commit: f5615b674dcdbddefac76b816a12458dd895fcb6 Author: Justin Lecher <jlec <AT> gentoo <DOT> org> AuthorDate: Wed Sep 23 10:15:57 2015 +0000 Commit: Justin Lecher <jlec <AT> gentoo <DOT> org> CommitDate: Wed Sep 23 10:15:57 2015 +0000 URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=f5615b67
sci-biology/bambus: Drop unnecessary dep on python Package-Manager: portage-2.2.21 Signed-off-by: Justin Lecher <jlec <AT> gentoo.org> sci-biology/bambus/bambus-2.33.ebuild | 58 ++++++++++++++++++----------------- 1 file changed, 30 insertions(+), 28 deletions(-) diff --git a/sci-biology/bambus/bambus-2.33.ebuild b/sci-biology/bambus/bambus-2.33.ebuild index d5b7c7f..13b7b62 100644 --- a/sci-biology/bambus/bambus-2.33.ebuild +++ b/sci-biology/bambus/bambus-2.33.ebuild @@ -8,10 +8,12 @@ PERL_EXPORT_PHASE_FUNCTIONS=no inherit perl-module eutils toolchain-funcs 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/${PV}/${P}.tar.gz +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/${PV}/${P}.tar.gz http://mira-assembler.sourceforge.net/docs/scaffolding_MIRA_BAMBUS.pdf"; LICENSE="Artistic" @@ -19,25 +21,25 @@ SLOT="0" KEYWORDS="~amd64 ~x86" IUSE="" -DEPEND="sci-biology/tigr-foundation-libs" -RDEPEND="${DEPEND} - dev-lang/perl - dev-lang/python - dev-perl/XML-Parser - dev-perl/Config-IniFiles - dev-perl/GraphViz" +RDEPEND=" + sci-biology/tigr-foundation-libs + dev-lang/perl + dev-perl/XML-Parser + dev-perl/Config-IniFiles + dev-perl/GraphViz" +DEPEND="${RDEPEND}" src_prepare() { # epatch "${FILESDIR}"/amos-2.0.8-gcc44.patch sed -e 's:BASEDIR = /usr/local/packages/bambus:BASEDIR = /usr:' -i Makefile || die sed -e 's:PERL = /usr/local/bin/perl:PERL = /usr/bin/perl:' -i Makefile || die - sed -e 's:INSTDIR:DESTDIR:g' -i Makefile || die - sed -e 's:INSTDIR:DESTDIR:g' -i src/Makefile || die - sed -e 's:INSTDIR:DESTDIR:g' -i doc/Makefile || die + sed \ + -e 's:INSTDIR:DESTDIR:g' \ + -i Makefile src/Makefile doc/Makefile || die sed -e 's:make all;:make all || exit 255;:' -i src/Makefile || die - sed -e 's:INSTDIR:DESTDIR:g' -i src/IO/Makefile || die - sed -e 's:INSTDIR:DESTDIR:g' -i src/DotLib/Makefile || die - sed -e 's:INSTDIR:DESTDIR:g' -i src/grommit/Makefile || die + sed \ + -e 's:INSTDIR:DESTDIR:g' \ + -i src/IO/Makefile src/DotLib/Makefile src/grommit/Makefile || die sed -e "s:^CC\t=:CC=$(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 @@ -70,7 +72,7 @@ src_prepare() { } src_compile() { - emake DESTDIR="${D}/usr" || die "emake failed" + emake DESTDIR="${D}/usr" # TODO: #ld -L../TIGR_Foundation_CC/ -shared -fPIC -o grommit grommit.o -L. -lgraph -lTigrFoundation @@ -87,7 +89,7 @@ src_compile() { } src_install() { - emake DESTDIR="${D}/usr" install || die "emake install failed" + emake DESTDIR="${D}/usr" install # cvs HEAD of amos now contains even more updated files: /usr/bin/printScaff /usr/bin/untangle /usr/lib/TIGR/AsmLib.pm for f in FASTArecord.pm FASTAreader.pm Foundation.pm FASTAgrammar.pm AsmLib.pm; do rm "${D}"/usr/lib/TIGR/$f; done || die for f in printScaff untangle; do rm "${D}"/usr/bin/$f; done || die @@ -96,18 +98,18 @@ src_install() { # link against the libTigrFoundation.a provided by sci-biology/tigr-foundation-libs package for f in CategoryInformation.hh MessageLevel.hh ConfigFile.hh LogCategory.hh \ ConfigSection.hh TIGR_Foundation.hh OptionResult.hh Exceptions.hh \ - LogMsg.hh Options.hh Logger.hh FileSystem.hh; do \ - rm "${D}"/usr/include/$f; \ - done || die - rm "${D}"/usr/lib/libTigrFoundation.a || die + LogMsg.hh Options.hh Logger.hh FileSystem.hh; do + rm "${ED}"/usr/include/$f || die + done + rm "${ED}"/usr/lib/libTigrFoundation.a || die - mkdir -p "${D}"/usr/share/doc/"${P}" || die - mv "${D}"/usr/doc/* "${D}"/usr/share/doc/"${P}" || die - rmdir "${D}"/usr/doc || die + dodir /usr/share/doc/${P} + mv "${ED}"/usr/doc/* "${ED}"/usr/share/doc/${PF} || die + rmdir "${ED}"/usr/doc || die - dobin "${FILESDIR}"/goBambus.pl || die "Failed to install the alternative of goBambus.py written in perl" + dobin "${FILESDIR}"/goBambus.pl dodoc "${DISTDIR}"/scaffolding_MIRA_BAMBUS.pdf - rm -rf "${D}"/usr/lib + rm -rf "${ED}"/usr/lib || die } pkg_postinst(){
