1 files changed, 100 insertions, 0 deletions
diff --git a/sci-biology/bambus/bambus-2.33-r2.ebuild b/sci-biology/bambus/bambus-2.33-r2.ebuild
new file mode 100644
index 000000000..1cb7aad1b
--- /dev/null
+++ b/sci-biology/bambus/bambus-2.33-r2.ebuild
@@ -0,0 +1,100 @@
+# Copyright 1999-2022 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+inherit perl-module toolchain-funcs
+
+DESCRIPTION="Scaffolding Polymorphic Genomes and Metagenomes, a part of AMOS bundle"
+HOMEPAGE="
+	https://sourceforge.net/apps/mediawiki/amos/index.php?title=AMOS
+	https://sourceforge.net/projects/amos/files/bambus"
+SRC_URI="
+	https://sourceforge.net/projects/amos/files/bambus/${PV}/${P}.tar.gz
+	https://mira-assembler.sourceforge.net/docs/scaffolding_MIRA_BAMBUS.pdf"
+
+LICENSE="Artistic"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+
+RDEPEND="
+	sci-biology/tigr-foundation-libs
+	dev-perl/XML-Parser
+	dev-perl/Config-IniFiles
+	dev-perl/GraphViz"
+DEPEND="${RDEPEND}"
+
+PATCHES=(
+	"${FILESDIR}"/TigrFoundation-all-patches.patch
+)
+
+src_prepare() {
+	default
+#	eapply "${FILESDIR}"/amos-2.0.8-gcc44.patch
+	sed -e 's:BASEDIR = /usr/local/packages/bambus:BASEDIR = /usr:' -i Makefile || die
+	sed -e 's:PERL = /usr/local/bin/perl:PERL = /usr/bin/perl:' -i Makefile || die
+	sed \
+		-e 's:INSTDIR:DESTDIR:g' \
+			-i Makefile src/Makefile doc/Makefile || die
+	sed -e 's:make all;:make all || exit 255;:' -i src/Makefile || die
+	sed \
+		-e 's:INSTDIR:DESTDIR:g' \
+		-i src/IO/Makefile src/DotLib/Makefile src/grommit/Makefile || die
+	sed -e "s:^CC\t=:CC=$(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
+	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}:$ENV{PERL5LIB}:' -i src/goBambus.pl || die
+	sed -e 's:^#!.*:#!/usr/bin/perl:' -i src/goBambus.pl || die
+	sed -e 's:^#!.*:#!/usr/bin/perl:' -i src/IO/*.pl || die
+	einfo "Argh, cannot delete src/TIGR_Foundation_CC/ because it has some extra files getopt.* not present"
+	einfo "in sci-biology/tigr-foundation-libs. It seems bambus-2.33/src/TIGR_Foundation_CC/ contains"
+	einfo "the following 3 files getopt.cc   getopt.hh   getopt1.cc which were possibly copied"
+	einfo "over from some old GNU libc and maybe could be completely dropped?"
+	einfo "Affected would be:"
+	einfo "bambus-2.33/src/grommit/newgrp.cc:#include <getopt.h>"
+	einfo "bambus-2.33/src/TIGR_Foundation_CC/Options.hh:#include <getopt.h>"
+	einfo "bambus-2.33/src/TIGR_Foundation_CC/Options.hh:#include \"getopt.hh\""
+	einfo "bambus-2.33/src/TIGR_Foundation_CC/OptionResult.cc:/*! Uses same syntax as getopt"
+	#rm -rf src/TIGR_Foundation_CC || die "Failed to rm -rf src/TIGR_Foundation_CC/, we use it from sci-biology/tigr-foundation-libs"
+	#sed -i 's:TIGR_Foundation_CC::' src/Makefile || die "Failed to zap last pointer to local copy of tigr-foundation-libs"
+}
+
+src_install() {
+	pushd src/TIGR_Foundation_CC || die
+	sed -e "s:/export/usr/local:${ED}/usr:g" -i Makefile || die
+	popd || die
+	emake DESTDIR="${ED}/usr" install
+	# cvs HEAD of amos now contains even more updated files: /usr/bin/printScaff /usr/bin/untangle /usr/lib/TIGR/AsmLib.pm
+	for f in FASTArecord.pm FASTAreader.pm Foundation.pm FASTAgrammar.pm AsmLib.pm; do rm "${ED}"/usr/lib/TIGR/$f; done || die
+	for f in printScaff untangle; do rm "${ED}"/usr/bin/$f; done || die
+
+	# we compiled using locally provided TIGR_Foundation_CC/{cc,.hh} files but
+	# link against the libTigrFoundation.a provided by sci-biology/tigr-foundation-libs package
+	for f in CategoryInformation.hh MessageLevel.hh ConfigFile.hh LogCategory.hh \
+			ConfigSection.hh TIGR_Foundation.hh OptionResult.hh Exceptions.hh \
+			LogMsg.hh Options.hh Logger.hh FileSystem.hh; do
+				rm "${ED}"/usr/include/$f || die
+	done
+	rm "${ED}"/usr/lib/libTigrFoundation.a || die
+
+	dodir /usr/share/doc/${PF}
+	mv "${ED}"/usr/doc/* "${ED}"/usr/share/doc/${PF} || die
+	rmdir "${ED}"/usr/doc || die
+
+	dobin "${FILESDIR}"/goBambus.pl
+	dodoc "${DISTDIR}"/scaffolding_MIRA_BAMBUS.pdf
+	rm -r "${ED}"/usr/lib || die
+}
+
+pkg_postinst(){
+	einfo "For manual see http://mira-assembler.sourceforge.net/docs/scaffolding_MIRA_BAMBUS.pdf"
+}