@ -1,15 +1,17 @@ -# Copyright 1999-2014 Gentoo Foundation +# Copyright 1999-2015 Gentoo Foundation # Distributed under the terms of the GNU General Public License v2 # $Header: $ -EAPI=3 +EAPI=5 inherit eutils DESCRIPTION="Scaffolding Polymorphic Genomes and Metagenomes, a part of AMOS bundle" HOMEPAGE="http://sourceforge.net/apps/mediawiki/amos/index.php?title=AMOS + http://sourceforge.net/projects/amos/files/bambus http://www.tigr.org/software/bambus"; -SRC_URI="http://sourceforge.net/projects/amos/files/bambus/2.33/bambus-2.33.tar.gz"; +SRC_URI="http://sourceforge.net/projects/amos/files/bambus/${PV}/${P}.tar.gz + http://mira-assembler.sourceforge.net/docs/scaffolding_MIRA_BAMBUS.pdf"; LICENSE="Artistic" SLOT="0" @@ -26,28 +28,32 @@ RDEPEND="${DEPEND} src_prepare() { # epatch "${FILESDIR}"/amos-2.0.8-gcc44.patch - sed -i 's:BASEDIR = /usr/local/packages/bambus:BASEDIR = /usr:' Makefile || die - sed -i 's:PERL = /usr/local/bin/perl:PERL = /usr/bin/perl:' Makefile || die - sed -i 's:INSTDIR:DESTDIR:g' Makefile || die - sed -i 's:INSTDIR:DESTDIR:g' src/Makefile || die - sed -i 's:INSTDIR:DESTDIR:g' doc/Makefile || die - sed -i 's:INSTDIR:DESTDIR:g' src/IO/Makefile || die - sed -i 's:INSTDIR:DESTDIR:g' src/DotLib/Makefile || die - sed -i 's:INSTDIR:DESTDIR:g' src/grommit/Makefile || die - sed -i 's:^CC:#CC:' Makefile || die - sed -i 's:^CXX:#CXX:' Makefile || die - sed -i 's:^LD:#LD:' Makefile || die - sed -i 's:^AR:#AR:' Makefile || die - sed -i 's:^export:#export:' Makefile || die - sed -i 's:-Wl::' src/grommit/Makefile || die - sed -i 's:-L../TIGR_Foundation_CC/:-L../TIGR_Foundation_CC/ -shared -fPIC:' src/grommit/Makefile || die - sed -i 's:make all:make all DESTDIR=$(DESTDIR):' Makefile || die - sed -i 's:make install:make install DESTDIR=$(DESTDIR):' Makefile || die - sed -i 's:^LDFLAGS =$(STATIC_$(OSTYPE)):LDFLAGS += $(STATIC_$(OSTYPE)) -shared -fPIC:' src/grommit/Makefile || die - sed -i 's:CFLAGS = $(HEADERS) -g:CFLAGS += $(HEADERS):' src/grommit/Makefile || die - sed -i 's:^$ENV{PERLLIB}:$ENV{PERL5LIB}:' src/goBambus.pl || die + sed -e 's:BASEDIR = /usr/local/packages/bambus:BASEDIR = /usr:' -i Makefile || die + sed -e 's:PERL = /usr/local/bin/perl:PERL = /usr/bin/perl:' -i Makefile || die + sed -e 's:INSTDIR:DESTDIR:g' -i Makefile || die + sed -e 's:INSTDIR:DESTDIR:g' -i src/Makefile || die + sed -e 's:INSTDIR:DESTDIR:g' -i doc/Makefile || die + sed -e 's:make all;:make all || exit 255;:' -i src/Makefile || die + sed -e 's:INSTDIR:DESTDIR:g' -i src/IO/Makefile || die + sed -e 's:INSTDIR:DESTDIR:g' -i src/DotLib/Makefile || die + sed -e 's:INSTDIR:DESTDIR:g' -i src/grommit/Makefile || die + sed -e "s:^CC\t=:CC=$(tc-getCXX):" -i Makefile || die + sed -e "s:^CXX\t=:CXX=$(tc-getCXX):" -i Makefile || die + sed -e "s:^LD\t:LD=$(tc-getCXX):" -i Makefile || die + sed -e 's:^AR\t=:#AR=:' -i Makefile || die + sed -e 's:^export:#export:' -i Makefile || die + sed -e 's:-Wl::' -i src/grommit/Makefile || die + # sed -e 's:-L../TIGR_Foundation_CC/:-L../TIGR_Foundation_CC/:' -i src/grommit/Makefile || die + sed -e 's:make all:make all DESTDIR=$(DESTDIR):' -i Makefile || die + sed -e 's:make install:make install DESTDIR=$(DESTDIR):' -i Makefile || die + sed -e "s:# Main targets:LD=$(tc-getCXX):" -i src/grommit/Makefile || die + sed -e 's:^LDFLAGS =$(STATIC_$(OSTYPE)):LDFLAGS += $(STATIC_$(OSTYPE)):' -i src/grommit/Makefile || die + sed -e 's:CFLAGS = $(HEADERS) -g:CFLAGS += $(HEADERS) -fPIC:' -i src/grommit/Makefile || die + sed -e 's:^$ENV{PERLLIB}:$ENV{PERL5LIB}:' -i src/goBambus.pl || die + sed -e 's:^#!.*:#!/usr/bin/perl:' -i src/goBambus.pl || die + sed -e 's:^#!.*:#!/usr/bin/perl:' -i src/IO/*.pl || die einfo "Argh, cannot delete src/TIGR_Foundation_CC/ because it has some extra files getopt.* not present" - einfo "in sci-biology/tigr-foundation-libs. It sees bambus-2.33/src/TIGR_Foundation_CC/ contains" + einfo "in sci-biology/tigr-foundation-libs. It seems bambus-2.33/src/TIGR_Foundation_CC/ contains" einfo "the following 3 files getopt.cc getopt.hh getopt1.cc which were possibly copied" einfo "over from some old GNU libc and maybe could be completely dropped?" einfo "Affected would be:" @@ -59,7 +65,7 @@ src_prepare() { #sed -i 's:TIGR_Foundation_CC::' src/Makefile || die "Failed to zap last pointer to local copy of tigr-foundation-libs" cd src/TIGR_Foundation_CC || die "Failed to cd src/TIGR_Foundation_CC/" epatch "${FILESDIR}"/TigrFoundation-all-patches.patch || die - sed -i "s:/export/usr/local:${D}/usr:g" Makefile || die + sed -e "s:/export/usr/local:${D}/usr:g" -i Makefile || die } src_compile() { @@ -99,6 +105,7 @@ src_install() { rmdir "${D}"/usr/doc || die dobin "${FILESDIR}"/goBambus.pl || die "Failed to install the alternative of goBambus.py written in perl" + dodoc "${DISTDIR}"/scaffolding_MIRA_BAMBUS.pdf } pkg_postinst(){
