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