sci-biology/bambus: fix installation process and use current perl-module files from amos package instead

Package-Manager: portage-2.2.18

3 files changed, 41 insertions, 26 deletions

diff --git a/sci-biology/bambus/ChangeLog b/sci-biology/bambus/ChangeLog
new file mode 100644
index 000000000..9140d875d
--- /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 <mmokrejs@fold.natur.cuni.cz> 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/Manifest b/sci-biology/bambus/Manifest
index 1625f9a2b..117e5e97f 100644
--- a/sci-biology/bambus/Manifest
+++ b/sci-biology/bambus/Manifest
@@ -1 +1,2 @@
-DIST bambus-2.33.tar.gz 504535 SHA256 bc8e3c712719bccb00357001713e56f58aac57ae452fd73148eeccff291eefdc
+DIST bambus-2.33.tar.gz 504535 SHA256 bc8e3c712719bccb00357001713e56f58aac57ae452fd73148eeccff291eefdc SHA512 b31360439938bd88a19694af0addceafa658e144c2d6dcc156f7b5a3a2df0e806d55f4e4e7cd31dbbdd9464201506da61b3d0b288ba34138770d3023ab40795a WHIRLPOOL de070bc2b8972b2563446dc2f2b130310110926dc8e7e8f08477992b7f43aa5636a65ce66f21781fdb3a0751e49f5072f0080204b07d7ea866631c81b2902d62
+DIST scaffolding_MIRA_BAMBUS.pdf 181237 SHA256 1a86233ab1cfaef6b23a09267129fd3eeec0a81a4d90995d69c3c72da5cca68c SHA512 fcdf458917b09613dea2769921dee625528b08fbb92c5bc0d8b32bb0f29f6b8d163e4b0a2fdf6c338ba4a872cd29cffd7d0a7aeb8beb6c9afc76d0cc812bbc29 WHIRLPOOL 780bf5d38357377477becae03feee14c8f2603cd337716c12b9011785897830edf48a35423003b57e0bc1dc550a9921800d0ff64c49f44ca01c928bf3df36bbf
diff --git a/sci-biology/bambus/bambus-2.33.ebuild b/sci-biology/bambus/bambus-2.33.ebuild
index 2c05ad171..71ecb4b1b 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(){